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Search results 501 to 600 out of 859 for Palm

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Type Details Score
Protein
A0A3B2WAL6
Organism: Mus musculus/domesticus
Length: 102  
Fragment?: false
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Protein
Q5Q9H3
Organism: Mus musculus/domesticus
Length: 237  
Fragment?: false
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Publication
32438371 | -
First Author: Hillen HS
Year: 2020
Journal: Nature
Title: Structure of replicating SARS-CoV-2 polymerase.
Volume: 584
Issue: 7819
Pages: 154-156
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Protein Domain
IPR002934 | Polymerase_NTP_transf_dom
Type: Domain
Description: A small region that overlaps with a nuclear localization signal and binds to the RNA primer contains three aspartates that are essential for catalysis. Sequence and secondary structure comparisons of regions surrounding these aspartates with sequences of other polymerases revealed a significant homology to the palm structure of DNA polymerase beta, terminal deoxynucleotidyltransferase and DNA polymerase IV of Saccharomyces cerevisiae, all members of the family X of polymerases. This homology extends as far as cca: tRNA nucleotidyltransferase and streptomycin adenylyltransferase, an antibiotic resistance factor [, ].Proteins containing this domain include kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase inactivates antibiotics by catalysing the addition of a nucleotidyl group onto the drug. In experiments, Mn2+ strongly stimulated this reaction due to a 50-fold lower Ki for 8-azido-ATP in the presence of Mn2+. Mutations of the highly conservedAsp residues 113, 115, and 167, critical for metal binding in the catalytic domain of bovine poly(A) polymerase, led to a strongreduction of cross-linking efficiency, and Mn2+ no longer stimulated the reaction. Mutations in the region of the "helical turn motif"(a domain binding the triphosphate moiety of the nucleotide) and in the suspected nucleotide-binding helix of bovine poly(A) polymeraseimpaired ATP binding and catalysis. The results indicate that ATP is bound in part by the helical turn motif and in part by a region thatmay be a structural analogue of the fingers domain found in many polymerases.
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Protein Domain
IPR044347 | RdRp_HCoV_HKU1-like
Type: Domain
Description: This entry contains the RNA-dependent RNA polymerase (RdRp) of human coronavirus HKU1, murine hepatitis virus, and similar proteins from betacoronaviruses in the embecovirus subgenera (A lineage).Coronaviruses (CoVs) utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (NSPs) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as NSP12), catalyses the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, NSP7 and NSP8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir. NSP12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RpRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides [].
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Protein Domain
IPR044349 | RdRp_batCoV_HKU9-like
Type: Domain
Description: This entry contains the RNA-dependent RNA polymerase (RdRp) of bat coronavirus HKU9 and similar proteins from betacoronaviruses in the nobecovirus subgenera (D lineage).Coronaviruses (CoVs) utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (NSPs) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as NSP12), catalyses the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, NSP7 and NSP8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir. NSP12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RpRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides [].
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Protein Domain
IPR044350 | RdRp_MERS-CoV-like
Type: Domain
Description: This entry contains the RNA-dependent RNA polymerase (RdRp) of Middle East respiratory syndrome (MERS)-related CoV, bat-CoV HKU5, and similar proteins from betacoronaviruses in the merbecovirus subgenera (C lineage).Coronaviruses (CoVs) utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (NSPs) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as NSP12), catalyses the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, NSP7 and NSP8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir. NSP12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RpRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides [].
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Protein Domain
IPR044351 | RdRp_SARS-CoV-like
Type: Domain
Description: This entry contains the RNA-dependent RNA polymerase (RdRp) of Severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2 (also known as 2019 novel CoV (2019-nCoV) or COVID-19 virus), and similar proteins from betacoronaviruses in the sarbecovirus subgenera (B lineage).Coronaviruses (CoVs) utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (NSPs) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as NSP12), catalyses the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, NSP7 and NSP8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir. NSP12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RpRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides [].
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Protein Domain
IPR044354 | RdRp_deltaCoV
Type: Domain
Description: This entry contains the RNA-dependent RNA polymerase (RdRp) of deltacoronaviruses.Coronaviruses (CoVs) utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (NSPs) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as NSP12), catalyses the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, NSP7 and NSP8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir. NSP12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RpRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides [].
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Protein Domain
IPR044356 | RdRp_alphaCoV
Type: Domain
Description: This entry contains the RNA-dependent RNA polymerase (RdRp) of alphacoronaviruses, including human coronaviruses (HCoVs), HCoV-NL63, and HCoV-229E.CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as NSP12), catalyses the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, NSP7 and NSP8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir [].NSP12 containsa RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RpRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides [].
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Protein Domain
IPR044358 | RdRp_gammaCoV
Type: Domain
Description: This entry contains the RNA-dependent RNA polymerase (RdRp) of gammacoronaviruses, including the RdRp of avian infectious bronchitis virus (IBV) and similar proteins.CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as NSP12), catalyses the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, NSP7 and NSP8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir [].NSP12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RpRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides [].
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Protein
Q9CY52
Organism: Mus musculus/domesticus
Length: 298  
Fragment?: false
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Protein
Q9CQT0
Organism: Mus musculus/domesticus
Length: 238  
Fragment?: false
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Protein
Q8BT63
Organism: Mus musculus/domesticus
Length: 279  
Fragment?: false
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Protein
Q9D999
Organism: Mus musculus/domesticus
Length: 150  
Fragment?: false
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Publication
33190493 | -
First Author: Wakchaure PD
Year: 2020
Journal: J Phys Chem B
Title: Revealing the Inhibition Mechanism of RNA-Dependent RNA Polymerase (RdRp) of SARS-CoV-2 by Remdesivir and Nucleotide Analogues: A Molecular Dynamics Simulation Study.
Volume: 124
Issue: 47
Pages: 10641-10652
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Publication
32531208 | -
First Author: Peng Q
Year: 2020
Journal: Cell Rep
Title: Structural and Biochemical Characterization of the nsp12-nsp7-nsp8 Core Polymerase Complex from SARS-CoV-2.
Volume: 31
Issue: 11
Pages: 107774
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Publication
33116300 | -
First Author: V'kovski P
Year: 2021
Journal: Nat Rev Microbiol
Title: Coronavirus biology and replication: implications for SARS-CoV-2.
Volume: 19
Issue: 3
Pages: 155-170
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Publication
19734957 | -
First Author: Ye Y
Year: 2009
Journal: Mol Biosyst
Title: Dissection of USP catalytic domains reveals five common insertion points.
Volume: 5
Issue: 12
Pages: 1797-808
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Protein
Q3UY73
Organism: Mus musculus/domesticus
Length: 256  
Fragment?: true
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Protein
Q9QWY2
Organism: Mus musculus/domesticus
Length: 1252  
Fragment?: false
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Protein
Q9QYM3
Organism: Mus musculus/domesticus
Length: 1219  
Fragment?: false
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Protein
Q3TQ92
Organism: Mus musculus/domesticus
Length: 267  
Fragment?: true
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Protein
Q5Q9H4
Organism: Mus musculus/domesticus
Length: 275  
Fragment?: false
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Publication
1377403 | -
First Author: Kohlstaedt LA
Year: 1992
Journal: Science
Title: Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor.
Volume: 256
Issue: 5065
Pages: 1783-90
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Publication
32443810 | -
 
First Author: Romano M
Year: 2020
Journal: Cells
Title: A Structural View of SARS-CoV-2 RNA Replication Machinery: RNA Synthesis, Proofreading and Final Capping.
Volume: 9
Issue: 5
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Publication
30383829 | -
First Author: Saberi A
Year: 2018
Journal: PLoS Pathog
Title: A planarian nidovirus expands the limits of RNA genome size.
Volume: 14
Issue: 11
Pages: e1007314
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Publication
28174054 | -
 
First Author: Posthuma CC
Year: 2017
Journal: Virus Res
Title: Nidovirus RNA polymerases: Complex enzymes handling exceptional RNA genomes.
Volume: 234
Pages: 58-73
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Publication
26304538 | -
First Author: Lehmann KC
Year: 2015
Journal: Nucleic Acids Res
Title: Discovery of an essential nucleotidylating activity associated with a newly delineated conserved domain in the RNA polymerase-containing protein of all nidoviruses.
Volume: 43
Issue: 17
Pages: 8416-34
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Protein Domain
IPR028889 | USP_dom
Type: Domain
Description: Protein ubiquitination is a reversible posttranslational modification, whichaffects a large number of cellular processes including protein degradation,trafficking, cell signaling and the DNA damage response. Ubiquitination isreversible, and dedicated deubiquitinases exist which hydrolyze isopeptidebonds. Ubiquitin specific proteases (USPs) () are the largest family of deubiquitinating enzymes. USP domains consist of a common conserved catalytic core which is interspersed at five points with insertions, some of which as large as the catalytic domain itself. The insertions can fold into independent domains that can be involved in the regulation of deubiquitinase activity. As commonly found in signaling proteins, many USP deubiquitinases have a modular architecture, and not only contain a catalytic domain but also additional protein-protein interaction and localisation domains. Most USP domains cleave the isopeptide linkage between two ubiquitin molecules, and hence contain (at least) two ubiquitin-binding sites, one for the distal ubiquitin, the C terminus of which is linked to the Lys residue on the proximal ubiquitin in a second, proximal binding site []. The USP domain forms the peptidase family C19 [].The USP catalytic core can be divided into six conserved boxes that arepresent in all USP domains. Box 1 contains the catalytic Cys residue, box 5contains the catalytic His, and box 6 contains the catalytic Asp/Asn residue.All boxes show several additional conserved features and residues. Boxes 3 and4 contain a Cys-X-X-Cys motif each, which have been shown to constitute afunctional zinc-binding motif. Potentially, zinc-binding facilitates foldingof the USP core, helping the interaction of sequence motifs some few hundredresidues apart. USP domains share a common conserved fold.The USP domain resembles an open hand containing Thumb, Palm and Fingerssubdomains. The catalytic triad resides between the Thumb (Cys) and Palmsubdomains (His/Asp) [].This entry represents the entire USP domain.
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Protein Domain
IPR042087 | DNA_pol_B_thumb
Type: Homologous_superfamily
Description: DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases ) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known, however, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate []. The DNA polymerase structure resembles a right hand with fingers, palm, and thumb, with an active site formed by a palm holding the catalytic residues, a thumb that binds the primer:template DNA and fingers interacting with incoming nucleotide, and the N and Exo domains extend from the finger toward the thumb [, , ].This superfamily represents the thumb domain found at the C-terminal of the DNA polymerase family B proteins.
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Protein Domain
IPR044863 | NIRAN
Type: Domain
Description: Positive-stranded RNA (+RNA) viruses that belong to the order Nidovirales infect a wide range of vertebrates (families Arteriviridae and Coronaviridae) or invertebrates (Mesoniviridae and Roniviridae). Examples of nidoviruses with high economic and societal impact are the arterivirus porcine reproductive and respiratory syndrome virus (PRRSV) and the zoonotic coronaviruses (CoVs) causing severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS) and Covid-19 (SARS-CoV-2) in humans. In all nidoviruses, at least two-thirds of the capacity of the polycistronic genome is occupied by the two large open reading frames (ORFs; 1a and 1b) that together constitute the replicase gene. The two polyproteins produced, pp1a (ORF1a-encoded) and pp1ab (ORF1a/ORF1b-encoded), are processed to a dozen or more proteins by the virus main protease (3CLpro, encoded in ORF1a) with possible involvement of other protease(s). These and other proteins form a membrane-bound replication-transcription complex (RTC) that invariably includes two key ORF1b-encoded subunits: the RNA-dependent RNA polymerase (RdRp) and a superfamily 1 helicase domain (HEL1), which is fused with a multinuclear Zn-binding domain (ZBD). The RNA-dependent RNA polymerase (RdRp) domain of nidoviruses resides in a cleavage product of the replicase polyprotein named non- structural protein (nsp) 12 in coronaviruses and nsp9 in arteriviruses. In all nidoviruses, the C-terminal RdRp domain is linked to a conserved N-terminal domain, which has been coined NiRAN (nidovirus RdRp-associated nucleotidyl transferase). The NiRAN domain has an essential nucleotidylation activity and its potential functions in nidovirus replication may include RNA ligation, protein-primed RNA synthesis, and the guanylyl-transferase function that is necessary for mRNA capping [, , , , ].The NiRAN domain is characterised by an α+β fold composed of eight α-helices and a five stranded β-sheet. In addition, an N-terminal β-hairpin interacts with the palm subdomain of the RdRp domain [, ].
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Protein Domain
IPR006134 | DNA-dir_DNA_pol_B_multi_dom
Type: Domain
Description: DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases ) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known, however, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate []. The DNA polymerase structure resembles a right hand with fingers, palm, and thumb, with an active site formed by a palm holding the catalytic residues, a thumb that binds the primer:template DNA and fingers interacting with incoming nucleotide, and the N and Exo domains extend from the finger toward the thumb [, , ].This domain of DNA polymerase B appears to consist of more than one activities, possibly including elongation, DNA-binding and dNTP binding [].
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Protein Domain
IPR018200 | USP_CS
Type: Conserved_site
Description: Protein ubiquitination is a reversible posttranslational modification, whichaffects a large number of cellular processes including protein degradation,trafficking, cell signaling and the DNA damage response. Ubiquitination isreversible, and dedicated deubiquitinases exist which hydrolyze isopeptidebonds. Ubiquitin specific proteases (USPs) ) are the largest family of deubiquitinating enzymes. USP domains consist of a common conserved catalytic core which is interspersed at five points with insertions, some of which as large as the catalytic domain itself. The insertions can fold into independent domains that can be involved in the regulation of deubiquitinase activity. As commonly found in signaling proteins, many USP deubiquitinases have a modular architecture, and not only contain a catalytic domain but also additional protein-protein interaction and localization domains. Most USP domains cleave the isopeptide linkage between two ubiquitin molecules, and hence contain (at least) two ubiquitin-binding sites, one for the distal ubiquitin, the C terminus of which is linked to the Lys residue on the proximal ubiquitin in a second, proximal binding site []. The USP domain forms the peptidase family C19 [].The USP catalytic core can be divided into six conserved boxes that arepresent in all USP domains. Box 1 contains the catalytic Cys residue, box 5contains the catalytic His, and box 6 contains the catalytic Asp/Asn residue.All boxes show several additional conserved features and residues. Boxes 3 and4 contain a Cys-X-X-Cys motif each, which have been shown to constitute afunctional zinc-binding motif. Potentially, zinc-binding facilitates foldingof the USP core, helping the interaction of sequence motifs some few hundredresidues apart. USP domains share a common conserved fold.The USP domain resembles an open hand containing Thumb, Palm and Fingerssubdomains. The catalytic triad resides between the Thumb (Cys) and Palmsubdomains (His/Asp) [].This entry represents two conserved sites for the USP domain. The first oneis around the catalytic cysteine in box 1, and the second around the catalytichistidine in box 5.
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Publication
28345656 | -
 
First Author: Zhao B
Year: 2017
Journal: Nat Commun
Title: Structure and function of the Zika virus full-length NS5 protein.
Volume: 8
Pages: 14762
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Publication
1875194 | -
 
First Author: Demler SA
Year: 1991
Journal: J Gen Virol
Title: The nucleotide sequence and luteovirus-like nature of RNA 1 of an aphid non-transmissible strain of pea enation mosaic virus.
Volume: 72 ( Pt 8)
Pages: 1819-34
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Publication
2823471 | -
First Author: Wu SX
Year: 1987
Journal: Virology
Title: Sequence and organization of southern bean mosaic virus genomic RNA.
Volume: 161
Issue: 1
Pages: 73-80
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Protein Domain
IPR001795 | RNA-dir_pol_luteovirus
Type: Family
Description: RNA-directed RNA polymerase (RdRp) () is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [, ]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear.The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product []. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb []. Only the catalytic palm subdomain, composed of a four-stranded antiparallel β-sheet with two α-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA [].The domain organisation []and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues.There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage:Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families.Mononegavirales (negative-strand RNA viruses with non-segmented genomes).Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses.Birnaviridae family of dsRNA viruses.The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups:All positive-strand RNA eukaryotic viruses with no DNA stage.All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages).Reoviridae family of dsRNA viruses.The nucleotide sequence for the RNA of Potato leafroll virus (PLrV) has been determined [, ]. The sequence contains six large open reading frames (ORFs). The 5' coding region encodes two polypeptides of 28K and 70K, which overlap in different reading frames; it is suggested that the third ORF in the 5' block is translated by frameshift read through near the end of the 70K protein, yielding a 118K polypeptide []. The C-terminal part of the 118K protein contains a consensus sequence for RNA-dependent RNA-polymerases [].The genomic RNA sequence of Southern bean mosaic virus (SBMV) has been determined []. The genome contains four ORFs. The largest ORF encodes the two largest proteins translated in cell-free extracts from full-length virion RNA []. Segments of the predicted amino acid sequence of this ORF resemble those of known viral RNA-polymerases, ATP-binding proteins and viral genome-linked proteins [].The genome sequence of Pea enation mosaic virus (PEMV) RNA 1 shows strong organisational relationships and sequence similarities to the Beet western yellows virus (BWYV) and PLrV []. Sequence analysis reveals five predominant ORFs. The third ORF is characterised by a number of RNA-polymerase motifs and a helicase-like motif typical of RNA-dependent RNA-polymerases []. It overlaps (out of frame) the ORF 2 product and is proposed to be expressed by a frameshift fusion of ORF 2 and ORF 3 [].The PLrV sequence shows some similarities to the putative polymerase of SBMV [], and more extensive similarities to the corresponding BWYV polypeptide [].
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Publication
2466700 | -
First Author: van der Wilk F
Year: 1989
Journal: FEBS Lett
Title: Nucleotide sequence and organization of potato leafroll virus genomic RNA.
Volume: 245
Issue: 1-2
Pages: 51-6
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Publication
3194229 | -
First Author: Veidt I
Year: 1988
Journal: Nucleic Acids Res
Title: Nucleotide sequence of beet western yellows virus RNA.
Volume: 16
Issue: 21
Pages: 9917-32
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Publication
31138817 | -
First Author: Kirchdoerfer RN
Year: 2019
Journal: Nat Commun
Title: Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors.
Volume: 10
Issue: 1
Pages: 2342
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Protein
P11369
Organism: Mus musculus/domesticus
Length: 1281  
Fragment?: false
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Protein
O08906
Organism: Mus musculus/domesticus
Length: 1300  
Fragment?: true
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Protein
Q9D196
Organism: Mus musculus/domesticus
Length: 462  
Fragment?: true
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•
•
•
•
Protein
Q61785
Organism: Mus musculus/domesticus
Length: 1300  
Fragment?: false
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•
•
•
Protein
Q9QWY3
Organism: Mus musculus/domesticus
Length: 1281  
Fragment?: false
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•
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•
Protein
O88915
Organism: Mus musculus/domesticus
Length: 1281  
Fragment?: false
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•
Protein
Q9QWY0
Organism: Mus musculus/domesticus
Length: 1281  
Fragment?: false
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Protein
Q91Z89
Organism: Mus musculus/domesticus
Length: 1281  
Fragment?: false
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Protein
O54850
Organism: Mus musculus/domesticus
Length: 1281  
Fragment?: false
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•
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•
Protein
Q9QUI2
Organism: Mus musculus/domesticus
Length: 1281  
Fragment?: false
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•
•
•
Protein
Q792I9
Organism: Mus musculus/domesticus
Length: 1281  
Fragment?: false
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•
•
Protein
F6TLB0
Organism: Mus musculus/domesticus
Length: 393  
Fragment?: true
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•
Protein
Q91Z88
Organism: Mus musculus/domesticus
Length: 1281  
Fragment?: false
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Protein
O88913
Organism: Mus musculus/domesticus
Length: 1281  
Fragment?: false
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Protein
O88914
Organism: Mus musculus/domesticus
Length: 1281  
Fragment?: false
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•
Publication
14633974 | -
First Author: Gu W
Year: 2003
Journal: Genes Dev
Title: tRNAHis maturation: an essential yeast protein catalyzes addition of a guanine nucleotide to the 5' end of tRNAHis.
Volume: 17
Issue: 23
Pages: 2889-901
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Publication
20080734 | -
First Author: Abad MG
Year: 2010
Journal: Proc Natl Acad Sci U S A
Title: Template-dependent 3'-5' nucleotide addition is a shared feature of tRNAHis guanylyltransferase enzymes from multiple domains of life.
Volume: 107
Issue: 2
Pages: 674-9
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Publication
16731615 | -
First Author: Jackman JE
Year: 2006
Journal: Proc Natl Acad Sci U S A
Title: tRNAHis guanylyltransferase catalyzes a 3'-5' polymerization reaction that is distinct from G-1 addition.
Volume: 103
Issue: 23
Pages: 8640-5
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Protein Domain
IPR017891 | Insulin_GF-bd_Cys-rich_CS
Type: Conserved_site
Description: The insulin-like growth factors (IGF-I and IGF-II) bind to specific binding proteins in extracellular fluids with high affinity [, ]. These IGF-binding proteins (IGFBP) prolong the half-life of the IGFs and have been shown to either inhibit or stimulate the growth promoting effects of the IGFs on cells culture. They seem to alter the interaction of IGFs with their cell surface receptors. The IGFBP family comprises six proteins (IGFBP-1 to -6) that bind to IGFs with high affinity. The precursor forms of all six IGFBPs have secretory signal peptides. All IGFBPs share a common domain organisation and also a high degree of similarity in their primary protein structure. The highest conservation is found in the N- and C-terminal cysteine-rich regions. Twelve conserved cysteines (ten in IGFBP-6) are found in the N-terminal domain, and six are found in the C-terminal domain. Both the N- and C-terminal domains participate in binding to IGFs, although the specific roles each of these domains in IGF binding have not been decisively established. In general, the strongest binding to IGFs is shown by amino-terminal fragments, which, however bind to IGF with 10- to 1000-fold lower affinity than full length IGFBPs. The central weakly conserved part (L domain) contains most of the cleavage sites for specific proteases [, ].The N-terminal domain is about 80 residues in length and has an L-like structure. It can be divided into two subdomains that are connected by a short stretch of amino acids. The two subdomains are perpendicular to each other, creating the "L"shape for the whole N-terminal domain. The core of the first subdomain presents a novel fold stabilised by a short two-stranded beta sheet and four disulphide bridges forming a disulphide bond ladder-like structure. The beta sheet and disulphide bridges are all in one plane, making the structure appear flat from one side like the "palm"of a hand. The palm is extended with a "thumb"segment in various IGFBPs. The thumb segment consists of the very N-terminal residues and contains a consensus XhhyC motif, where h is a hydrophobic amino acid and y is positively charged. The second subdomain adopts a globular fold whose scaffold is secured by an inside packing of two cysteines bridges stabilised by a three-stranded beta sheet [, ].The following growth-factor inducible proteins are structurally related to IGFBPs and could function as growth-factor binding proteins [, ]:Mouse protein cyr61 and its probable chicken homologue, protein CEF-10.Human connective tissue growth factor (CTGF) and its mouse homologue, protein FISP-12.Vertebrate protein NOV.This entry represents a conserved cysteine-rich region located in the N-terminal IGFBP domain.
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Publication
2732710 | -
 
First Author: Mayo MA
Year: 1989
Journal: J Gen Virol
Title: Nucleotide sequence of potato leafroll luteovirus RNA.
Volume: 70 ( Pt 5)
Pages: 1037-51
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Protein
Q6PB75
Organism: Mus musculus/domesticus
Length: 542  
Fragment?: false
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Protein
Q68ED3
Organism: Mus musculus/domesticus
Length: 633  
Fragment?: false
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•
•
Protein
Q3ULM6
Organism: Mus musculus/domesticus
Length: 1089  
Fragment?: false
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•
•
•
•
Protein
O70372
Organism: Mus musculus/domesticus
Length: 1122  
Fragment?: false
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•
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•
•
Protein
Q8CAG1
Organism: Mus musculus/domesticus
Length: 90  
Fragment?: true
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Protein
E9QLC6
Organism: Mus musculus/domesticus
Length: 1089  
Fragment?: false
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•
•
•
•
Protein
E9QJT6
Organism: Mus musculus/domesticus
Length: 680  
Fragment?: false
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•
•
•
•
Protein
A0A0G2JDV2
Organism: Mus musculus/domesticus
Length: 785  
Fragment?: false
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•
•
•
•
Protein
Q3U7R5
Organism: Mus musculus/domesticus
Length: 541  
Fragment?: false
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•
•
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•
Protein
D3YW34
Organism: Mus musculus/domesticus
Length: 1075  
Fragment?: false
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•
•
•
•
Protein
Q3V059
Organism: Mus musculus/domesticus
Length: 306  
Fragment?: true
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•
•
•
Protein
B7ZMU2
Organism: Mus musculus/domesticus
Length: 590  
Fragment?: false
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•
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•
Protein
E9QAY4
Organism: Mus musculus/domesticus
Length: 168  
Fragment?: false
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•
•
Protein
A0A0R4J244
Organism: Mus musculus/domesticus
Length: 293  
Fragment?: false
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•
•
Protein
D3Z324
Organism: Mus musculus/domesticus
Length: 142  
Fragment?: true
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Protein
Q5Q9G9
Organism: Mus musculus/domesticus
Length: 434  
Fragment?: false
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•
Protein
A0A0R4J1P9
Organism: Mus musculus/domesticus
Length: 890  
Fragment?: false
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•
•
Protein
A0JNY9
Organism: Mus musculus/domesticus
Length: 584  
Fragment?: false
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•
•
•
Protein
F8WI26
Organism: Mus musculus/domesticus
Length: 637  
Fragment?: false
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•
•
•
Protein
E9Q4D8
Organism: Mus musculus/domesticus
Length: 257  
Fragment?: true
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Publication
8396668 | -
First Author: Baker SC
Year: 1993
Journal: J Virol
Title: Identification of the catalytic sites of a papain-like cysteine proteinase of murine coronavirus.
Volume: 67
Issue: 10
Pages: 6056-63
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Protein
Q9D9M2
Organism: Mus musculus/domesticus
Length: 370  
Fragment?: false
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•
Protein
E9Q9U0
Organism: Mus musculus/domesticus
Length: 468  
Fragment?: false
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•
•
•
Protein
Q80TQ2
Organism: Mus musculus/domesticus
Length: 952  
Fragment?: false
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•
•
•
Protein
P70398
Organism: Mus musculus/domesticus
Length: 2559  
Fragment?: false
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•
Protein
Q8BW70
Organism: Mus musculus/domesticus
Length: 1042  
Fragment?: false
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•
Protein
Q8BUM9
Organism: Mus musculus/domesticus
Length: 1132  
Fragment?: false
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•
•
•
Protein
Q3UN04
Organism: Mus musculus/domesticus
Length: 517  
Fragment?: false
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•
•
•
Protein
Q6P8X6
Organism: Mus musculus/domesticus
Length: 390  
Fragment?: false
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•
•
•
Protein
Q8BWR4
Organism: Mus musculus/domesticus
Length: 1235  
Fragment?: false
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•
•
•
Protein
Q5I043
Organism: Mus musculus/domesticus
Length: 1051  
Fragment?: false
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•
•
•
Protein
Q8BY87
Organism: Mus musculus/domesticus
Length: 1376  
Fragment?: false
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•
•
•
•
Protein
Q7M764
Organism: Mus musculus/domesticus
Length: 540  
Fragment?: false
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•
•
•
Protein
Q9ES63
Organism: Mus musculus/domesticus
Length: 869  
Fragment?: false
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•
•
Protein
Q8BJQ2
Organism: Mus musculus/domesticus
Length: 784  
Fragment?: false
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Protein
Q61068
Organism: Mus musculus/domesticus
Length: 526  
Fragment?: false
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Protein
B2RQC2
Organism: Mus musculus/domesticus
Length: 1324  
Fragment?: false
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Protein
O88623
Organism: Mus musculus/domesticus
Length: 613  
Fragment?: false
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•
•
Protein
Q9WTV6
Organism: Mus musculus/domesticus
Length: 368  
Fragment?: false
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•




MouseMine is a collaboration between MGI at The Jackson Laboratory and the InterMine project at the Cambridge Systems Biology Centre. MouseMine is funded through a grant from the NIH/NHGRI.The Jackson Laboratory makes no representation about the suitability or accuracy of this software or data for any purpose, and makes no warranties, either express or implied, including merchantability and fitness for a particular purpose or that the use of this software or data will not infringe any third party patents, copyrights, trademarks, or other rights. the software and data are provided "as is". This software and data are provided to enhance knowledge and encourage progress in the scientific community and are to be used only for research and educational purposes. Any reproduction or use for commercial purpose is prohibited without the prior express written permission of the Jackson Laboratory.

Copyright © 2017 by The Jackson Laboratory. All Rights Reserved

© 2002 - 2017 Department of Genetics, University of Cambridge, Downing Street,
Cambridge CB2 3EH, United Kingdom