1R0K | pdb_00001r0k

Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Zymomonas mobilis

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	d1r0ka1	All alpha proteins	Left-handed superhelix	1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain	1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain	1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain	(Zymomonas mobilis ) [TaxId: 542 ],	SCOPe (2.08)
A	d1r0ka2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	1-deoxy-D-xylulose-5-phosphate reductoisomerase	(Zymomonas mobilis ) [TaxId: 542 ],	SCOPe (2.08)
A	d1r0ka3	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Dihydrodipicolinate reductase-like	1-deoxy-D-xylulose-5-phosphate reductoisomerase	(Zymomonas mobilis ) [TaxId: 542 ],	SCOPe (2.08)
B	d1r0kb1	All alpha proteins	Left-handed superhelix	1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain	1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain	1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain	(Zymomonas mobilis ) [TaxId: 542 ],	SCOPe (2.08)
B	d1r0kb2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	1-deoxy-D-xylulose-5-phosphate reductoisomerase	(Zymomonas mobilis ) [TaxId: 542 ],	SCOPe (2.08)
B	d1r0kb3	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Dihydrodipicolinate reductase-like	1-deoxy-D-xylulose-5-phosphate reductoisomerase	(Zymomonas mobilis ) [TaxId: 542 ],	SCOPe (2.08)
C	d1r0kc1	All alpha proteins	Left-handed superhelix	1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain	1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain	1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain	(Zymomonas mobilis ) [TaxId: 542 ],	SCOPe (2.08)
C	d1r0kc2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	1-deoxy-D-xylulose-5-phosphate reductoisomerase	(Zymomonas mobilis ) [TaxId: 542 ],	SCOPe (2.08)
C	d1r0kc3	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Dihydrodipicolinate reductase-like	1-deoxy-D-xylulose-5-phosphate reductoisomerase	(Zymomonas mobilis ) [TaxId: 542 ],	SCOPe (2.08)
D	d1r0kd1	All alpha proteins	Left-handed superhelix	1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain	1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain	1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain	(Zymomonas mobilis ) [TaxId: 542 ],	SCOPe (2.08)
D	d1r0kd2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	1-deoxy-D-xylulose-5-phosphate reductoisomerase	(Zymomonas mobilis ) [TaxId: 542 ],	SCOPe (2.08)
D	d1r0kd3	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Dihydrodipicolinate reductase-like	1-deoxy-D-xylulose-5-phosphate reductoisomerase	(Zymomonas mobilis ) [TaxId: 542 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	DXP reductoisomerase-like	8056157	4000096	SCOP2 (2022-06-29)
A	SCOP2 Family	DXP reductoisomerase C-terminal domain-like	8091676	4007753	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	GAPDH-like	8056158	3000043	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DXP reductoisomerase C-terminal domain-like	8056159	3000022	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	GAPDH-like	8056158	3000043	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DXP reductoisomerase C-terminal domain-like	8056159	3000022	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DXP reductoisomerase C-terminal domain-like	8056159	3000022	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GAPDH-like	8056158	3000043	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DXP reductoisomerase C-terminal domain-like	8056159	3000022	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	GAPDH-like	8056158	3000043	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		e1r0kA1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: tRNA-binding arm	T: tRNA-binding arm	F:	ECOD (v294.1)
A	FAD_binding_3	e1r0kA3	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (v294.1)
A	Cobalamin_bind	e1r0kA2	A: a/b three-layered sandwiches	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: Cobalamin_bind	ECOD (v294.1)
B		e1r0kB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: tRNA-binding arm	T: tRNA-binding arm	F:	ECOD (v294.1)
B	FAD_binding_3	e1r0kB3	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (v294.1)
B	Cobalamin_bind	e1r0kB2	A: a/b three-layered sandwiches	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: Cobalamin_bind	ECOD (v294.1)
C	JmjC,JmjN	e1r0kC3	A: a/b three-layered sandwiches	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: JmjC,JmjN	ECOD (v294.1)
C	PI3K_rbd,PIK3CG_ABD	e1r0kC1	A: a/b three-layered sandwiches	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: PI3K_rbd,PIK3CG_ABD	ECOD (v294.1)
D		e1r0kD1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: tRNA-binding arm	T: tRNA-binding arm	F:	ECOD (v294.1)
D	FAD_binding_3	e1r0kD3	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (v294.1)
D	Cobalamin_bind	e1r0kD2	A: a/b three-layered sandwiches	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: Cobalamin_bind	ECOD (v294.1)

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)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	1.10.1740.10	Mainly Alpha	Orthogonal Bundle	Rna Polymerase Sigma Factor	Chain: A	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	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, C, D	PF02670	1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXP_reductoisom)	1-deoxy-D-xylulose 5-phosphate reductoisomerase	-	Family
A, B, C, D	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, C, D	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, C, D	1-deoxy-D-xylulose 5-phosphate reductoisomerase	cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding nucleotide binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding NADPH binding cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding nucleotide binding nucleoside phosphate binding purine nucleotide 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	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR026877	DXP reductoisomerase, C-terminal domain	Domain
A, B, C, D	IPR003821	1-deoxy-D-xylulose 5-phosphate reductoisomerase	Family
A, B, C, D	IPR036169	DXP reductoisomerase, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR013644	1-deoxy-D-xylulose 5-phosphate reductoisomerase, C-terminal	Domain
A, B, C, D	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.