5EVI

Crystal Structure of Beta-Lactamase/D-Alanine Carboxypeptidase from Pseudomonas syringae

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5evia_	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	automated matches	automated matches	(Pseudomonas syringae pv. tomato str. DC3000 ) [TaxId: 223283 ],	SCOPe (2.08)
B	d5evib_	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	automated matches	automated matches	(Pseudomonas syringae pv. tomato str. DC3000 ) [TaxId: 223283 ],	SCOPe (2.08)
C	d5evic_	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	automated matches	automated matches	(Pseudomonas syringae pv. tomato str. DC3000 ) [TaxId: 223283 ],	SCOPe (2.08)
D	d5evid_	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	automated matches	automated matches	(Pseudomonas syringae pv. tomato str. DC3000 ) [TaxId: 223283 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	beta-Lactamase/D-ala carboxypeptidase	8069926	4002685	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	beta-lactamase/transpeptidase-like	8069927	3001604	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8069927	3001604	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8069927	3001604	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8069927	3001604	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)
A	Beta-lactamase_1st	e5eviA2	A: alpha complex topology	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Beta-lactamase_1st	ECOD (1.6)
A	Beta-lactamase_2nd	e5eviA1	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Beta-lactamase_2nd	ECOD (1.6)
B	Beta-lactamase_1st	e5eviB1	A: alpha complex topology	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Beta-lactamase_1st	ECOD (1.6)
B	Beta-lactamase_2nd	e5eviB2	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Beta-lactamase_2nd	ECOD (1.6)
C	Beta-lactamase_1st	e5eviC2	A: alpha complex topology	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Beta-lactamase_1st	ECOD (1.6)
C	Beta-lactamase_2nd	e5eviC1	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Beta-lactamase_2nd	ECOD (1.6)
D	Beta-lactamase_1st	e5eviD2	A: alpha complex topology	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Beta-lactamase_1st	ECOD (1.6)
D	Beta-lactamase_2nd	e5eviD1	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Beta-lactamase_2nd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
B	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
C	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
D	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00144	Beta-lactamase (Beta-lactamase)	Beta-lactamase	This family appears to be distantly related to Pfam:PF00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.	Domain
B	PF00144	Beta-lactamase (Beta-lactamase)	Beta-lactamase	This family appears to be distantly related to Pfam:PF00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.	Domain
C	PF00144	Beta-lactamase (Beta-lactamase)	Beta-lactamase	This family appears to be distantly related to Pfam:PF00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.	Domain
D	PF00144	Beta-lactamase (Beta-lactamase)	Beta-lactamase	This family appears to be distantly related to Pfam:PF00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Beta-Lactamase/D-Alanine Carboxypeptidase	beta-lactamase activity hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	antibiotic metabolic process catabolic process metabolic process antibiotic catabolic process response to stimulus response to chemical response to antibiotic	outer membrane-bounded periplasmic space cell envelope periplasmic space cellular anatomical entity
B	Beta-Lactamase/D-Alanine Carboxypeptidase	beta-lactamase activity hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	antibiotic metabolic process catabolic process metabolic process antibiotic catabolic process response to stimulus response to chemical response to antibiotic	outer membrane-bounded periplasmic space cell envelope periplasmic space cellular anatomical entity
C	Beta-Lactamase/D-Alanine Carboxypeptidase	beta-lactamase activity hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	antibiotic metabolic process catabolic process metabolic process antibiotic catabolic process response to stimulus response to chemical response to antibiotic	outer membrane-bounded periplasmic space cell envelope periplasmic space cellular anatomical entity
D	Beta-Lactamase/D-Alanine Carboxypeptidase	beta-lactamase activity hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	antibiotic metabolic process catabolic process metabolic process antibiotic catabolic process response to stimulus response to chemical response to antibiotic	outer membrane-bounded periplasmic space cell envelope periplasmic space cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001466	Beta-lactamase-related	Domain
A	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
A	IPR001586	Beta-lactamase, class-C active site	Active Site
B	IPR001466	Beta-lactamase-related	Domain
B	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
B	IPR001586	Beta-lactamase, class-C active site	Active Site
C	IPR001466	Beta-lactamase-related	Domain
C	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
C	IPR001586	Beta-lactamase, class-C active site	Active Site
D	IPR001466	Beta-lactamase-related	Domain
D	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
D	IPR001586	Beta-lactamase, class-C active site	Active Site

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	MLY	Parent Component: LYS RESID: AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084
A	MSE	Parent Component: MET RESID: AA0075
B	MLY	Parent Component: LYS RESID: AA0075 , AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084 , N6,N6-dimethyl-L-lysine MOD:00084
B	MSE	Parent Component: MET RESID: AA0075 , AA0075
C	MLY	Parent Component: LYS RESID: AA0075 , AA0075 , AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084 , N6,N6-dimethyl-L-lysine MOD:00084 , N6,N6-dimethyl-L-lysine MOD:00084
C	MSE	Parent Component: MET RESID: AA0075 , AA0075 , AA0075
D	MLY	Parent Component: LYS RESID: AA0075 , AA0075 , AA0075 , AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084 , N6,N6-dimethyl-L-lysine MOD:00084 , N6,N6-dimethyl-L-lysine MOD:00084 , N6,N6-dimethyl-L-lysine MOD:00084
D	MSE	Parent Component: MET RESID: AA0075 , AA0075 , AA0075 , AA0075

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.