1GK0 | pdb_00001gk0

Structure-based prediction of modifications in glutarylamidase to allow single-step enzymatic production of 7-aminocephalosporanic acid from cephalosporin C

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D	d1gk0.2	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Penicillin acylase, catalytic domain	Cephalosporin acylase	(Pseudomonas sp. ) [TaxId: 306 ],	SCOPe (2.08)
B	d1gk0.1	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Penicillin acylase, catalytic domain	Cephalosporin acylase	(Pseudomonas sp. ) [TaxId: 306 ],	SCOPe (2.08)
A	d1gk0.1	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Penicillin acylase, catalytic domain	Cephalosporin acylase	(Pseudomonas sp. ) [TaxId: 306 ],	SCOPe (2.08)
C	d1gk0.2	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Penicillin acylase, catalytic domain	Cephalosporin acylase	(Pseudomonas sp. ) [TaxId: 306 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Penicil_amidase	e1gk0D01	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Penicil_amidase	ECOD (v294.1)
B	Penicil_amidase	e1gk0B01	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Penicil_amidase	ECOD (v294.1)
A	Penicil_amidase	e1gk0A01	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Penicil_amidase	ECOD (v294.1)
C	Penicil_amidase	e1gk0C01	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Penicil_amidase	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	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)
D	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)
D	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	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	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)
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)
A	1.10.439.10	Mainly Alpha	Orthogonal Bundle	Penicillin Amidohydrolase	domain 1	CATH (4.3.0)
C	1.10.439.10	Mainly Alpha	Orthogonal Bundle	Penicillin Amidohydrolase	domain 1	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	CEPHALOSPORIN ACYLASE	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity glutaryl-7-aminocephalosporanic-acid acylase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	response to stimulus response to chemical response to antibiotic antibiotic metabolic process biosynthetic process metabolic process cellular process antibiotic biosynthetic process	cellular anatomical structure extracellular region periplasmic space
A, C	CEPHALOSPORIN ACYLASE	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity glutaryl-7-aminocephalosporanic-acid acylase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	response to stimulus response to chemical response to antibiotic antibiotic metabolic process biosynthetic process metabolic process cellular process antibiotic biosynthetic process	cellular anatomical structure extracellular region periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

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

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.