3RAS

Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) complexed with a lipophilic phosphonate inhibitor

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
A	DXPR_C	e3rasA3	A: alpha superhelices	X: 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C (From Topology)	H: 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C (From Topology)	T: 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C	F: DXPR_C	ECOD (1.6)
A	DXP_redisom_C	e3rasA1	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology)	T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	F: DXP_redisom_C	ECOD (1.6)
A	DXP_reductoisom	e3rasA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: DXP_reductoisom	ECOD (1.6)
B	DXPR_C	e3rasB3	A: alpha superhelices	X: 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C (From Topology)	H: 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C (From Topology)	T: 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C	F: DXPR_C	ECOD (1.6)
B	DXP_redisom_C	e3rasB1	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology)	T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	F: DXP_redisom_C	ECOD (1.6)
B	DXP_reductoisom	e3rasB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: DXP_reductoisom	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	1.10.1740.10	Mainly Alpha	Orthogonal Bundle	Rna Polymerase Sigma Factor	Chain: A	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	1.10.1740.10	Mainly Alpha	Orthogonal Bundle	Rna Polymerase Sigma Factor	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02670	1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXP_reductoisom)	1-deoxy-D-xylulose 5-phosphate reductoisomerase	-	Family
A, B	PF13288	DXP reductoisomerase C-terminal domain (DXPR_C)	DXP reductoisomerase C-terminal domain	This is the C-terminal domain of the 1-deoxy-D-xylulose-5-phosphate reductoisomerase enzyme. This domain forms a left handed super-helix.	Domain
A, B	PF08436	1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal domain (DXP_redisom_C)	1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal domain	This domain is found to the C-terminus of Pfam:PF02670 domains in bacterial and plant 1-deoxy-D-xylulose 5-phosphate reductoisomerases which catalyse the formation of 2-C-methyl-D-erythritol 4-phosphate from 1-deoxy-D-xylulose-5-phosphate in the pres ...	This domain is found to the C-terminus of Pfam:PF02670 domains in bacterial and plant 1-deoxy-D-xylulose 5-phosphate reductoisomerases which catalyse the formation of 2-C-methyl-D-erythritol 4-phosphate from 1-deoxy-D-xylulose-5-phosphate in the presence of NADPH [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	1-deoxy-D-xylulose 5-phosphate reductoisomerase	cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding magnesium ion binding nucleotide binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding magnesium ion binding nucleotide binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding heterocyclic compound binding NADPH binding NADP binding 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors catalytic activity manganese ion binding	isoprenoid biosynthetic process cellular biosynthetic process cellular metabolic process lipid biosynthetic process terpenoid biosynthetic process, mevalonate-independent primary metabolic process terpenoid biosynthetic process biosynthetic process cellular lipid metabolic process metabolic process cellular process terpenoid metabolic process lipid metabolic process isoprenoid metabolic process isoprenoid biosynthetic process cellular biosynthetic process cellular metabolic process lipid biosynthetic process terpenoid biosynthetic process, mevalonate-independent primary metabolic process terpenoid biosynthetic process biosynthetic process cellular lipid metabolic process metabolic process cellular process terpenoid metabolic process lipid metabolic process isoprenoid metabolic process isopentenyl diphosphate biosynthetic process carbohydrate derivative metabolic process glyceraldehyde-3-phosphate metabolic process phospholipid metabolic process cellular aldehyde metabolic process phosphate-containing compound metabolic process phosphorus metabolic process isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway phospholipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway involved in terpenoid biosynthetic process isopentenyl diphosphate metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR026877	DXP reductoisomerase, C-terminal domain	Domain
A, B	IPR003821	1-deoxy-D-xylulose 5-phosphate reductoisomerase	Family
A, B	IPR036169	DXP reductoisomerase, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR013644	1-deoxy-D-xylulose 5-phosphate reductoisomerase, C-terminal	Domain
A, B	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B	IPR013512	1-deoxy-D-xylulose 5-phosphate reductoisomerase, N-terminal	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.