1GKF | pdb_00001gkf

Crystal structures of penicillin acylase enzyme-substrate complexes: Structural insights into the catalytic mechanism

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d1gkf.1	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Penicillin acylase, catalytic domain	Penicillin acylase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1gkf.1	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Penicillin acylase, catalytic domain	Penicillin acylase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.439.10	Mainly Alpha	Orthogonal Bundle	Penicillin Amidohydrolase	domain 1	CATH (4.3.0)
A	1.10.287.150	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
B	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
B	2.30.120.10	Mainly Beta	Roll	Penicillin G acylase, beta-roll domain	Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region	CATH (4.3.0)
B	1.10.1400.10	Mainly Alpha	Orthogonal Bundle	Penicillin amidase (Acylase) alpha subunit, N-terminal domain	Aminohydrolase, alpha-helical knob region	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01804	Penicillin amidase (Penicil_amidase)	Penicillin amidase	-	Family
B	PF01804	Penicillin amidase (Penicil_amidase)	Penicillin amidase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	PENICILLIN G ACYLASE ALPHA SUBUNIT	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity penicillin amidase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding ion binding binding metal ion binding small molecule binding	response to stimulus response to chemical response to antibiotic antibiotic metabolic process biosynthetic process metabolic process cellular process antibiotic biosynthetic process	cellular anatomical structure periplasmic space
B	PENICILLIN G ACYLASE BETA SUBUNIT	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity penicillin amidase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding ion binding binding metal ion binding small molecule binding	response to stimulus response to chemical response to antibiotic antibiotic metabolic process biosynthetic process metabolic process cellular process antibiotic biosynthetic process	cellular anatomical structure periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR043146	Penicillin amidase type, N-terminal domain, B-knob	Homologous Superfamily
A	IPR029055	Nucleophile aminohydrolases, N-terminal	Homologous Superfamily
A	IPR033813	Penicillin G acylase, C-terminal	Domain
A	IPR002692	Penicillin/GL-7-ACA/AHL/aculeacin-A acylase	Family
A	IPR014395	Penicillin/GL-7-ACA/AHL acylase	Family
A	IPR023343	Penicillin amidase type, domain 1	Homologous Superfamily
A	IPR043147	Penicillin amidase type, A-knob	Homologous Superfamily
B	IPR043146	Penicillin amidase type, N-terminal domain, B-knob	Homologous Superfamily
B	IPR029055	Nucleophile aminohydrolases, N-terminal	Homologous Superfamily
B	IPR033813	Penicillin G acylase, C-terminal	Domain
B	IPR002692	Penicillin/GL-7-ACA/AHL/aculeacin-A acylase	Family
B	IPR014395	Penicillin/GL-7-ACA/AHL acylase	Family
B	IPR023343	Penicillin amidase type, domain 1	Homologous Superfamily
B	IPR043147	Penicillin amidase type, A-knob	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	SME	Parent Component: MET RESID: AA0581 PSI-MOD : L-methionine (S)-sulfoxide MOD:00721

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.