3DR7 | pdb_00003dr7

GDP-perosamine synthase from Caulobacter crescentus with bound GDP-3-deoxyperosamine

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
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3dr7a1	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Caulobacter vibrioides CB15 ) [TaxId: 190650 ],	SCOPe (2.08)
A	d3dr7a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Caulobacter vibrioides CB15 ) [TaxId: 190650 ],	SCOPe (2.08)
B	d3dr7b1	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Caulobacter vibrioides CB15 ) [TaxId: 190650 ],	SCOPe (2.08)
B	d3dr7b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Caulobacter vibrioides CB15 ) [TaxId: 190650 ],	SCOPe (2.08)
D	d3dr7d1	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Caulobacter vibrioides CB15 ) [TaxId: 190650 ],	SCOPe (2.08)
D	d3dr7d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Caulobacter vibrioides CB15 ) [TaxId: 190650 ],	SCOPe (2.08)
C	d3dr7c1	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Caulobacter vibrioides CB15 ) [TaxId: 190650 ],	SCOPe (2.08)
C	d3dr7c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Caulobacter vibrioides CB15 ) [TaxId: 190650 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	PLP-dependent transferases	8063304	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8063304	3000954	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PLP-dependent transferases	8063304	3000954	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8063304	3000954	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		e3dr7A2	A: Subtilisin-like	X: Subtilisin-like	H: Subtilisin-like	T: Pyridoxal_deC	F:	ECOD (20:10:01)
B		e3dr7B2	A: Subtilisin-like	X: Subtilisin-like	H: Subtilisin-like	T: Pyridoxal_deC	F:	ECOD (20:10:01)
D		e3dr7D2	A: Subtilisin-like	X: Subtilisin-like	H: Subtilisin-like	T: Pyridoxal_deC	F:	ECOD (20:10:01)
C		e3dr7C2	A: Subtilisin-like	X: Subtilisin-like	H: Subtilisin-like	T: Pyridoxal_deC	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
A	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
B	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
B	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
D	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
D	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
C	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
C	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01041	DegT/DnrJ/EryC1/StrS aminotransferase family (DegT_DnrJ_EryC1)	DegT/DnrJ/EryC1/StrS aminotransferase family	The members of this family are probably all pyridoxal-phosphate-dependent aminotransferase enzymes with a variety of molecular functions. The family includes StsA Swiss:P72454, StsC Swiss:P77952 and StsS [1]. The aminotransferase activity was demons ...	The members of this family are probably all pyridoxal-phosphate-dependent aminotransferase enzymes with a variety of molecular functions. The family includes StsA Swiss:P72454, StsC Swiss:P77952 and StsS [1]. The aminotransferase activity was demonstrated for purified StsC protein as the L-glutamine:scyllo-inosose aminotransferase EC:2.6.1.50, which catalyses the first amino transfer in the biosynthesis of the streptidine subunit of streptomycin [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Putative perosamine synthetase	vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding transferase activity, transferring nitrogenous groups GDP-4-dehydro-6-deoxy-D-mannose-4-aminotransferase activity transaminase activity transferase activity catalytic activity	lipopolysaccharide biosynthetic process carbohydrate derivative biosynthetic process carbohydrate metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process liposaccharide metabolic process lipid biosynthetic process carbohydrate derivative metabolic process primary metabolic process macromolecule biosynthetic process O antigen biosynthetic process lipopolysaccharide metabolic process polysaccharide metabolic process biosynthetic process lipopolysaccharide biosynthetic process carbohydrate derivative biosynthetic process carbohydrate metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process liposaccharide metabolic process lipid biosynthetic process carbohydrate derivative metabolic process primary metabolic process macromolecule biosynthetic process O antigen biosynthetic process lipopolysaccharide metabolic process polysaccharide metabolic process biosynthetic process metabolic process cellular process macromolecule metabolic process lipid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B, C, D	IPR000653	DegT/DnrJ/EryC1/StrS aminotransferase	Family
A, B, C, D	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B, C, D	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D	LLP	Parent Component: LYS RESID: AA0119 PSI-MOD : N6-pyridoxal phosphate-L-lysine MOD:00128

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.