7U35

Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from Pseudomonas aeruginosa PAO1 in complex with ADP

External Resource: Annotation

Domain Annotation: ECOD Classification
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)
C	NAD_binding_8_1	e7u35C2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: MurCD/PglD N-terminal domain-like	F: NAD_binding_8_1	ECOD (1.6)
C	Mur_ligase_M	e7u35C1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Mur_ligase_M	ECOD (1.6)
C	Mur_ligase_C	e7u35C3	A: a/b three-layered sandwiches	X: MurD-like peptide ligases, peptide-binding domain (From Topology)	H: MurD-like peptide ligases, peptide-binding domain (From Topology)	T: MurD-like peptide ligases, peptide-binding domain	F: Mur_ligase_C	ECOD (1.6)
A	NAD_binding_8_1	e7u35A3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: MurCD/PglD N-terminal domain-like	F: NAD_binding_8_1	ECOD (1.6)
A	Mur_ligase_M	e7u35A2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Mur_ligase_M	ECOD (1.6)
A	Mur_ligase_C	e7u35A1	A: a/b three-layered sandwiches	X: MurD-like peptide ligases, peptide-binding domain (From Topology)	H: MurD-like peptide ligases, peptide-binding domain (From Topology)	T: MurD-like peptide ligases, peptide-binding domain	F: Mur_ligase_C	ECOD (1.6)
B	NAD_binding_8_1	e7u35B2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: MurCD/PglD N-terminal domain-like	F: NAD_binding_8_1	ECOD (1.6)
B	Mur_ligase_M	e7u35B3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Mur_ligase_M	ECOD (1.6)
B	Mur_ligase_C	e7u35B1	A: a/b three-layered sandwiches	X: MurD-like peptide ligases, peptide-binding domain (From Topology)	H: MurD-like peptide ligases, peptide-binding domain (From Topology)	T: MurD-like peptide ligases, peptide-binding domain	F: Mur_ligase_C	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF08245	Mur ligase middle domain (Mur_ligase_M)	Mur ligase middle domain	-	Domain
A, B, C	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
A, B, C	PF02875	Mur ligase family, glutamate ligase domain (Mur_ligase_C)	Mur ligase family, glutamate ligase domain	This family contains a number of related ligase enzymes which have EC numbers 6.3.2.*. This family includes: MurC (Swiss:P17952), MurD (Swiss:P14900), MurE (Swiss:P22188), MurF (Swiss:P11880), Mpl (Swiss:P37773) and FolC (Swiss:P08192). MurC, MurD, ...	This family contains a number of related ligase enzymes which have EC numbers 6.3.2.*. This family 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. This family also includes Folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	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 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 cycle cell division 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 cycle cell division cellular component organization cell wall organization or biogenesis cell wall organization cellular component organization or biogenesis external encapsulating structure organization cellular biosynthetic process glycosaminoglycan metabolic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process cellular component biogenesis organic substance metabolic process peptidoglycan metabolic process organic substance biosynthetic process nitrogen compound metabolic process glycosaminoglycan biosynthetic process carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis organonitrogen compound metabolic process cellular metabolic process macromolecule biosynthetic process peptidoglycan biosynthetic process cell wall biogenesis biosynthetic process cell wall macromolecule biosynthetic process aminoglycan metabolic process aminoglycan biosynthetic process metabolic process macromolecule metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.