1R44

Crystal Structure of VanX

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
AMR Gene: CARD Annotation
AMR Gene Family: CARD Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d1r44c_	Alpha and beta proteins (a+b)	Hedgehog/DD-peptidase	Hedgehog/DD-peptidase	VanX-like	D-Ala-D-Ala dipeptidase VanX	(Enterococcus faecium ) [TaxId: 1352 ],	SCOPe (2.08)
A	d1r44a_	Alpha and beta proteins (a+b)	Hedgehog/DD-peptidase	Hedgehog/DD-peptidase	VanX-like	D-Ala-D-Ala dipeptidase VanX	(Enterococcus faecium ) [TaxId: 1352 ],	SCOPe (2.08)
B	d1r44b_	Alpha and beta proteins (a+b)	Hedgehog/DD-peptidase	Hedgehog/DD-peptidase	VanX-like	D-Ala-D-Ala dipeptidase VanX	(Enterococcus faecium ) [TaxId: 1352 ],	SCOPe (2.08)
D	d1r44d_	Alpha and beta proteins (a+b)	Hedgehog/DD-peptidase	Hedgehog/DD-peptidase	VanX-like	D-Ala-D-Ala dipeptidase VanX	(Enterococcus faecium ) [TaxId: 1352 ],	SCOPe (2.08)
E	d1r44e_	Alpha and beta proteins (a+b)	Hedgehog/DD-peptidase	Hedgehog/DD-peptidase	VanX-like	D-Ala-D-Ala dipeptidase VanX	(Enterococcus faecium ) [TaxId: 1352 ],	SCOPe (2.08)
F	d1r44f_	Alpha and beta proteins (a+b)	Hedgehog/DD-peptidase	Hedgehog/DD-peptidase	VanX-like	D-Ala-D-Ala dipeptidase VanX	(Enterococcus faecium ) [TaxId: 1352 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Hedgehog/DD-peptidase	8038729	3001458	SCOP2B (2022-06-29)
A	SCOP2 Family	VanX-like	8026350	4002577	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Hedgehog/DD-peptidase	8038729	3001458	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Hedgehog/DD-peptidase	8038729	3001458	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Hedgehog/DD-peptidase	8038729	3001458	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Hedgehog/DD-peptidase	8038729	3001458	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Hedgehog/DD-peptidase	8038729	3001458	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	Peptidase_M15	e1r44C1	A: a+b two layers	X: Hedgehog/DD-peptidase (From Topology)	H: Hedgehog/DD-peptidase (From Topology)	T: Hedgehog/DD-peptidase	F: Peptidase_M15	ECOD (1.6)
A	Peptidase_M15	e1r44A1	A: a+b two layers	X: Hedgehog/DD-peptidase (From Topology)	H: Hedgehog/DD-peptidase (From Topology)	T: Hedgehog/DD-peptidase	F: Peptidase_M15	ECOD (1.6)
B	Peptidase_M15	e1r44B1	A: a+b two layers	X: Hedgehog/DD-peptidase (From Topology)	H: Hedgehog/DD-peptidase (From Topology)	T: Hedgehog/DD-peptidase	F: Peptidase_M15	ECOD (1.6)
D	Peptidase_M15	e1r44D1	A: a+b two layers	X: Hedgehog/DD-peptidase (From Topology)	H: Hedgehog/DD-peptidase (From Topology)	T: Hedgehog/DD-peptidase	F: Peptidase_M15	ECOD (1.6)
E	Peptidase_M15	e1r44E1	A: a+b two layers	X: Hedgehog/DD-peptidase (From Topology)	H: Hedgehog/DD-peptidase (From Topology)	T: Hedgehog/DD-peptidase	F: Peptidase_M15	ECOD (1.6)
F	Peptidase_M15	e1r44F1	A: a+b two layers	X: Hedgehog/DD-peptidase (From Topology)	H: Hedgehog/DD-peptidase (From Topology)	T: Hedgehog/DD-peptidase	F: Peptidase_M15	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.30.1380.10	Alpha Beta	2-Layer Sandwich	Muramoyl-pentapeptide Carboxypeptidase	domain 2	CATH (4.3.0)
A	3.30.1380.10	Alpha Beta	2-Layer Sandwich	Muramoyl-pentapeptide Carboxypeptidase	domain 2	CATH (4.3.0)
B	3.30.1380.10	Alpha Beta	2-Layer Sandwich	Muramoyl-pentapeptide Carboxypeptidase	domain 2	CATH (4.3.0)
D	3.30.1380.10	Alpha Beta	2-Layer Sandwich	Muramoyl-pentapeptide Carboxypeptidase	domain 2	CATH (4.3.0)
E	3.30.1380.10	Alpha Beta	2-Layer Sandwich	Muramoyl-pentapeptide Carboxypeptidase	domain 2	CATH (4.3.0)
F	3.30.1380.10	Alpha Beta	2-Layer Sandwich	Muramoyl-pentapeptide Carboxypeptidase	domain 2	CATH (4.3.0)

AMR Gene: CARD Annotation CARD Database Homepage

Chains	Accession	Short Name	Description	Provenance Source (Version)
A, B, C, D, E A, B, C, D, E, F	ARO:3002949	vanX gene in vanA cluster	Also known as vanXA, is a vanX variant found in the vanA gene cluster.	CARD (3.2.9)

AMR Gene Family: CARD Annotation CARD Database Homepage

Chains	Accession	Gene Family	Drug Class	Resistance Machanism	Provenance Source (Version)
A, B, C, D, E A, B, C, D, E, F	ARO:3000234	glycopeptide resistance gene cluster	glycopeptide antibiotic	antibiotic target alteration	CARD (3.2.9)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF01427	D-ala-D-ala dipeptidase (Peptidase_M15)	D-ala-D-ala dipeptidase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	D-alanyl-D-alanine dipeptidase	peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding exopeptidase activity dipeptidase activity	organic substance metabolic process organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process cellular component organization cell wall organization or biogenesis cell wall organization cellular process cellular component organization or biogenesis external encapsulating structure organization response to stimulus organic substance metabolic process organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process cellular component organization cell wall organization or biogenesis cell wall organization cellular process cellular component organization or biogenesis external encapsulating structure organization response to stimulus response to chemical response to antibiotic	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR009045	Hedgehog signalling/DD-peptidase zinc-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR000755	D-alanyl-D-alanine dipeptidase	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	D-Ala-D-Ala dipeptidase M-CSA #706	VanX is a Zn(II)-containing metalloenzyme that cleaves D-alanyl-D-alanine dipeptide (D-ala-D-ala), increasing the cytoplasmic pool of free D-ala available for use by VanA to form D-ala-D-lac. The enzyme is stereospecific and is found in solution as a mixture of monomers and dimers. The dipeptidase is a critical component of a system that mediates transposon-based, high-level vancomycin resistance in enterococci. Vancomycin acts by binding to the terminal D-ala-D-ala moiety of the bacterial peptidoglycan precursor, interfering with growth of the peptidoglycan chain and normal cell wall formation. The substitution of D-ala-D-ala by D-ala-D-lac at the extracellular terminus of the peptidoglycan chain diminishes the affinity of vancomycin by 1000-fold.	Defined by 5 residues: ARG:A-71HIS:A-116ASP:A-123GLU:A-181HIS:A-184 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.4.13 (PDB Primary Data) Search M-CSA Motif + EC 3.4.13

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.