1VPB

CRYSTAL STRUCTURE OF A PUTATIVE MODULATOR OF DNA GYRASE (BT3649) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 1.75 A RESOLUTION

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1vpba_	Alpha and beta proteins (a+b)	Putative modulator of DNA gyrase, PmbA/TldD	Putative modulator of DNA gyrase, PmbA/TldD	Putative modulator of DNA gyrase, PmbA/TldD	Putative modulator of DNA gyrase BT3649	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Putative modulator of DNA gyrase, PmbA/TldD	8030820	4002916	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Putative modulator of DNA gyrase, PmbA/TldD	8043199	3001895	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PmbA_TldD_3rd	e1vpbA1	A: beta barrels	X: barrel domain in putative modulator of DNA gyrase, PmbA/TldD (From Topology)	H: barrel domain in putative modulator of DNA gyrase, PmbA/TldD (From Topology)	T: barrel domain in putative modulator of DNA gyrase, PmbA/TldD	F: PmbA_TldD_3rd	ECOD (1.6)
A	PmbA_TldD_1st	e1vpbA2	A: a+b two layers	X: a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) (From Topology)	H: a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) (From Topology)	T: a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523)	F: PmbA_TldD_1st	ECOD (1.6)
A	PmbA_TldD_2nd	e1vpbA3	A: a+b two layers	X: a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) (From Topology)	H: a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) (From Topology)	T: a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523)	F: PmbA_TldD_2nd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.2290.10	Alpha Beta	2-Layer Sandwich	PmbA/TldD fold	PmbA/TldD superfamily	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF19289	PmbA/TldA metallopeptidase C-terminal domain (PmbA_TldD_3rd)	PmbA/TldA metallopeptidase C-terminal domain	This entry represents a group of metalloproteases. The tertiary structure of the Escherichia coli TdlD/TdlE complex has been solved, and shows that the TdlD subunit is the active peptidase, binding a single zinc ion at an HEXXXH motif in which the gl ...	This entry represents a group of metalloproteases. The tertiary structure of the Escherichia coli TdlD/TdlE complex has been solved, and shows that the TdlD subunit is the active peptidase, binding a single zinc ion at an HEXXXH motif in which the glutamic acid is a substrate-binding residue and the two histidines are zinc ligands. The third zinc ligand is a cysteine, C-terminal to the HEXXXH motif. The TldE (also known as PmbA) by itself has no catalytic activity, does not bind zinc, and does not carry the HEXXXH motif [1]. TldD and TldE were originally identified as regulators of DNA gyrase. Later, they are shown to be metalloproteases involved in CcdA degradation [2-3].	Domain
A	PF19290	PmbA/TldA metallopeptidase central domain (PmbA_TldD_2nd)	PmbA/TldA metallopeptidase central domain	This entry represents a group of metalloproteases. The tertiary structure of the Escherichia coli TdlD/TdlE complex has been solved, and shows that the TdlD subunit is the active peptidase, binding a single zinc ion at an HEXXXH motif in which the gl ...	This entry represents a group of metalloproteases. The tertiary structure of the Escherichia coli TdlD/TdlE complex has been solved, and shows that the TdlD subunit is the active peptidase, binding a single zinc ion at an HEXXXH motif in which the glutamic acid is a substrate-binding residue and the two histidines are zinc ligands. The third zinc ligand is a cysteine, C-terminal to the HEXXXH motif. The TldE (also known as PmbA) by itself has no catalytic activity, does not bind zinc, and does not carry the HEXXXH motif [1]. TldD and TldE were originally identified as regulators of DNA gyrase. Later, they are shown to be metalloproteases involved in CcdA degradation [2-3].	Domain
A	PF01523	PmbA/TldA metallopeptidase domain 1 (PmbA_TldD_1st)	PmbA/TldA metallopeptidase domain 1	This entry represents a group of metalloproteases. The tertiary structure of the Escherichia coli TdlD/TdlE complex has been solved, and shows that the TdlD subunit is the active peptidase, binding a single zinc ion at an HEXXXH motif in which the gl ...	This entry represents a group of metalloproteases. The tertiary structure of the Escherichia coli TdlD/TdlE complex has been solved, and shows that the TdlD subunit is the active peptidase, binding a single zinc ion at an HEXXXH motif in which the glutamic acid is a substrate-binding residue and the two histidines are zinc ligands. The third zinc ligand is a cysteine, C-terminal to the HEXXXH motif. The TldE (also known as PmbA) by itself has no catalytic activity, does not bind zinc, and does not carry the HEXXXH motif [1]. TldD and TldE were originally identified as regulators of DNA gyrase. Later, they are shown to be metalloproteases involved in CcdA degradation [2-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	putative modulator of DNA gyrase	peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR002510	Metalloprotease TldD/E, N-terminal domain	Domain
A	IPR036059	Metalloprotease TldD/PmbA superfamily	Homologous Superfamily
A	IPR035068	Metalloprotease TldD/PmbA, N-terminal	Homologous Superfamily
A	IPR045570	Metalloprotease TldD/E, central domain	Domain
A	IPR045569	Metalloprotease TldD/E, C-terminal domain	Domain
A	IPR047657	Metalloprotease PmbA	Family

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.