3SXP

Crystal Structure of Helicobacter pylori ADP-L-glycero-D-manno-heptose-6-epimerase (rfaD, HP0859)

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	d3sxpa_	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Helicobacter pylori G27 ) [TaxId: 563041 ],	SCOPe (2.08)
B	d3sxpb_	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Helicobacter pylori G27 ) [TaxId: 563041 ],	SCOPe (2.08)
C	d3sxpc_	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Helicobacter pylori G27 ) [TaxId: 563041 ],	SCOPe (2.08)
D	d3sxpd_	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Helicobacter pylori G27 ) [TaxId: 563041 ],	SCOPe (2.08)
E	d3sxpe_	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Helicobacter pylori G27 ) [TaxId: 563041 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	UDP-glucose 4-epimerase GalE-lke	8077512	4000088	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	SDR-like	8077513	3000038	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	SDR-like	8077513	3000038	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SDR-like	8077513	3000038	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	SDR-like	8077513	3000038	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	SDR-like	8077513	3000038	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	GDP_Man_Dehyd_1	e3sxpA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: GDP_Man_Dehyd_1	ECOD (1.6)
B	GDP_Man_Dehyd_1	e3sxpB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: GDP_Man_Dehyd_1	ECOD (1.6)
C	GDP_Man_Dehyd_1	e3sxpC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: GDP_Man_Dehyd_1	ECOD (1.6)
D	GDP_Man_Dehyd_1	e3sxpD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: GDP_Man_Dehyd_1	ECOD (1.6)
E	GDP_Man_Dehyd_1	e3sxpE1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: GDP_Man_Dehyd_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	3.90.25.10	Alpha Beta	Alpha-Beta Complex	UDP-galactose 4-epimerase	domain 1	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	3.90.25.10	Alpha Beta	Alpha-Beta Complex	UDP-galactose 4-epimerase	domain 1	CATH (4.3.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	3.90.25.10	Alpha Beta	Alpha-Beta Complex	UDP-galactose 4-epimerase	domain 1	CATH (4.3.0)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	3.90.25.10	Alpha Beta	Alpha-Beta Complex	UDP-galactose 4-epimerase	domain 1	CATH (4.3.0)
E	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
E	3.90.25.10	Alpha Beta	Alpha-Beta Complex	UDP-galactose 4-epimerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E	PF01370	NAD dependent epimerase/dehydratase family (Epimerase)	NAD dependent epimerase/dehydratase family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E	ADP-L-glycero-D-mannoheptose-6-epimerase	hydro-lyase activity lyase activity UDP-glucose 4,6-dehydratase activity catalytic activity carbon-oxygen lyase activity isomerase activity racemase and epimerase activity ADP-glyceromanno-heptose 6-epimerase activity racemase and epimerase activity, acting on carbohydrates and derivatives UDP-L-rhamnose synthase activity transferase activity binding nucleoside phosphate binding purine nucleotide binding hydro-lyase activity lyase activity UDP-glucose 4,6-dehydratase activity catalytic activity carbon-oxygen lyase activity isomerase activity racemase and epimerase activity ADP-glyceromanno-heptose 6-epimerase activity racemase and epimerase activity, acting on carbohydrates and derivatives UDP-L-rhamnose synthase activity transferase activity binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding dTDP-glucose 4,6-dehydratase activity	nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process UDP-rhamnose biosynthetic process UDP-rhamnose metabolic process nucleotide-sugar metabolic process cellular metabolic process carbohydrate derivative metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleobase-containing compound metabolic process biosynthetic process organophosphate metabolic process nucleobase-containing small molecule metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process UDP-rhamnose biosynthetic process UDP-rhamnose metabolic process nucleotide-sugar metabolic process cellular metabolic process carbohydrate derivative metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleobase-containing compound metabolic process biosynthetic process organophosphate metabolic process nucleobase-containing small molecule metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process nucleoside phosphate biosynthetic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process nucleotide-sugar biosynthetic process pigment metabolic process flavonoid metabolic process organic hydroxy compound metabolic process pigment biosynthetic process flavonol biosynthetic process flavonoid biosynthetic process organic hydroxy compound biosynthetic process flavonol metabolic process flavone biosynthetic process flavone metabolic process carbohydrate metabolic process cellular response to stimulus auxin-activated signaling pathway regulation of cellular process response to stimulus transport signaling regulation of signal transduction export across plasma membrane hormone-mediated signaling pathway cellular response to auxin stimulus cell communication response to auxin localization cellular response to endogenous stimulus response to hormone regulation of biological quality signal transduction auxin export across the plasma membrane cellular response to hormone stimulus regulation of biological process regulation of signaling regulation of auxin mediated signaling pathway regulation of hormone levels response to endogenous stimulus biological regulation export from cell establishment of localization transmembrane transport cellular response to chemical stimulus regulation of response to stimulus response to chemical auxin transport hormone transport regulation of cell communication	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D, E	IPR001509	NAD-dependent epimerase/dehydratase	Domain
A, B, C, D, E	IPR011912	ADP-L-glycero-D-manno-heptose-6-epimerase	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 R01GM133198.