6FQB | pdb_00006fqb

MurT/GatD peptidoglycan amidotransferase complex from Streptococcus pneumoniae R6

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)
F [auth G]	GATase	e6fqbG1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: GATase	ECOD (1.6)
H	GATase	e6fqbH1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: GATase	ECOD (1.6)
D [auth F]	GATase	e6fqbF1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: GATase	ECOD (1.6)
B [auth E]	GATase	e6fqbE1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: GATase	ECOD (1.6)
G [auth D]	Mur_ligase_M	e6fqbD1	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)
G [auth D]	UNK_F_TYPE	e6fqbD2	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: UNK_F_TYPE	ECOD (1.6)
E [auth C]	Mur_ligase_M	e6fqbC2	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)
E [auth C]	UNK_F_TYPE	e6fqbC1	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: UNK_F_TYPE	ECOD (1.6)
C [auth B]	Mur_ligase_M	e6fqbB1	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 [auth B]	UNK_F_TYPE	e6fqbB2	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: UNK_F_TYPE	ECOD (1.6)
A	Mur_ligase_M	e6fqbA1	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	UNK_F_TYPE	e6fqbA2	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: UNK_F_TYPE	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth E], D [auth F], F [auth G], H	PF07685	CobB/CobQ-like glutamine amidotransferase domain (GATase_3)	CobB/CobQ-like glutamine amidotransferase domain		Domain
A, C [auth B], E [auth C], G [auth D]	PF08245	Mur ligase middle domain (Mur_ligase_M)	Mur ligase middle domain		Domain
A, C [auth B], E [auth C], G [auth D]	PF08353	MurT ligase C-terminal (MurT_C)	MurT ligase C-terminal	This entry represents the C-terminal domain of MurT ligase from Gram-positive bacteria. MurT is part of the bi-enzymatic complex MurT-GatD involved in the amidation of the alpha-carboxyl group of the D-isoglutamate residue in Lipid II in the peptidog ...	This entry represents the C-terminal domain of MurT ligase from Gram-positive bacteria. MurT is part of the bi-enzymatic complex MurT-GatD involved in the amidation of the alpha-carboxyl group of the D-isoglutamate residue in Lipid II in the peptidoglycan layer to produce D-isoglutamine. This domain contains an aspartate at position 349, the third residue in the catalytic triad GatD-C94, GatD-H189, MurT-D349. This C-terminal domain is built around a central six-stranded, predominantly parallel beta-sheet that is sandwiched between four alpha-helices on one side and two alpha-helices on the other. The MurT-GatD heterodimer adopts a boomerang-shaped conformation, with GatD packing against the C-terminal domain of MurT [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth E], D [auth F], F [auth G], H	Cobyric acid synthase	carbon-nitrogen ligase activity on lipid II carbon-nitrogen ligase activity, with glutamine as amido-N-donor catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides glutaminase activity hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	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 cobalamin metabolic process cobalamin biosynthetic process water-soluble vitamin biosynthetic process 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 cobalamin metabolic process cobalamin biosynthetic process water-soluble vitamin biosynthetic process tetrapyrrole metabolic process small molecule biosynthetic process vitamin biosynthetic process vitamin metabolic process tetrapyrrole biosynthetic process biosynthetic process small molecule metabolic process metabolic process cellular process carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis cell wall organization or biogenesis glycosaminoglycan metabolic process carbohydrate derivative metabolic process macromolecule biosynthetic process cellular component biogenesis peptidoglycan biosynthetic process cell wall biogenesis cell wall macromolecule biosynthetic process aminoglycan metabolic process peptidoglycan metabolic process aminoglycan biosynthetic process glycosaminoglycan biosynthetic process cellular component organization or biogenesis macromolecule metabolic process cell wall macromolecule metabolic process cellular component organization cell wall organization external encapsulating structure organization	-
A, C [auth B], E [auth C], G [auth D]	Mur ligase family protein	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding transition metal ion binding zinc ion binding metal ion binding acid-amino acid ligase activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity carbon-nitrogen ligase activity on lipid II carbon-nitrogen ligase activity, with glutamine as amido-N-donor	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 carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis cell wall organization or biogenesis 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 carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis cell wall organization or 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 cellular process metabolic process glycosaminoglycan biosynthetic process cellular component organization or biogenesis macromolecule metabolic process cell wall macromolecule metabolic process cellular component organization cell wall organization external encapsulating structure organization	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth E], D [auth F], F [auth G], H	IPR029062	Class I glutamine amidotransferase-like	Homologous Superfamily
B [auth E], D [auth F], F [auth G], H	IPR033949	Cobyric acid synthase, glutamine amidotransferase type 1	Domain
B [auth E], D [auth F], F [auth G], H	IPR054859	Lipid II isoglutaminyl synthase subunit GatD	Family
B [auth E], D [auth F], F [auth G], H	IPR011698	CobB/CobQ-like glutamine amidotransferase	Domain
B [auth E], D [auth F], F [auth G], H	IPR043702	Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD	Family
A, C [auth B], E [auth C], G [auth D]	IPR054853	Lipid II isoglutaminyl synthase subunit MurT	Family
A, C [auth B], E [auth C], G [auth D]	IPR013564	Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT, C-terminal	Domain
A, C [auth B], E [auth C], G [auth D]	IPR043703	Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT	Family
A, C [auth B], E [auth C], G [auth D]	IPR013221	Mur ligase, central	Domain
A, C [auth B], E [auth C], G [auth D]	IPR036565	Mur-like, catalytic domain superfamily	Homologous Superfamily

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.