3QTD

Crystal structure of putative modulator of gyrase (PmbA) from Pseudomonas aeruginosa PAO1

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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	e3qtdA1	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	e3qtdA3	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	e3qtdA2	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)
B	PmbA_TldD_3rd	e3qtdB1	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)
B	PmbA_TldD_1st	e3qtdB3	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)
B	PmbA_TldD_2nd	e3qtdB2	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)
C	PmbA_TldD_3rd	e3qtdC1	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)
C	PmbA_TldD_1st	e3qtdC3	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)
C	PmbA_TldD_2nd	e3qtdC2	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)
D	PmbA_TldD_3rd	e3qtdD1	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)
D	PmbA_TldD_1st	e3qtdD3	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)
D	PmbA_TldD_2nd	e3qtdD2	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)
B	3.30.2290.10	Alpha Beta	2-Layer Sandwich	PmbA/TldD fold	PmbA/TldD superfamily	CATH (4.3.0)
C	3.30.2290.10	Alpha Beta	2-Layer Sandwich	PmbA/TldD fold	PmbA/TldD superfamily	CATH (4.3.0)
D	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, B, C, D	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, B, C, D	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, B, C, D	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, B, C, D	PmbA protein	peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity	organic substance metabolic process organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.