1P3D

Crystal Structure of UDP-N-acetylmuramic acid:L-alanine ligase (MurC) in Complex with UMA and ANP.

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
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1p3da1	Alpha and beta proteins (a/b)	MurCD N-terminal domain	MurCD N-terminal domain	MurCD N-terminal domain	UDP-N-acetylmuramate-alanine ligase MurC	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
A	d1p3da2	Alpha and beta proteins (a/b)	MurD-like peptide ligases, peptide-binding domain	MurD-like peptide ligases, peptide-binding domain	MurCDEF C-terminal domain	UDP-N-acetylmuramate-alanine ligase MurC	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
A	d1p3da3	Alpha and beta proteins (a/b)	Ribokinase-like	MurD-like peptide ligases, catalytic domain	MurCDEF	UDP-N-acetylmuramate-alanine ligase MurC	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
B	d1p3db1	Alpha and beta proteins (a/b)	MurCD N-terminal domain	MurCD N-terminal domain	MurCD N-terminal domain	UDP-N-acetylmuramate-alanine ligase MurC	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
B	d1p3db2	Alpha and beta proteins (a/b)	MurD-like peptide ligases, peptide-binding domain	MurD-like peptide ligases, peptide-binding domain	MurCDEF C-terminal domain	UDP-N-acetylmuramate-alanine ligase MurC	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
B	d1p3db3	Alpha and beta proteins (a/b)	Ribokinase-like	MurD-like peptide ligases, catalytic domain	MurCDEF	UDP-N-acetylmuramate-alanine ligase MurC	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	MurCD	8058589	4000154	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	MurD peptide-binding domain-like	8091455	3001290	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	MurCD N-terminal domain	8058590	3000082	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	MurD catalytic domain-like	8058591	3000107	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	MurD peptide-binding domain-like	8091455	3001290	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	MurD catalytic domain-like	8058591	3000107	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	MurCD N-terminal domain	8058590	3000082	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	Mur_ligase	e1p3dA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: MurCD/PglD N-terminal domain-like	F: Mur_ligase	ECOD (1.6)
A	Mur_ligase_M	e1p3dA2	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	e1p3dA3	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	Mur_ligase	e1p3dB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: MurCD/PglD N-terminal domain-like	F: Mur_ligase	ECOD (1.6)
B	Mur_ligase_M	e1p3dB2	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	e1p3dB3	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	3.40.1190.10	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Mur-like, catalytic domain	CATH (4.3.0)
A	3.90.190.20	Alpha Beta	Alpha-Beta Complex	Protein-Tyrosine Phosphatase	Chain A	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	3.40.1190.10	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Mur-like, catalytic domain	CATH (4.3.0)
B	3.90.190.20	Alpha Beta	Alpha-Beta Complex	Protein-Tyrosine Phosphatase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF08245	Mur ligase middle domain (Mur_ligase_M)	Mur ligase middle domain	-	Domain
A, B	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
A, B	PF01225	Mur ligase family, catalytic domain (Mur_ligase)	Mur ligase family, catalytic 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	UDP-N-acetylmuramate--alanine 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 UDP-N-acetylmuramate-L-alanine ligase activity catalytic 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 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	IPR005758	UDP-N-acetylmuramate--L-alanine ligase	Family
A, B	IPR004101	Mur ligase, C-terminal	Domain
A, B	IPR036565	Mur-like, catalytic domain superfamily	Homologous Superfamily
A, B	IPR000713	Mur ligase, N-terminal catalytic domain	Domain
A, B	IPR036615	Mur ligase, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR013221	Mur ligase, central	Domain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	UDP-N-acetylmuramate---L-alanine ligase M-CSA #876	UDP-N-acetylmuramate-alanine ligase (MurC) is an essential, cytoplasmic peptidoglycan biosynthetic enzyme that catalyses the ATP-dependent ligation of L-alanine (Ala) and UDP-N-acetylmuramic acid (UNAM) to form UDP-N-acetylmuramyl-L-alanine (UNAM-Ala). This reaction is part of the biosynthesis of cell walls in bacteria. MurC is a nonribosomal peptide ligase which utilises ATP to form an amide bond between L-alanine and UNAM. Mechanistic studies on the Escherichia coli enzyme demonstrated that the enzyme-catalysed reaction proceeds through an acyl phosphate UNAM intermediate prior to L-alanine addition.	Defined by 3 residues: LYS:A-129THR:A-130GLU:A-173 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 6.3.2.8 (PDB Primary Data) Search M-CSA Motif + EC 6.3.2.8

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.