4WKU

n-Alkylboronic Acid Inhibitors Reveal Determinants of Ligand Specificity in the Quorum-Quenching and Siderophore Biosynthetic Enzyme PvdQ

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Penicil_amidase	e4wkuA1	A: a+b four layers	X: Ntn/PP2C	H: Ntn	T: Penicillin acylase, catalytic domain	F: Penicil_amidase	ECOD (1.6)
B	Penicil_amidase	e4wkuB1	A: a+b four layers	X: Ntn/PP2C	H: Ntn	T: Penicillin acylase, catalytic domain	F: Penicil_amidase	ECOD (1.6)

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)
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
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	Acyl-homoserine lactone acylase PvdQ	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds oxidoreductase activity, acting on the CH-CH group of donors, with a flavin as acceptor oxidoreductase activity short-chain fatty acyl-CoA dehydrogenase activity acyl-CoA dehydrogenase activity oxidoreductase activity, acting on the CH-CH group of donors identical protein binding protein binding binding	regulation of biological process response to stimulus signaling quorum sensing biological regulation cell-cell signaling detection of cell density detection of biotic stimulus response to biotic stimulus cell communication detection of stimulus cellular process response to chemical response to antibiotic regulation of biological process response to stimulus signaling quorum sensing biological regulation cell-cell signaling detection of cell density detection of biotic stimulus response to biotic stimulus cell communication detection of stimulus cellular process response to chemical response to antibiotic antibiotic metabolic process biosynthetic process metabolic process antibiotic biosynthetic process amide biosynthetic process secondary metabolic process pyoverdine biosynthetic process siderophore biosynthetic process peptide biosynthetic process secondary metabolite biosynthetic process siderophore metabolic process amide metabolic process nonribosomal peptide biosynthetic process peptide metabolic process bacterial-type flagellum-dependent swarming motility bacterial-type flagellum-dependent cell motility cell motility archaeal or bacterial-type flagellum-dependent cell motility cilium or flagellum-dependent cell motility cell aggregation biofilm formation biological process involved in intraspecies interaction between organisms single-species biofilm formation aggregation of unicellular organisms	cellular anatomical structure periplasmic space intracellular anatomical structure cytoplasm
B	Acyl-homoserine lactone acylase PvdQ	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds oxidoreductase activity, acting on the CH-CH group of donors, with a flavin as acceptor oxidoreductase activity short-chain fatty acyl-CoA dehydrogenase activity acyl-CoA dehydrogenase activity oxidoreductase activity, acting on the CH-CH group of donors identical protein binding protein binding binding	regulation of biological process response to stimulus signaling quorum sensing biological regulation cell-cell signaling detection of cell density detection of biotic stimulus response to biotic stimulus cell communication detection of stimulus cellular process response to chemical response to antibiotic regulation of biological process response to stimulus signaling quorum sensing biological regulation cell-cell signaling detection of cell density detection of biotic stimulus response to biotic stimulus cell communication detection of stimulus cellular process response to chemical response to antibiotic antibiotic metabolic process biosynthetic process metabolic process antibiotic biosynthetic process amide biosynthetic process secondary metabolic process pyoverdine biosynthetic process siderophore biosynthetic process peptide biosynthetic process secondary metabolite biosynthetic process siderophore metabolic process amide metabolic process nonribosomal peptide biosynthetic process peptide metabolic process bacterial-type flagellum-dependent swarming motility bacterial-type flagellum-dependent cell motility cell motility archaeal or bacterial-type flagellum-dependent cell motility cilium or flagellum-dependent cell motility cell aggregation biofilm formation biological process involved in intraspecies interaction between organisms single-species biofilm formation aggregation of unicellular organisms	cellular anatomical structure periplasmic space intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

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