2Q85

Crystal Structure of E. Coli Mur B bound to a Naphthyl Tetronic Acid inihibitor

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2q85a1	Alpha and beta proteins (a+b)	FAD-binding/transporter-associated domain-like	FAD-binding/transporter-associated domain-like	Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase (MurB), N-terminal domain	Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase (MurB), N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2q85a2	Alpha and beta proteins (a+b)	Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain	Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain	Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain	Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain	8036714	3000935	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	FAD-binding/transporter-associated domain-like	8036705	3000913	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	FAD_binding_4	e2q85A1	A: a+b complex topology	X: FAD-binding domain-like	H: FAD-binding domain (From Topology)	T: FAD-binding domain	F: FAD_binding_4	ECOD (1.6)
A	MurB_C	e2q85A2	A: a+b complex topology	X: Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain (From Topology)	H: Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain (From Topology)	T: Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain	F: MurB_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.43.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 2	CATH (4.3.0)
A	3.30.465.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 3	CATH (4.3.0)
A	3.90.78.10	Alpha Beta	Alpha-Beta Complex	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01565	FAD binding domain (FAD_binding_4)	FAD binding domain	This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, call ...	This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110 [1]. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyses the oxidation of a wide variety of substrates, ranging form aromatic amines to 4-alkylphenols. Other members of this family include D-lactate dehydrogenase, this enzyme catalyses the conversion of D-lactate to pyruvate using FAD as a co-factor; mitomycin radical oxidase, this enzyme oxidises the reduced form of mitomycins and is involved in mitomycin resistance. This family includes MurB an UDP-N-acetylenolpyruvoylglucosamine reductase enzyme EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan [2].	Domain
A	PF02873	UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain (MurB_C)	UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain	Members of this family are UDP-N-acetylenolpyruvoylglucosamine reductase enzymes EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	UDP-N-acetylenolpyruvoylglucosamine reductase	UDP-N-acetylmuramate dehydrogenase activity oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors catalytic activity FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding UDP-N-acetylmuramate dehydrogenase activity oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors catalytic activity FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding small molecule binding	developmental process regulation of biological process regulation of developmental process biological regulation regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis cellular process cell division cellular component organization developmental process regulation of biological process regulation of developmental process biological regulation regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis cellular process cell division cellular component organization cell wall organization or biogenesis cell wall organization cellular component organization or biogenesis external encapsulating structure organization carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis glycosaminoglycan metabolic process carbohydrate derivative metabolic process macromolecule biosynthetic process cellular component biogenesis peptidoglycan biosynthetic process cell wall biogenesis biosynthetic process cell wall macromolecule biosynthetic process aminoglycan metabolic process peptidoglycan metabolic process aminoglycan biosynthetic process metabolic process glycosaminoglycan biosynthetic process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR016167	FAD-binding, type PCMH, subdomain 1	Homologous Superfamily
A	IPR006094	FAD linked oxidase, N-terminal	Domain
A	IPR003170	UDP-N-acetylenolpyruvoylglucosamine reductase	Family
A	IPR016166	FAD-binding domain, PCMH-type	Domain
A	IPR036635	UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain superfamily	Homologous Superfamily
A	IPR036318	FAD-binding, type PCMH-like superfamily	Homologous Superfamily
A	IPR016169	FAD-binding, type PCMH, subdomain 2	Homologous Superfamily
A	IPR011601	UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal	Domain

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.