| Type |
Details |
Score |
| Publication |
| First Author: |
Justino MC |
| Year: |
2005 |
| Journal: |
J Biol Chem |
| Title: |
New genes implicated in the protection of anaerobically grown Escherichia coli against nitric oxide. |
| Volume: |
280 |
| Issue: |
4 |
| Pages: |
2636-43 |
|
•
•
•
•
•
|
| Publication |
| First Author: |
van der Ploeg JR |
| Year: |
1997 |
| Journal: |
J Bacteriol |
| Title: |
Involvement of CysB and Cbl regulatory proteins in expression of the tauABCD operon and other sulfate starvation-inducible genes in Escherichia coli. |
| Volume: |
179 |
| Issue: |
24 |
| Pages: |
7671-8 |
|
•
•
•
•
•
|
| Publication |
| First Author: |
Seeger C |
| Year: |
1995 |
| Journal: |
J Bacteriol |
| Title: |
Identification and characterization of genes (xapA, xapB, and xapR) involved in xanthosine catabolism in Escherichia coli. |
| Volume: |
177 |
| Issue: |
19 |
| Pages: |
5506-16 |
|
•
•
•
•
•
|
| Publication |
| First Author: |
van Der Ploeg JR |
| Year: |
1999 |
| Journal: |
J Biol Chem |
| Title: |
The Escherichia coli ssuEADCB gene cluster is required for the utilization of sulfur from aliphatic sulfonates and is regulated by the transcriptional activator Cbl. |
| Volume: |
274 |
| Issue: |
41 |
| Pages: |
29358-65 |
|
•
•
•
•
•
|
| Publication |
| First Author: |
Fukami-Kobayashi K |
| Year: |
1999 |
| Journal: |
J Mol Biol |
| Title: |
Domain dislocation: a change of core structure in periplasmic binding proteins in their evolutionary history. |
| Volume: |
286 |
| Issue: |
1 |
| Pages: |
279-90 |
|
•
•
•
•
•
|
| Publication |
| First Author: |
Maddocks SE |
| Year: |
2008 |
| Journal: |
Microbiology |
| Title: |
Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins. |
| Volume: |
154 |
| Issue: |
Pt 12 |
| Pages: |
3609-23 |
|
•
•
•
•
•
|
| Publication |
| First Author: |
Felder CB |
| Year: |
1999 |
| Journal: |
AAPS PharmSci |
| Title: |
The Venus flytrap of periplasmic binding proteins: an ancient protein module present in multiple drug receptors. |
| Volume: |
1 |
| Issue: |
2 |
| Pages: |
E2 |
|
•
•
•
•
•
|
| Publication |
| First Author: |
Hill M |
| Year: |
2011 |
| Journal: |
PLoS One |
| Title: |
Penicillin binding proteins as danger signals: meningococcal penicillin binding protein 2 activates dendritic cells through Toll-like receptor 4. |
| Volume: |
6 |
| Issue: |
10 |
| Pages: |
e23995 |
|
•
•
•
•
•
|
| Publication |
| First Author: |
Nicholas RA |
| Year: |
2003 |
| Journal: |
J Biol Chem |
| Title: |
Crystal structure of wild-type penicillin-binding protein 5 from Escherichia coli: implications for deacylation of the acyl-enzyme complex. |
| Volume: |
278 |
| Issue: |
52 |
| Pages: |
52826-33 |
|
•
•
•
•
•
|
| Publication |
| First Author: |
Nohno T |
| Year: |
1986 |
| Journal: |
Mol Gen Genet |
| Title: |
Cloning and complete nucleotide sequence of the Escherichia coli glutamine permease operon (glnHPQ). |
| Volume: |
205 |
| Issue: |
2 |
| Pages: |
260-9 |
|
•
•
•
•
•
|
| Publication |
| First Author: |
Hing AW |
| Year: |
1994 |
| Journal: |
Biochemistry |
| Title: |
An investigation of the ligand-binding site of the glutamine-binding protein of Escherichia coli using rotational-echo double-resonance NMR. |
| Volume: |
33 |
| Issue: |
29 |
| Pages: |
8651-61 |
|
•
•
•
•
•
|
| Protein Domain |
| Type: |
Domain |
| Description: |
GlnH belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor []. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggersthe ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis [, ]. |
|
•
•
•
•
•
|
| Protein Domain |
| Type: |
Homologous_superfamily |
| Description: |
This superfamily represents a structural motif found at the C-terminal of penicillin-binding proteins 4 (PBP4) and 5 (PBP5), as well as at the C-terminal of D-Ala-D-Ala carboxypeptidase A, a member of the MEROPS S11 peptidase family (PBP4 and PBP5 also belong to this peptidase family). These domains share a similar structure, consisting of a β-sandwich of six strands in two sheets [, ].Penicillin-binding proteins are beta-lactam antibiotic-sensitive bacterial enzymes required for the growth and maintenance of the peptidoglycan layer of the bacterial cell wall that protects the cell from osmotic stress. PBP4 functions as a transpeptidase, acting co-operatively with PBP2 in staphylococcal cell wall biosynthesis and susceptibility to antimicrobial agents []. |
|
•
•
•
•
•
|
| Publication |
| First Author: |
Choi YG |
| Year: |
2011 |
| Journal: |
Gene |
| Title: |
Changes of gene expression profiles in the cervical spinal cord by acupuncture in an MPTP-intoxicated mouse model: microarray analysis. |
| Volume: |
481 |
| Issue: |
1 |
| Pages: |
7-16 |
|
•
•
•
•
•
|
| Publication |
| First Author: |
Zhao GS |
| Year: |
1992 |
| Journal: |
J Biol Chem |
| Title: |
Cyclohexadienyl dehydratase from Pseudomonas aeruginosa. Molecular cloning of the gene and characterization of the gene product. |
| Volume: |
267 |
| Issue: |
4 |
| Pages: |
2487-93 |
|
•
•
•
•
•
|
| Publication |
| First Author: |
Zhao G |
| Year: |
1993 |
| Journal: |
J Gen Microbiol |
| Title: |
Cyclohexadienyl dehydratase from Pseudomonas aeruginosa is a periplasmic protein. |
| Volume: |
139 |
| Issue: |
4 |
| Pages: |
807-13 |
|
•
•
•
•
•
|
| Publication |
| First Author: |
Imperial J |
| Year: |
1998 |
| Journal: |
Biochim Biophys Acta |
| Title: |
Molybdate binding by ModA, the periplasmic component of the Escherichia coli mod molybdate transport system. |
| Volume: |
1370 |
| Issue: |
2 |
| Pages: |
337-46 |
|
•
•
•
•
•
|
| Publication |
| First Author: |
Schiefner A |
| Year: |
2004 |
| Journal: |
J Biol Chem |
| Title: |
Structural basis for the binding of compatible solutes by ProX from the hyperthermophilic archaeon Archaeoglobus fulgidus. |
| Volume: |
279 |
| Issue: |
46 |
| Pages: |
48270-81 |
|
•
•
•
•
•
|
| Protein Domain |
| Type: |
Family |
| Description: |
This entry includes TRAP transporters that binds to ketoacids such as pyruvate and alpha-ketobutyrate, xylulose, and other unknown ligands [, , ]. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP; often called the P subunit) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process (the M subunit) and a smaller membrane of unknown function (the Q subunit). The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap []. |
|
•
•
•
•
•
|
| Protein Domain |
| Type: |
Family |
| Description: |
This entry includes a lactate binding TRAP transporter TTHA0766 and related proteins []. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP; often called the P subunit) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process (the M subunit) and a smaller membrane of unknown function (the Q subunit). The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap []. |
|
•
•
•
•
•
|
| Protein Domain |
| Type: |
Domain |
| Description: |
This entry represents the substrate-binding domain found in ProX from the hyperthermophilic archaeon Archaeoglobus fulgidus and its related proteins. AfProX is involved in uptake of compatible solutes such as the trimethylammonium compound glycine betaine and the dimethylammonium compound proline betaine, but the relative substrate preference is not known. To counteract the efflux of water, many microorganisms accumulate the compatible solutes for a sustained adjustment to high osmolarity surroundings []. AfProX belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap []. |
|
•
•
•
•
•
|
| Protein Domain |
| Type: |
Domain |
| Description: |
This entry represents the substrate binding domainfound in the putative ABC transporter substrate-binding lipoprotein YvgL. It is a ModA-like protein that belong to the PBP2 superfamilyof periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge []. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap [].ModA proteins, which serve as initial receptors in the ABC transport of molybdate in eubacteria and archaea []. Bacteria and archaea import molybdenum and tungsten from the environment in the form of the oxyanions molybdate (MoO(4) (2-)) and tungstate (WO(4) (2-)). After binding molybdate and tungstate with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis []. |
|
•
•
•
•
•
|
| Protein Domain |
| Type: |
Domain |
| Description: |
This entry represents the periplasmic binding protein type 2 (PBP2) domain found in cyclohexadienyl dehydratase PheC []. Proteins containing this domain catalyze the decarboxylation of prephenate to phenylpyruvate in the alternative phenylalanine biosynthesis pathway in some proteobacteria and archaea []. The PheC proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap []. Since the PheC proteins are so similar to periplasmic binding proteins, (PBP), it is evolutionary plausible that several pre-existing PBP proteins might have been recruited to perform the enzymatic function. |
|
•
•
•
•
•
|
| Publication |
| First Author: |
Self WT |
| Year: |
2001 |
| Journal: |
Res Microbiol |
| Title: |
Molybdate transport. |
| Volume: |
152 |
| Issue: |
3-4 |
| Pages: |
311-21 |
|
•
•
•
•
•
|
| Publication |
| First Author: |
Morlot C |
| Year: |
2005 |
| Journal: |
J Biol Chem |
| Title: |
Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from Streptococcus pneumoniae. |
| Volume: |
280 |
| Issue: |
16 |
| Pages: |
15984-91 |
|
•
•
•
•
•
|
| Publication |
| First Author: |
Gonin S |
| Year: |
2007 |
| Journal: |
BMC Struct Biol |
| Title: |
Crystal structures of an Extracytoplasmic Solute Receptor from a TRAP transporter in its open and closed forms reveal a helix-swapped dimer requiring a cation for alpha-keto acid binding. |
| Volume: |
7 |
|
| Pages: |
11 |
|
•
•
•
•
•
|
| Publication |
| First Author: |
Akiyama N |
| Year: |
2009 |
| Journal: |
J Mol Biol |
| Title: |
Crystal structure of a periplasmic substrate-binding protein in complex with calcium lactate. |
| Volume: |
392 |
| Issue: |
3 |
| Pages: |
559-65 |
|
•
•
•
•
•
|
| Publication |
| First Author: |
Pernil R |
| Year: |
2010 |
| Journal: |
J Bacteriol |
| Title: |
A TRAP transporter for pyruvate and other monocarboxylate 2-oxoacids in the cyanobacterium Anabaena sp. strain PCC 7120. |
| Volume: |
192 |
| Issue: |
22 |
| Pages: |
6089-92 |
|
•
•
•
•
•
|
| Publication |
| First Author: |
Chan S |
| Year: |
2010 |
| Journal: |
Acta Crystallogr Sect F Struct Biol Cryst Commun |
| Title: |
Apo and ligand-bound structures of ModA from the archaeon Methanosarcina acetivorans. |
| Volume: |
66 |
| Issue: |
Pt 3 |
| Pages: |
242-50 |
|
•
•
•
•
•
|
| Publication |
| First Author: |
Bevers LE |
| Year: |
2006 |
| Journal: |
J Bacteriol |
| Title: |
Tungsten transport protein A (WtpA) in Pyrococcus furiosus: the first member of a new class of tungstate and molybdate transporters. |
| Volume: |
188 |
| Issue: |
18 |
| Pages: |
6498-505 |
|
•
•
•
•
•
|
| Protein Domain |
| Type: |
Domain |
| Description: |
In general, ModA serves as initial receptors in the ABC transport of molybdate in eubacteria and archaea. Bacteria and archaea import molybdenum and tungsten from the environment in the form of the oxyanions molybdate (MoO(4) (2-)) and tungstate (WO(4) (2-)). After binding molybdate with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis [].In contrast to the structure of the two ModA homologues from Escherichia coli and Azotobacter vinelandii, where the oxygen atoms are tetrahedrally arranged around the metal centre, the structure of Pyrococcus furiosus ModA/WtpA (PfModA) has shown that a binding site for molybdate and tungstate is where the central metal atom is in a hexacoordinate configuration. This octahedral geometry was rather unexpected [].The ModA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap [, , ].This entry represents a domain found in the ModA protein from Azotobacter vinelandii and its homologues. |
|
•
•
•
•
•
|
| Publication |
| First Author: |
Kishida H |
| Year: |
2006 |
| Journal: |
Biochemistry |
| Title: |
Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics. |
| Volume: |
45 |
| Issue: |
3 |
| Pages: |
783-92 |
|
•
•
•
•
•
|
| Publication |
| First Author: |
Hu Y |
| Year: |
1997 |
| Journal: |
Nat Struct Biol |
| Title: |
Crystal structure of the molybdate binding protein ModA. |
| Volume: |
4 |
| Issue: |
9 |
| Pages: |
703-7 |
|
•
•
•
•
•
|
| Publication |
| First Author: |
Maeda S |
| Year: |
2000 |
| Journal: |
J Biol Chem |
| Title: |
Bicarbonate binding activity of the CmpA protein of the cyanobacterium Synechococcus sp. strain PCC 7942 involved in active transport of bicarbonate. |
| Volume: |
275 |
| Issue: |
27 |
| Pages: |
20551-5 |
|
•
•
•
•
•
|
| Publication |
| First Author: |
Nagore D |
| Year: |
2003 |
| Journal: |
Biochim Biophys Acta |
| Title: |
Characterization of the N-terminal domain of NrtC, the ATP-binding subunit of ABC-type nitrate transporter of the cyanobacterium Phormidium laminosum. |
| Volume: |
1623 |
| Issue: |
2-3 |
| Pages: |
143-53 |
|
•
•
•
•
•
|
| Publication |
| First Author: |
Maeda S |
| Year: |
1997 |
| Journal: |
J Biol Chem |
| Title: |
Substrate-binding lipoprotein of the cyanobacterium Synechococcus sp. strain PCC 7942 involved in the transport of nitrate and nitrite. |
| Volume: |
272 |
| Issue: |
5 |
| Pages: |
3036-41 |
|
•
•
•
•
•
|
| Protein Domain |
| Type: |
Domain |
| Description: |
This entry includes a domain found in nitrate (Nrt) and bicarbonate (Cmp) receptors. This domain is found in eubacterial periplasmic-binding proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates []. After binding its ligand with high affinity, it interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energised by ATP hydrolysis. These binding proteins belong to the PBP2 superfamily of periplasmic-binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap [].In cyanobacteria, nitrate transport takes place through NRT system, a multicomponent ABC transporter. NRT consists of 4 proteins: a periplasmic substrate-binding protein (NrtA) involved in the specific and high affinity binding of nitrate and nitrite. NrtB is a hydrophobic protein with structural similarities to integral membrane subunits of ABC transporters []. It is thought to form a pore across the membrane to allow the translocation of nitrate and nitrite. Finally, NrtC and NrtD are proposed to form a heterodimer associated to the inner side of the cytoplasmic membrane, and to be responsible of energising the transport system via ATP hydrolysis. In NrtC the binding site for ATP in found at the N-terminal [].The cmpA, cmpB, cmpC, and cmpD genes are strongly similar to the genes encoding the nitrate/nitrite transporter, nrtA, nrtB, nrtC, and nrtD, respectively. NrtB and CmpB are hydrophobic proteins with structural similarities to the integral membrane components of ABC transporters. CmpC and CmpD are ATP-binding cassette proteins strongly similar to NrtC and NrtD, respectively. CmpA is a cytoplasmic membrane protein, which is 46.5% identical to NrtA that functions as the membrane-anchored substrate (nitrate and nitrite)-binding protein []. The similarity of CmpA to NrtA and its involvement in HCO(3)(-) uptake suggest that CmpA is the substrate-binding protein of the HCO(3)(-) transporter []. |
|
•
•
•
•
•
|
| Publication |
| First Author: |
Tam R |
| Year: |
1993 |
| Journal: |
Microbiol Rev |
| Title: |
Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria. |
| Volume: |
57 |
| Issue: |
2 |
| Pages: |
320-46 |
|
•
•
•
•
•
|
| Publication |
| First Author: |
Higgins CF |
| Year: |
1992 |
| Journal: |
Annu Rev Cell Biol |
| Title: |
ABC transporters: from microorganisms to man. |
| Volume: |
8 |
|
| Pages: |
67-113 |
|
•
•
•
•
•
|
