1E8C

Structure of MurE the UDP-N-acetylmuramyl tripeptide synthetase from E. coli

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	d1e8ca2	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-acetylmuramyl tripeptide synthetase MurE	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1e8ca3	Alpha and beta proteins (a/b)	Ribokinase-like	MurD-like peptide ligases, catalytic domain	MurCDEF	UDP-N-acetylmuramyl tripeptide synthetase MurE	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1e8ca1	Alpha and beta proteins (a/b)	MurF and HprK N-domain-like	MurE/MurF N-terminal domain	MurE/MurF N-terminal domain	UDP-N-acetylmuramyl tripeptide synthetase MurE	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1e8ca4	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1e8cb2	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-acetylmuramyl tripeptide synthetase MurE	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1e8cb3	Alpha and beta proteins (a/b)	Ribokinase-like	MurD-like peptide ligases, catalytic domain	MurCDEF	UDP-N-acetylmuramyl tripeptide synthetase MurE	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1e8cb1	Alpha and beta proteins (a/b)	MurF and HprK N-domain-like	MurE/MurF N-terminal domain	MurE/MurF N-terminal domain	UDP-N-acetylmuramyl tripeptide synthetase MurE	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1e8cb4	Artifacts	Tags	Tags	Tags	C-terminal Tags	(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	MurD catalytic domain-like	8003704	3000107	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	MurD peptide-binding domain-like	8091453	3001290	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	MurE/MurF N-terminal domain	8003715	3000146	SCOP2B (2022-06-29)
B	SCOP2 Family	MurEF	8003702	4000234	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	MurD catalytic domain-like	8003704	3000107	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	MurE/MurF N-terminal domain	8003715	3000146	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	MurD peptide-binding domain-like	8091453	3001290	SCOP2 (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_M	e1e8cA1	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_1	e1e8cA3	A: a/b three-layered sandwiches	X: MurF and HprK N-domain-like (From Topology)	H: MurF and HprK N-domain-like (From Topology)	T: MurF and HprK N-domain-like	F: Mur_ligase_1	ECOD (1.6)
A	Mur_ligase_C	e1e8cA2	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_M	e1e8cB1	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_1	e1e8cB3	A: a/b three-layered sandwiches	X: MurF and HprK N-domain-like (From Topology)	H: MurF and HprK N-domain-like (From Topology)	T: MurF and HprK N-domain-like	F: Mur_ligase_1	ECOD (1.6)
B	Mur_ligase_C	e1e8cB2	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	3.40.1390.10	Alpha Beta	3-Layer(aba) Sandwich	Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase	Chain: A, domain 1	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	3.40.1390.10	Alpha Beta	3-Layer(aba) Sandwich	Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase	Chain: A, domain 1	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, 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, 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-ACETYLMURAMOYLALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase activity acid-amino acid 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 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, B	IPR004101	Mur ligase, C-terminal	Domain
A, B	IPR035911	MurE/MurF, N-terminal	Homologous Superfamily
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
A, B	IPR005761	UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase	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.