|  Help  |  About  |  Contact Us

Search our database by keyword

- or -

Examples

  • Search this entire website. Enter identifiers, names or keywords for genes, diseases, strains, ontology terms, etc. (e.g. Pax6, Parkinson, ataxia)
  • Use OR to search for either of two terms (e.g. OR mus) or quotation marks to search for phrases (e.g. "dna binding").
  • Boolean search syntax is supported: e.g. Balb* for partial matches or mus AND NOT embryo to exclude a term

Search results 1 to 43 out of 43 for Tat

Category restricted to ProteinDomain (x)

0.027s

Categories

Category: ProteinDomain
Type Details Score
Protein Domain
Type: Homologous_superfamily
Description: Like other lentiviruses, Human immunodeficiency virus 1 (HIV-1) encodes a trans-activating regulatory protein (Tat), which is essential for efficient transcription of the viral genome [, ]. Tat acts by binding to an RNA stem-loop structure, the trans-activating response element (TAR), found at the 5' ends of nascent HIV-1 transcripts. In binding to TAR, Tat alters the properties of the transcription complex, recruits a positive transcription elongation complex (P-TEFb) and hence increases the production of full-length viral RNA []. Tat protein also associates with RNA polymerase II complexes during early transcription elongation afterthe promoter clearance and before the synthesis of full-length TAR RNA transcript. This interaction of Tat with RNA polymerase II elongationcomplexes is P-TEFb-independent. There are two Tat binding sites on each transcription elongation complex; one is located onTAR RNA and the other one on RNA polymerase II near the exit site for nascent mRNA transcripts which suggests that two Tat molecules areinvolved in performing various functions during a single round of HIV-1 mRNA synthesis []. The minimum Tat sequence that can mediate specific TAR binding in vitrohas been mapped to a basic domain of 10 amino acids, comprising mostly Arg and Lys residues. Regulatory activity, however, also requires the 47 N-terminal residues, which interact with components of the transcription complex and function as a transcriptional activation domain [, , ].
Protein Domain
Type: Family
Description: DmsD is essential for the biogenesis/assembly of dimethyl sulfoxide (DMSO) reductase in Escherichia coli. DmsD binds the signal peptide of DmsA - the catalytic subunit of the DMSO reductase and a substrate for the Twin-arginine translocase (Tat) pathway - but it is not required for the interaction of the DmsA signal peptide with the Tat system [, ]. DmsD may be part of a chaperone cascade complex that facilitates a folding-maturation pathway for the substrate protein [].
Protein Domain
Type: Family
Description: Members of this uncharacterised protein family are all small, extending 70 or fewer residues from their respective likely start codon. All have the twin-arginine-dependent transport (TAT) signal sequence at the N terminus and a conserved 20-residue C-terminal region that includes the motif Y-[HRK]-X-[TS]-X-H-[IV]-X-X-[YF]-Y. The TAT signal sequence suggests a bound cofactor. All members are encoded near genes for subunits of format dehydrogenase, and may themselves be a subunit or accessory protein of another protein complex.
Protein Domain
Type: Domain
Description: This entry represents a forty-five residue domain in which the last six residues represent the start of a TAT (Twin-Arginine Translocation) sorting signal. TAT allows proteins already folded, with cofactor already bound, to transit the membrane and reach the periplasm with the ability to perform redox or other cofactor-dependent activities. TAT signals are not normally seen so far from a well-supported start site. Proteins containing this domain may all be mutually homologous, with both a molybdenum cofactor-binding domain and a 4Fe-4S dicluster-binding domain.
Protein Domain
Type: Family
Description: DmsD binds to the twin-arginine signal peptide of DmsA and TorA [], although this latter binding is controversial []. It could be required for the biogenesis of DMSO reductase rather than for the targeting of DmsA to the inner membrane [, , ]. It may be part of a chaperone cascade complex that facilitates a folding-maturation pathway for the substrate protein []. This family also includes the chaperon protein YcdY []. YcdY acts as a chaperone that increases YcdX activity, maybe by facilitating the correct insertion of the zinc ions into the catalytic site of YcdX. It is involved in the swarming motility process [].
Protein Domain
Type: Domain
Description: This entry represents the TAT-signal region found in the iron-sulphur subunit of Ubiquinol-cytochrome C reductase (also known as the cytochrome bc1 complex). This enzymex is an oligomeric membrane protein complex that is a component of respiratory and photosynthetic electron transfer chains. It couples the transfer of electrons from ubiquinol to cytochrome c with the generation of a protein gradient across the membrane []. This entry is associated with , and .
Protein Domain
Type: Family
Description: TatD is a Mg(2+)-dependent 3'-5' exonuclease that not only degrades chromosomal DNA during apoptosis but also processes single-stranded DNA during DNA repair [].In E. coli TatD is encoded by a operon that encodes Tat proteins, including TatA, TatB, and TatC, for protein transport via the Tat (Twin-Arginine Translocation) pathway. However, TatD is not involved in the protein export in the Tat pathway [].
Protein Domain
Type: Conserved_site
Description: The twin-arginine translocation (Tat) pathway serves the role of transporting folded proteins across energy-transducing membranes []. Homologues of the genes that encode the transport apparatus occur in archaea, bacteria, chloroplasts, and plant mitochondria []. In bacteria, the Tat pathway catalyses the export of proteins from the cytoplasm across the inner/cytoplasmic membrane. In chloroplasts, the Tat components are found in the thylakoid membrane and direct the import of proteins from the stroma. The Tat pathway acts separately from the general secretory (Sec) pathway, which transports proteins in an unfolded state [].It is generally accepted that the primary role of the Tat system is to translocate fully folded proteins across membranes. An example of proteins that need to be exported in their 3D conformation are redox proteins that have acquired complex multi-atom cofactors in the bacterial cytoplasm (or the chloroplast stroma or mitochondrial matrix). They include hydrogenases, formate dehydrogenases, nitrate reductases, trimethylamine N-oxide (TMAO) reductases and dimethyl sulphoxide (DMSO) reductases [, ]. The Tat system can also export whole heteroligomeric complexes in which some proteins have no Tat signal. This is the case of the DMSO reductase or formate dehydrogenase complexes. But there are also other cases where the physiological rationale for targeting a protein to the Tat signal is less obvious. Indeed, there are examples of homologous proteins that are in some cases targeted to the Tat pathway and in other cases to the Sec apparatus. Some examples are: copper nitrite reductases, flavin domains of flavocytochrome c and N-acetylmuramoyl-L-alanine amidases [].In halophilic archaea such as Halobacterium almost all secreted proteins appear to be Tat targeted. It has been proposed to be a response to the difficulties these organisms would otherwise face in successfully folding proteins extracellularly at high ionic strength [].The Tat signal peptide consists of three motifs: the positively charged N-terminal motif, the hydrophobic region and the C-terminal region that generally ends with a consensus short motif (A-x-A) specifying cleavage by signal peptidase. Sequence analysis revealed that signal peptides capable of targeting the Tat protein contain the consensus sequence [ST]-R-R-x-F-L-K. The nearly invariant twin-arginine gave rise to the pathway's name. In addition the h-region of Tat signal peptides is typically less hydrophobic than that of Sec-specific signal peptides [, ].This entry represents the Tat signal, from the methionine to the A-x-A short motif.
Protein Domain
Type: Family
Description: Like other lentiviruses, Human immunodeficiency virus 1 (HIV-1) encodes a trans-activating regulatory protein (Tat), which is essential for efficient transcription of the viral genome [, ]. Tat acts by binding to an RNA stem-loop structure, the trans-activating response element (TAR), found at the 5' ends of nascent HIV-1 transcripts. In binding to TAR, Tat alters the properties of the transcription complex, recruits a positive transcription elongation complex (P-TEFb) and hence increases the production of full-length viral RNA []. Tat protein also associates with RNA polymerase II complexes during early transcription elongation afterthe promoter clearance and before the synthesis of full-length TAR RNA transcript. This interaction of Tat with RNA polymerase II elongationcomplexes is P-TEFb-independent. There are two Tat binding sites on each transcription elongation complex; one is located onTAR RNA and the other one on RNA polymerase II near the exit site for nascent mRNA transcripts which suggests that two Tat molecules areinvolved in performing various functions during a single round of HIV-1 mRNA synthesis []. The minimum Tat sequence that can mediate specific TAR binding in vitrohas been mapped to a basic domain of 10 amino acids, comprising mostly Arg and Lys residues. Regulatory activity, however, also requires the 47 N-terminal residues, which interact with components of the transcription complex and function as a transcriptional activation domain [, , ].
Protein Domain
Type: Conserved_site
Description: The twin-arginine translocation (Tat) pathway serves the role of transporting folded proteins across energy-transducing membranes []. Homologues of the genes that encode the transport apparatus occur in archaea, bacteria, chloroplasts, and plant mitochondria []. In bacteria, the Tat pathway catalyses the export of proteins from the cytoplasm across the inner/cytoplasmic membrane. In chloroplasts, the Tat components are found in the thylakoid membrane and direct the import of proteins from the stroma. The Tat pathway acts separately from the general secretory (Sec) pathway, which transports proteins in an unfolded state [].It is generally accepted that the primary role of the Tat system is to translocate fully folded proteins across membranes. An example of proteins that need to be exported in their 3D conformation are redox proteins that have acquired complex multi-atom cofactors in the bacterial cytoplasm (or the chloroplast stroma or mitochondrial matrix). They include hydrogenases, formate dehydrogenases, nitrate reductases, trimethylamine N-oxide (TMAO) reductases and dimethyl sulphoxide (DMSO) reductases [, ]. The Tat system can also export whole heteroligomeric complexes in which some proteins have no Tat signal. This is the case of the DMSO reductase or formate dehydrogenase complexes. But there are also other cases where the physiological rationale for targeting a protein to the Tat signal is less obvious. Indeed, there are examples of homologous proteins that are in some cases targeted to the Tat pathway and in other cases to the Sec apparatus. Some examples are: copper nitrite reductases, flavin domains of flavocytochrome c and N-acetylmuramoyl-L-alanine amidases [].In halophilic archaea such as Halobacterium almost all secreted proteins appear to be Tat targeted. It has been proposed to be a response to the difficulties these organisms would otherwise face in successfully folding proteins extracellularly at high ionic strength [].The Tat signal peptide consists of three motifs: the positively charged N-terminal motif, the hydrophobic region and the C-terminal region that generally ends with a consensus short motif (A-x-A) specifying cleavage by signal peptidase. Sequence analysis revealed that signal peptides capable of targeting the Tat protein contain the consensus sequence [ST]-R-R-x-F-L-K. The nearly invariant twin-arginine gave rise to the pathway's name. In addition the h-region of Tat signal peptides is typically less hydrophobic than that of Sec-specific signal peptides [, ].
Protein Domain
Type: Family
Description: The Sec-independent protein export system TAT, or twin-arginine translocation, is composed of TatA, TatB, and TatC. The TAT system is unusual in Leptospira, with Lys replacing Arg in the second position of the twin-Arg motif. This protein, restricted to Leptospira and showing distant homology to the phosphoserine phosphatases RsbU and SpoIIE, is always encoded immediately downstream of the tatC gene and appears to be part of the variant TAT system. It lacks a TAT signal itself, and so is more likely to be part of the Sec-independent translocation machinery than to be a substrate. The suggested symbol is rktP, for RK-Translocation Phosphatase.
Protein Domain
Type: Family
Description: These sequences represent the CopA copper resistance protein family. CopA is related to laccase (benzenediol:oxygen oxidoreductase) and L-ascorbate oxidase, both copper-containing enzymes. Most members have a typical TAT (twin-arginine translocation) signal sequence with an Arg-Arg pair. Twin-arginine translocation is observed for a large number of periplasmic proteins that cross the inner membrane with metal-containing cofactors already bound. The combination of copper-binding sites and TAT translocation motif suggests a mechanism of resistance by packaging and export.
Protein Domain
Type: Family
Description: This protein family includes 3'-5' ssDNA/RNA exonuclease TatD and many uncharacterised deoxyribonucleases and metal-dependent hydrolases. The family is related to a large superfamily of metalloenzymes []. TatD has been shown to be a 3'-5' exonuclease that processes single-stranded DNA in DNA repair [, ].In E. coli TatD, which adopts a TIM-barrel fold, is encoded by a operon that encodes Tat proteins, including TatA, TatB, and TatC, for protein transport via the Tat (Twin-Arginine Translocation) pathway. However, TatD is not involved in the protein export in the Tat pathway [].Deoxyribonuclease TATDN1 from Danio rerio (Zebrafish) catalyses (in vitro) the decatenation of kinetoplast DNA producing linear DNA molecules. It is involved in chromosomal segregation and cell cycle progression during eye development []. TATDN1 has been related to several types of cancer [, , ].
Protein Domain
Type: Homologous_superfamily
Description: Aralkylamine dehydrogenase light chain and methylamine dehydrogenase light chain are aromatic amine dehydrogenases that form heterotetramers with their respective heavy chains, and catalyse the oxidative deamination of amines to their corresponding aldehydes.The light subunit possesses an apparent Tat signal peptide. This subunit is dominated by beta structure [].
Protein Domain
Type: Family
Description: This entry describes a small collection of probable metallophosphoresterases, related to . Members of this protein family usually have a Sec-independent TAT (twin-arginine translocation) signal sequence, N-terminal to the region modeled by this HMM. This model and divide a narrow clade of -related enzymes.
Protein Domain
Type: Family
Description: This entry describes a small collection of probable metallophosphoresterases, related to but with long inserts separating some of the shared motifs such that the homology is apparent only through multiple sequence alignment. Members of this protein family, in general, have a Sec-independent TAT (twin-arginine translocation) signal sequence, N-terminal to the region modeled by this HMM. Members include YP_056203.1 from Propionibacterium acnes KPA171202.
Protein Domain
Type: Family
Description: Homologous-pairing protein 2 (Hop2) is required for proper homologous pairing and efficient cross-over and intragenic recombination during meiosis [, , ].The mammalian HOP2 homologue, TBPIP, was first identified as a factor interacting with TBP-1, which binds to the human immunodeficiency virus, type 1 Tat protein []. Later, TBPIP was found to be an activator that specifically stimulates the homologous pairing catalyzed by DMC1 [].
Protein Domain
Type: Family
Description: Nitrous-oxide reductase is part of a bacterial respiratory system which is activated under anaerobic conditions in the presence of nitrate or nitrous oxide. NosZ, one of the members of this family, is the nitrous-oxide reductase structural protein, with an N-terminal twin-arginine translocation (TAT) signal sequence. The TAT system replaces the Sec system for export of proteins with bound cofactor [].
Protein Domain
Type: Family
Description: Proteins encoded by the mttABC operon (formerly yigTUW), mediate a novel Sec-independent membrane targeting and translocation system in Escherichia coli that interacts with cofactor-containing redox proteins having a S/TRRXFLK "twin arginine"leader motif. This family contains the E. coli mttB gene (TATC) [].A functional Tat system or Delta pH-dependent pathway requires three integral membrane proteins: TatA/Tha4, TatB/Hcf106 and TatC/cpTatC. The TatC protein is essential for the function of both pathways. It might be involved in twin-arginine signal peptide recognition, protein translocation and proton translocation. Sequence analysis predicts that TatC contains six transmembrane helices (TMHs), and experimental data confirmed that N and C termini of TatC or cpTatC are exposed to the cytoplasmic or stromal face of the membrane. The cytoplasmic N terminus and the first cytoplasmic loop region of the E. coli TatC protein are essential for protein export. At least two TatC molecules co-exist within each Tat translocon [, ].
Protein Domain
Type: Conserved_site
Description: Proteins encoded by the mttABC operon (formerly yigTUW), mediate a novel Sec-independent membrane targeting and translocation system in Escherichia coli that interacts with cofactor-containing redox proteins having a S/TRRXFLK "twin arginine"leader motif. This family contains the E. coli mttB gene (TATC) [].A functional Tat system or Delta pH-dependent pathway requires three integral membrane proteins: TatA/Tha4, TatB/Hcf106 and TatC/cpTatC. The TatC protein is essential for the function of both pathways. It might be involved in twin-arginine signal peptide recognition, protein translocation and proton translocation. Sequence analysis predicts that TatC contains six transmembrane helices (TMHs), and experimental data confirmed that N and C termini of TatC or cpTatC are exposed to the cytoplasmic or stromal face of the membrane. The cytoplasmic N terminus and the first cytoplasmic loop region of the E. coli TatC protein are essential for protein export. At least two TatC molecules co-exist within each Tat translocon [, ].This entry represents a conserved site from the central section of these proteins.
Protein Domain
Type: Family
Description: This very narrowly defined family represents trimethylamine-N-oxide (TMAO) reductase TorA. TorA typically is located in the periplasm, has a Tat (twin-arginine translocation)-dependent signal sequence, and is encoded in a torCAD operon. TorA reduces TMAO into trimethylamine; an anaerobic reaction coupled to energy-yielding reactions [, ]. The torC gene, located upstream from torA encodes a pentahemic c-type cytochrome, likely to be involved in electron transfer to the TorA terminal reductase [].
Protein Domain
Type: Family
Description: This entry represents a putative redox-active protein of about 140 residues, with four perfectly conserved Cys residues. It includes a CGAXXG motif. Most members are found within one or two loci of transporter or oxidoreductase genes. A member from Geobacter sulfurreducens, located in a molybdenum transporter operon, has a TAT (twin-arginine translocation) signal sequence for Sec-independent transport across theplasma membrane, a hallmark of bound prosthetic groups such as FeS clusters.
Protein Domain
Type: Domain
Description: Homologous-pairing protein 2 (Hop2) is required for proper homologous pairing and efficient cross-over and intragenic recombination during meiosis [, , ].The mammalian HOP2 homologue, TBPIP, was first identified as a factor interacting with TBP-1, which binds to the human immunodeficiency virus, type 1 Tat protein []. Later, TBPIP was found to be an activator that specifically stimulates the homologous pairing catalyzed by DMC1 []. This entry represents the winged helix domain found in Hop2.
Protein Domain
Type: Domain
Description: This region contains a probable site of ubiquitination that ensures rapid degradation of tyrosine aminotransferase in rats. The half life of the enzyme in vivois about 2-4 hours. The enzyme contains at least 2 phosphorylation sites including CAPK at Ser29 and, at the other end of the protein, a casein kinase II site at S*QEECDK. This region of TAT is probably primarily related to regulatory events. Most other transaminases are much more stable and are not phosphorylated.
Protein Domain
Type: Family
Description: Translocation of proteins across the two membranes of Gram-negative bacteriacan be carried out via a number of routes. Most proteins marked for export carry a secretion signal at their N terminus, and are secreted by the general secretory pathway. The signal peptide is cleaved as they pass through the outer membrane. Other secretion systems include the type III system found in a select group of Gram-negative plant and animal pathogens, and the CagA system of Helicobacter pylori [].In some bacterial species, however, there exists a system that operates independently of the Sec pathway []. It selectively translocates periplasmic-bound molecules that are synthesised with, or are in close association with, "partner"proteins bearing an (S/T)RRXFLK twin arginine motif at the N terminus. The pathway is therefore termed the Twin-Arginine Translocation or TAT system. Surprisingly, the four components that make up the TAT system are structurally and mechanistically related to a pH-dependent import system in plant chloroplast thylakoid membranes []. Thegene products responsible for the Sec-independent pathway are called TatA,TatB, TatC and TatE.This entry represents Sec-independent protein translocase protein TatB (TatB) and similar proteins predominantly found in Proteobacteria. TatB is essential for the secretion of large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes. It may form an oligomeric binding site that transiently accommodates folded Tat precursor proteins before their translocation []. It may form a circular arrangement with TatC [].
Protein Domain
Type: Family
Description: This entry represents a group of prokaryotic molybdopterin-containing oxidoreductases, including Arsenite oxidase subunit AioB from Alcaligenes faecalis and Iodate reductase subunit IdrB from Pseudomonas sp. AioB is the small subunit of an arsenite oxidase complex. It is a Rieske protein and appears to rely on the Tat (twin-arginine translocation) system to cross the membrane. Although this enzyme could run in the direction of arsenate reduction to arsenite in principle, the relevant biological function is arsenite oxidation for energy metabolism, not arsenic resistance [, ]. IdrB, a Rieske-type protein with a [2Fe-2S]-binding motif, is involved in iodate respiration [, ].
Protein Domain
Type: Domain
Description: This entry represents the RNA recognition motif 1 (RRM1) of Tat-SF1, which interacts with components of both the transcription and splicing machineries []. It has been shown to be a cofactor for human immunodeficiency virus-type 1 (HIV-1) Tat, which stimulates transcription elongation of HIV-1 through a series of events termed Tat transactivation [, ]. It contains two RNA recognition motifs (RRMs) and a highly acidic carboxyl-terminal half. Proteins containing this domain also include Cus2, a yeast homologue of human Tat-SF1. Cus2 interacts with U2 snRNA and Prp11, a subunit of the conserved splicing factor SF3a []. Like Tat-SF1, Cus2 contains two RRMs.
Protein Domain
Type: Family
Description: Tat-SF1 (HIV Tat-specific factor 1) interacts with components of both the transcription and splicing machineries []. It has been shown to be a cofactor for human immunodeficiency virus-type 1 (HIV-1) Tat, which stimulates transcription elongation of HIV-1 through a series of events termed Tat transactivation [, ]. It contains two RNA recognition motifs (RRMs) and a highly acidic carboxyl-terminal half. This entry also includes Cus2, a yeast homologue of human Tat-SF1. Cus2 interacts with U2 snRNA and Prp11, a subunit of the conserved splicing factor SF3a []. Like Tat-SF1, Cus2 contains two RRMs.
Protein Domain
Type: Domain
Description: This entry represents the C-terminal methyltransferase domain of TARBP1 and Trm3 [].Yeast tRNA (guanosine(18)-2'-O)-methyltransferase Trm3 catalyses the formation of 2'-O-methylguanosine at position 18 (Gm18) in various tRNAs []. Trm3 is similar to C-terminal domain of TAR (HIV-1) RNA binding protein 1 (TARBP1), a protein binding to TAR, which functions as a RNA regulatory signal by forming a stable stem-loop structure to which transactivator protein Tat binds. The role of TARBP1 is believed to be to disengage RNA polymerase II from TAR during transcriptional elongation [, ].
Protein Domain
Type: Family
Description: Members of this family are radical SAM proteins found in about 5 percent of microbial genomes. A portion occur as gene fusions with, or adjacent to, members of the TatD family of hydrolases (). The TatD family may have several paralogs per genome, including TatD itself from E. coli (a soluble protein not actually part of the twin-arginine translocation complex), which appears to act in quality control for TAT, directing turnover of misfolded TAT substrates. The functions of TatD family hydrolases in general (other than TatD itself, which may be exceptional within its larger family), and of this radical SAM domain protein modeled here, are unknown.
Protein Domain
Type: Family
Description: Translocation of proteins across the two membranes of Gram-negative bacteriacan be carried out via a number of routes. Most proteins marked for export carry a secretion signal at their N terminus, and are secreted by the general secretory pathway. The signal peptide is cleaved as they pass through the outer membrane. Other secretion systems include the type III system found in a select group of Gram-negative plant and animal pathogens, and the CagA system of Helicobacter pylori [].In some bacterial species, however, there exists a system that operates independently of the Sec pathway []. It selectively translocates periplasmic-bound molecules that are synthesised with, or are in close association with, "partner"proteins bearing an (S/T)RRXFLK twin arginine motif at the N terminus. The pathway is therefore termed the Twin-Arginine Translocation or TAT system. Surprisingly, the four components that make up the TAT system are structurally and mechanistically related to a pH-dependent import system in plant chloroplast thylakoid membranes []. Thegene products responsible for the Sec-independent pathway are called TatA,TatB, TatC and TatE.This entry represents the related TatA, TatB and TatE proteins.
Protein Domain
Type: Family
Description: Translocation of proteins across the two membranes of Gram-negative bacteriacan be carried out via a number of routes. Most proteins marked for export carry a secretion signal at their N terminus, and are secreted by the general secretory pathway. The signal peptide is cleaved as they pass through the outer membrane. Other secretion systems include the type III system found in a select group of Gram-negative plant and animal pathogens, and the CagA system of Helicobacter pylori [].In some bacterial species, however, there exists a system that operates independently of the Sec pathway []. It selectively translocates periplasmic-bound molecules that are synthesised with, or are in close association with, "partner"proteins bearing an (S/T)RRXFLK twin arginine motif at the N terminus. The pathway is therefore termed the Twin-Arginine Translocation or TAT system. Surprisingly, the four components that make up the TAT system are structurally and mechanistically related to a pH-dependent import system in plant chloroplast thylakoid membranes []. Thegene products responsible for the Sec-independent pathway are called TatA,TatB, TatC and TatE.TatE is highly related to TatA and these proteins appear to overlap in functionality []. Translocation occurred in single mutants of either TatA or TatE, though much less efficiently, but double mutants showed no detectable translocation.
Protein Domain
Type: Family
Description: Translocation of proteins across the two membranes of Gram-negative bacteriacan be carried out via a number of routes. Most proteins marked for export carry a secretion signal at their N terminus, and are secreted by the general secretory pathway. The signal peptide is cleaved as they pass through the outer membrane. Other secretion systems include the type III system found in a select group of Gram-negative plant and animal pathogens, and the CagA system of Helicobacter pylori [].In some bacterial species, however, there exists a system that operates independently of the Sec pathway []. It selectively translocates periplasmic-bound molecules that are synthesised with, or are in close association with, "partner"proteins bearing an (S/T)RRXFLK twin arginine motif at the N terminus. The pathway is therefore termed the Twin-Arginine Translocation or TAT system. Surprisingly, the four components that make up the TAT system are structurally and mechanistically related to a pH-dependent import system in plant chloroplast thylakoid membranes []. Thegene products responsible for the Sec-independent pathway are called TatA,TatB, TatC and TatE.TatA and TatE are highly related proteins and appear to overlap in functionality []. Translocation occurred in single mutants of either TatA or TatE, though much less efficiently, but double mutants showed no detectable translocation.
Protein Domain
Type: Family
Description: Glucose-fructose oxidoreductase (GFOR) catalyses the formation of D-gluconolactone and D-glucitol from D-glucose and D-fructose. It hasone tightly-bound NADP(H) per enzyme subunit, it exists as a homotetramer,and is one of the pivotal proteins in the sorbitol-gluconate pathway. It istargeted to the periplasm of the Gram-negative cell envelope, and belongs tothe GFO/IDH/MOCA superfamily. First discovered in Zymomonas mobilis, homologues have also been found in Caulobacter crescentus and Deinococcus radiodurans.GFOR is of great interest as its mechanism of secretion into the bacterialperiplasm differs from other precursor proteins of the Twin ArginineTranslocation (TAT) pathway []. Although it exhibits the consensus TAT signal motif (S/T-R-R-x-L-F-K) at its N terminus, unlike other TAT proteins that can be universally secreted across a number of Gram-negative microbes, GFOR is only translocated in Z. mobilis. However, replacing the Z. mobilis signal peptide with one from Escherichia coli restores this function. This observation has led to the suggestion that TAT-dependent precursors are optimally adapted only to their particular cognate secretion apparatus [].Recently, the crystal structure of Z. mobilis GFOR was resolved to 2.5A bymeans of X-ray crystallography. This revealed that the protein indeed exists as a homotetramer, and has 4 active sites. There are 2 distinct domains: a classical dinucleotide binding fold at the N terminus and a 9-stranded β-sheet at the C terminus. NADP(H) is bound to the N terminus of the first α-helix.
Protein Domain
Type: Family
Description: The purine-rich element binding (Pur) protein family protein consists PURalpha/beta/gamma in humans. Pur-alpha is a highly conserved, sequence-specific DNA- and RNA-binding protein involved in diverse cellular and viral functions including transcription, replication, and cell growth. Pur-alpha has a modular structure with alternating three basic aromatic class I and two acidic leucine-rich class II repeats in the central region of the protein []. In addition to its involved in basic cellular function, Pur-alpha, has been implicated in the development of blood cells and cells of the central nervous system; it has also been implicated in the inhibition of oncogenic transformation and along with Pur-beta in myelodysplastic syndrome progressing to acute myelogenous leukemia. Pur-alpha can influence viral interaction through functional associations, for example with the Tat protein and TAR RNA of HIV-1, and with large T-antigen and DNA regulatory regions of JC virus. JC virus causes opportunistic infections in the brains of certain HIV-1-infected individuals [].
Protein Domain
Type: Family
Description: This family consists of MyoD family inhibitor (I-mfa, MDFI) and MyoD family inhibitor domain-containing protein. I-mfa acts as a transcriptional activator or repressor. It retains nuclear Zic family proteins (ZIC1, ZIC2 and ZIC3) in the cytoplasm and consequently inhibits their transcriptional activation ability []. I-mfa domain-containing protein interacts with HAND1 (bHLH transcription factor), leading to sequester HAND1 into the nucleolus and prevent its activity []. In humans modulates the expression from both cellular and viral promoters. It down-regulates Tat-dependent transcription of the human immunodeficiency virus type 1 (HIV-1) LTR by interacting with HIV-1 Tat and Rev and impairing their nuclear import, probably by rendering the NLS domains inaccessible to importin-beta. It also stimulates activation of human T-cell leukemia virus type I (HTLV-I) LTR [, , ]. Both I-mfa and I-mfa domain-containing protein interact with the axin complex and affect axin regulation of both the Wnt and the JNK activation pathways [].
Protein Domain
Type: Family
Description: Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). This entry represents cyclin-T1 and cyclin-T.Cyclin-T associates with CDK9. Both cyclin-T and CDK9 are subunits of the positive-transcription elongation factor (P-TEFb), which facilitates transcription elongation by phosphorylating the carboxy-terminal domain (CTD) of the largest subunit of pol II []. In humans, there are three T-type cyclins: cyclins T1, T2a and T2b. Cyclins T2a and T2b are splice variants of a primary transcript []. Each of the T-type cyclin/CDK9 complexes can phosphorylate the C-terminal domain of the large subunit of RNA polymerase II. However, only human cyclin T1/CDK9 complexes can bind HIV Tat and promote RNA Pol II activation, allowing transcription of viral genes [, , , ].
Protein Domain
Type: Family
Description: This entry represents a small family of proteins with a typical Tat (twin-arginine translocation) signal sequence, suggesting that the family is exported in a folded state, perhaps with a bound redox cofactor. Proteins in this family include deferrochelatase/peroxidase EfeB, which is involved in the recovery of exogenous heme iron. It extracts iron from heme while preserving the tetrapyrrole ring intact [, ]. Crystal structure of EfeB revealed that it has ferredoxin-like fold domains (N- and C-terminal) consisting of an α+β fold that contains an antiparallel β-sheet composed of four β-strands. A large heme binding pocket is located in the C-terminal domain []. This entry also includes deferrochelatase/peroxidase EfeN from Bacillus subtilis, which shows two domains with a ferredoxin-fold and best activity in the acidic range of pH [].
Protein Domain
Type: Domain
Description: Alkaline phosphatase D (PhoD) []catalyses the reaction: phosphate monoester + H(2)O = an alcohol + phosphate. PhoD is similar to Ca(2+)-dependent phospholipase D [], which catalyses the hydrolysis of the ester bond between the phosphatidic acid and alcohol moieties of phospholipids [, ].PhoD (also known as alkaline phosphatase D/APaseD in Bacillus subtilis) is a secreted phosphodiesterase encoded by phoD of the Pho regulon in Bacillus subtilis. PhoD homologs are found in prokaryotes, eukaryotes, and archaea. PhoD contains a twin arginine (RR) motif and is transported by the Tat (Twin-arginine translocation) translocation pathway machinery (TatAyCy) [, , , ]. Proteins containing this domain also includes the Fusarium oxysporum Fso1 protein []. PhoD belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but allshare a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double β-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination [].
Protein Domain
Type: Family
Description: This entry represents a family of proteins which are involved in enzymes assembly and/or maturation: The TorD protein is involved in the maturation of the the trimethylamine N-oxide reductase TorA (a DMSO reductase family member) in Escherichia coli []. TorA is a molybdenum-containing enzyme which requires the the insertion of a bis(molybdopterin guanine dinucleotide) molybdenum (bis(MGD)Mo) cofactor in its catalytic site to be active and translocated to the periplasm. TorD acts as a chaperone, binding to apoTorA and promoting efficient incorporation of the cofactor into the protein.Nitrate reductase delta subunit (NarJ). This subunit is not part of the nitrate reductase enzyme but is a chaperone required for proper molybdenum cofactor insertion and final assembly of the nitrate reductase [, , ]. NarJ exhibits sequence homology to chaperones involved in maturation and cofactor insertion of E. coli redox enzymes that are mediated by twin-arginine translocase (Tat) dependent translocation []. The archetypal Tat proofreading chaperones belong to the TorD family [].Twin-arginine leader-binding protein DmsD, which could be required for the biogenesis of DMSO reductase rather than for the targeting of DmsA to the inner membrane [, , ].Dimethyl sulphide dehydrogenase protein DdhD. This protein is thought to function as chaperone protein in the assembly of an active dimethyl sulphide dehydrogenase DdhABC [].
Protein Domain
Type: Domain
Description: This entry represents the RNA recognition motif 1 (RRM1) of SART3 (also known as Tip110), which is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver []. It is involved in the regulation of mRNA splicing probably via its complex formation with RNPS1 (an RNA-binding protein with a serine-rich domain), a pre-mRNA-splicing factor []. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication []. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies []. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro [].SART3 contains an N-terminal HAT (half-a-tetratricopeptide repeat)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs).
Protein Domain
Type: Domain
Description: This entry represents the RNA recognition motif 2 (RRM2) of SART3 (also known as Tip110), which is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver []. It is involved in the regulation of mRNA splicing probably via its complex formation with RNPS1 (an RNA-binding protein with a serine-rich domain), a pre-mRNA-splicing factor []. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication []. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies []. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro [].SART3 contains a HAT (N-terminal half-a-tetratricopeptide repeat)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs).
Protein Domain
Type: Family
Description: Many bacterial species are capable of anaerobic growth by using dimethylsulphoxide (DMSO) as the terminal electron acceptor, with DMSO reductase as the terminal elctron transfer enzyme. In Escherichia coli and many other Gram-negative bacteria DMSO reductase is a membrane-bound enzyme composed of three subunits; a catalytic molybdenum-containing subunit (DmsA), an electron transfer subunit containing a [4Fe-4S]cluster (DmsB), and a hydrophobic membrane-spanning anchor subunit which attaches the enzyme to the cytoplasmic membrane (DmsC) [, ]. It is generally thought now that DmsAB faces the periplasm, contradicting previous results suggesting a cytoplasmic location. The N-terminal region of DmsA contains a "twin-arginine"signal sequence, suggesting export to the periplasm occurs via the TAT secretion pathway.This entry represents known and predicted bacterial DmsA polypeptides. Several species contain one or more paralogs of DmsA. In E. coli, the two paralogs of DmsA, YnfE and YnfF, are encoded within the ynfEFGHI operon []. YnfE and YnfF cannot form a functional complex with DmsBC, but YnfFGH can restore growth on DMSO when DmABC is deleted. The function of YnfE is not known and it appears to prevent formation of the YnfFGH complex if present.