1RRV

X-ray crystal structure of TDP-vancosaminyltransferase GtfD as a complex with TDP and the natural substrate, desvancosaminyl vancomycin.

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	d1rrva_	Alpha and beta proteins (a/b)	UDP-Glycosyltransferase/glycogen phosphorylase	UDP-Glycosyltransferase/glycogen phosphorylase	Gtf glycosyltransferase	TDP-vancosaminyltransferase GftD	(Amycolatopsis orientalis ) [TaxId: 31958 ],	SCOPe (2.08)
B	d1rrvb_	Alpha and beta proteins (a/b)	UDP-Glycosyltransferase/glycogen phosphorylase	UDP-Glycosyltransferase/glycogen phosphorylase	Gtf glycosyltransferase	TDP-vancosaminyltransferase GftD	(Amycolatopsis orientalis ) [TaxId: 31958 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Gtf glycosyltransferase	8026553	4003450	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Type B glycosyltransferase-like	8038932	3001586	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Type B glycosyltransferase-like	8038932	3001586	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	Glyco_transf_28	e1rrvA2	A: a/b three-layered sandwiches	X: UDP-Glycosyltransferase/glycogen phosphorylase (From Topology)	H: UDP-Glycosyltransferase/glycogen phosphorylase (From Topology)	T: UDP-Glycosyltransferase/glycogen phosphorylase	F: Glyco_transf_28	ECOD (1.6)
A	UDPGT	e1rrvA1	A: a/b three-layered sandwiches	X: UDP-Glycosyltransferase/glycogen phosphorylase (From Topology)	H: UDP-Glycosyltransferase/glycogen phosphorylase (From Topology)	T: UDP-Glycosyltransferase/glycogen phosphorylase	F: UDPGT	ECOD (1.6)
B	Glyco_transf_28	e1rrvB1	A: a/b three-layered sandwiches	X: UDP-Glycosyltransferase/glycogen phosphorylase (From Topology)	H: UDP-Glycosyltransferase/glycogen phosphorylase (From Topology)	T: UDP-Glycosyltransferase/glycogen phosphorylase	F: Glyco_transf_28	ECOD (1.6)
B	UDPGT	e1rrvB2	A: a/b three-layered sandwiches	X: UDP-Glycosyltransferase/glycogen phosphorylase (From Topology)	H: UDP-Glycosyltransferase/glycogen phosphorylase (From Topology)	T: UDP-Glycosyltransferase/glycogen phosphorylase	F: UDPGT	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.2000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Glycogen Phosphorylase B	CATH (4.3.0)
B	3.40.50.2000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Glycogen Phosphorylase B	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF03033	Glycosyltransferase family 28 N-terminal domain (Glyco_transf_28)	Glycosyltransferase family 28 N-terminal domain	-	Family
A, B	PF06722	Erythromycin biosynthesis protein CIII-like, C-terminal domain (EryCIII-like_C)	Erythromycin biosynthesis protein CIII-like, C-terminal domain	This domain is found at the C-terminal of Erythromycin biosynthesis protein CIII (EryCIII) from Saccharopolyspora erythraea and similar proteins found in bacteria and eukaryotes. This protein is organised into two domains, both of them with a Rossman ...	This domain is found at the C-terminal of Erythromycin biosynthesis protein CIII (EryCIII) from Saccharopolyspora erythraea and similar proteins found in bacteria and eukaryotes. This protein is organised into two domains, both of them with a Rossmann-like alpha/beta fold. The C-terminal domain contains the nucleotide disphospho-sugar (NDP-sugar) binding site [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	DESVANCOSAMINYL VANCOMYCIN	-	-	-
A, B	GLYCOSYLTRANSFERASE GTFD	glycosyltransferase activity transferase activity hexosyltransferase activity catalytic activity UDP-glycosyltransferase activity	carbohydrate derivative biosynthetic process peptide antibiotic metabolic process carbohydrate derivative metabolic process amide biosynthetic process vancomycin metabolic process antibiotic biosynthetic process antibiotic metabolic process peptide antibiotic biosynthetic process peptide biosynthetic process biosynthetic process vancomycin biosynthetic process metabolic process cellular process amide metabolic process carbohydrate derivative biosynthetic process peptide antibiotic metabolic process carbohydrate derivative metabolic process amide biosynthetic process vancomycin metabolic process antibiotic biosynthetic process antibiotic metabolic process peptide antibiotic biosynthetic process peptide biosynthetic process biosynthetic process vancomycin biosynthetic process metabolic process cellular process amide metabolic process nonribosomal peptide biosynthetic process peptide metabolic process carbohydrate metabolic process primary metabolic process glycosylation lipid glycosylation lipid biosynthetic process lipid modification lipid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR004276	Glycosyltransferase family 28, N-terminal domain	Domain
A, B	IPR002213	UDP-glucuronosyl/UDP-glucosyltransferase	Family
A, B	IPR050426	Glycosyltransferase 28	Family
A, B	IPR010610	Erythromycin biosynthesis protein CIII-like, C-terminal domain	Domain

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.