1GG4

CRYSTAL STRUCTURE OF ESCHERICHIA COLI UDPMURNAC-TRIPEPTIDE D-ALANYL-D-ALANINE-ADDING ENZYME (MURF) AT 2.3 ANGSTROM RESOLUTION

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	d1gg4a1	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-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1gg4a4	Alpha and beta proteins (a/b)	Ribokinase-like	MurD-like peptide ligases, catalytic domain	MurCDEF	UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1gg4a3	Alpha and beta proteins (a/b)	MurF and HprK N-domain-like	MurE/MurF N-terminal domain	MurE/MurF N-terminal domain	UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1gg4b1	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-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1gg4b4	Alpha and beta proteins (a/b)	Ribokinase-like	MurD-like peptide ligases, catalytic domain	MurCDEF	UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1gg4b3	Alpha and beta proteins (a/b)	MurF and HprK N-domain-like	MurE/MurF N-terminal domain	MurE/MurF N-terminal domain	UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF	(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	SCOP2 Family	MurEF	8003727	4000234	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	MurD peptide-binding domain-like	8091454	3001290	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	MurD catalytic domain-like	8003728	3000107	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	MurE/MurF N-terminal domain	8003731	3000146	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	MurD catalytic domain-like	8003728	3000107	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	MurE/MurF N-terminal domain	8003731	3000146	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	MurD peptide-binding domain-like	8091454	3001290	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_M	e1gg4A1	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	e1gg4A3	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	e1gg4A2	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	e1gg4B1	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	e1gg4B3	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	e1gg4B2	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	3.90.190.20	Alpha Beta	Alpha-Beta Complex	Protein-Tyrosine Phosphatase	Chain A	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	3.40.1390.10	Alpha Beta	3-Layer(aba) Sandwich	Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase	Chain: A, domain 1	CATH (4.3.0)
B	3.90.190.20	Alpha Beta	Alpha-Beta Complex	Protein-Tyrosine Phosphatase	Chain A	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	3.40.1390.10	Alpha Beta	3-Layer(aba) Sandwich	Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase	Chain: A, domain 1	CATH (4.3.0)

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	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
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMYL-2,6-DIAMINOPIMELATE-D-ALANYL-D-ALANYL 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-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate-D-alanyl-D-alanine ligase activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine 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 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	IPR005863	UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase	Family

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.