9BN8

Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli in complex with UMA and inhibitor A19

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	MurCD N-terminal domain	8058462	3000082	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	MurD catalytic domain-like	8058463	3000107	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	MurD peptide-binding domain-like	8091456	3001290	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF08245	Mur ligase middle domain (Mur_ligase_M)	Mur ligase middle domain	-	Domain
A	PF02875	Mur ligase, glutamate ligase domain (Mur_ligase_C)	Mur ligase, glutamate ligase domain	This entry contains a number of related ligase enzymes which have EC numbers 6.3.2.* which includes: MurC (Swiss:P17952), MurD (Swiss:P14900), MurE (Swiss:P22188), MurF (Swiss:P11880), Mpl (Swiss:P37773) and FolC (Swiss:P08192). MurC, MurD, MurE and ...	This entry contains a number of related ligase enzymes which have EC numbers 6.3.2.* which includes: MurC (Swiss:P17952), MurD (Swiss:P14900), MurE (Swiss:P22188), MurF (Swiss:P11880), Mpl (Swiss:P37773) and FolC (Swiss:P08192). MurC, MurD, MurE and MurF catalyse consecutive steps in the synthesis of peptidoglycan. Peptidoglycan consists of a sheet of two sugar derivatives, with one of these N-acetylmuramic acid attaching to a small pentapeptide. The pentapeptide is is made of L-alanine, D-glutamic acid, Meso-diaminopimelic acid and D-alanyl alanine. The peptide moiety is synthesised by successively adding these amino acids to UDP-N-acetylmuramic acid. MurC transfers the L-alanine, MurD transfers the D-glutamate, MurE transfers the diaminopimelic acid, and MurF transfers the D-alanyl alanine [1,3,4]. This entry also includes folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate and cyanophycin synthetase that catalyses the biosynthesis of the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartate (cyanophycin) [2].	Domain
A	PF21799	Mur ligase MurD-like, N-terminal domain (MurD-like_N)	Mur ligase MurD-like, N-terminal domain	This domain is found at the N-terminal end of Mur ligases predominantly from proteobacteria, including UDP-N -acetylmuramoylalanine--D-glutamate ligase from Escherichia coli (MurD). Proteins in this family play a crucial role in the intracellular ste ...	This domain is found at the N-terminal end of Mur ligases predominantly from proteobacteria, including UDP-N -acetylmuramoylalanine--D-glutamate ligase from Escherichia coli (MurD). Proteins in this family play a crucial role in the intracellular steps leading to the synthesis of bacterial peptidoglycan. MurD shows a three-domain topology, with the N-terminal (this entry) responsible for binding the UDP-precursor. This domain shows a Rossmann fold [1-6].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	UDP-N-acetylmuramoylalanine--D-glutamate ligase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding identical protein binding protein binding acid-amino acid ligase activity catalytic activity UDP-N-acetylmuramoylalanine-D-glutamate ligase activity ligase activity, forming carbon-nitrogen bonds ligase activity	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR004101	Mur ligase, C-terminal	Domain
A	IPR036565	Mur-like, catalytic domain superfamily	Homologous Superfamily
A	IPR005762	UDP-N-acetylmuramoylalanine-D-glutamate ligase MurD	Family
A	IPR036615	Mur ligase, C-terminal domain superfamily	Homologous Superfamily
A	IPR013221	Mur ligase, central	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.