5NJF

E. coli Microcin-processing metalloprotease TldD/E (TldD H262A mutant) with pentapeptide bound

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
B	d5njfb_	Alpha and beta proteins (a+b)	Putative modulator of DNA gyrase, PmbA/TldD	Putative modulator of DNA gyrase, PmbA/TldD	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d5njfd_	Alpha and beta proteins (a+b)	Putative modulator of DNA gyrase, PmbA/TldD	Putative modulator of DNA gyrase, PmbA/TldD	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

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	e5njfA1	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_2nd	e5njfA2	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)
A	UNK_F_TYPE	e5njfA3	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: UNK_F_TYPE	ECOD (1.6)
C	PmbA_TldD_3rd	e5njfC2	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_2nd	e5njfC1	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	UNK_F_TYPE	e5njfC3	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: UNK_F_TYPE	ECOD (1.6)
B	PmbA_TldD_3rd	e5njfB3	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	e5njfB1	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	e5njfB2	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	e5njfD2	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	e5njfD1	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	e5njfD3	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)
B	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, C	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, C	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, C	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
B, 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
B, 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
B, 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
E, F	ALA-ALA-ALA-ALA-ALA	-	-	-
A, C	Metalloprotease TldD	peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding zinc ion binding	primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process	protein-containing complex catalytic complex peptidase complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
B, D	Metalloprotease PmbA	peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity	primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex peptidase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR051463	Peptidase U62 metalloprotease	Family
A, C	IPR036059	Metalloprotease TldD/PmbA superfamily	Homologous Superfamily
A, C	IPR045570	Metalloprotease TldD/E, central domain	Domain
A, C	IPR045569	Metalloprotease TldD/E, C-terminal domain	Domain
A, C	IPR002510	Metalloprotease TldD/E, N-terminal domain	Domain
A, C	IPR025502	TldD	Family
A, C	IPR035068	Metalloprotease TldD/PmbA, N-terminal	Homologous Superfamily
B, D	IPR002510	Metalloprotease TldD/E, N-terminal domain	Domain
B, D	IPR036059	Metalloprotease TldD/PmbA superfamily	Homologous Superfamily
B, D	IPR035068	Metalloprotease TldD/PmbA, N-terminal	Homologous Superfamily
B, D	IPR045570	Metalloprotease TldD/E, central domain	Domain
B, D	IPR045569	Metalloprotease TldD/E, C-terminal domain	Domain
B, D	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.