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Protein

1-deoxy-D-xylulose 5-phosphate reductoisomerase

Gene

dxr

Organism
Yersinia pseudotuberculosis serotype O:3 (strain YPIII)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP).UniRule annotation

Catalytic activityi

2-C-methyl-D-erythritol 4-phosphate + NADP+ = 1-deoxy-D-xylulose 5-phosphate + NADPH.UniRule annotation

Cofactori

a divalent metal cationUniRule annotation

Pathwayi: isopentenyl diphosphate biosynthesis via DXP pathway

This protein is involved in step 1 of the subpathway that synthesizes isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate.UniRule annotation
Proteins known to be involved in the 6 steps of the subpathway in this organism are:
  1. 1-deoxy-D-xylulose 5-phosphate reductoisomerase (dxr)
  2. 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (ispD)
  3. 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (ispE)
  4. 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (ispF)
  5. 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin) (ispG)
  6. 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (ispH)
This subpathway is part of the pathway isopentenyl diphosphate biosynthesis via DXP pathway, which is itself part of Isoprenoid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate, the pathway isopentenyl diphosphate biosynthesis via DXP pathway and in Isoprenoid biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei125 – 1251SubstrateUniRule annotation
Metal bindingi150 – 1501Divalent metal cationUniRule annotation
Metal bindingi152 – 1521Divalent metal cationUniRule annotation
Binding sitei152 – 1521SubstrateUniRule annotation
Binding sitei186 – 1861SubstrateUniRule annotation
Binding sitei209 – 2091SubstrateUniRule annotation
Metal bindingi231 – 2311Divalent metal cationUniRule annotation
Binding sitei231 – 2311SubstrateUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi7 – 3630NADPUniRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Isoprene biosynthesis

Keywords - Ligandi

Metal-binding, NADP

Enzyme and pathway databases

BioCyciYPSE502800:GH0W-1083-MONOMER.
UniPathwayiUPA00056; UER00092.

Names & Taxonomyi

Protein namesi
Recommended name:
1-deoxy-D-xylulose 5-phosphate reductoisomeraseUniRule annotation (EC:1.1.1.267UniRule annotation)
Short name:
DXP reductoisomeraseUniRule annotation
Alternative name(s):
1-deoxyxylulose-5-phosphate reductoisomeraseUniRule annotation
2-C-methyl-D-erythritol 4-phosphate synthaseUniRule annotation
Gene namesi
Name:dxrUniRule annotation
Ordered Locus Names:YPK_1070
OrganismiYersinia pseudotuberculosis serotype O:3 (strain YPIII)
Taxonomic identifieri502800 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeYersinia
Proteomesi
  • UP000000721 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 3983981-deoxy-D-xylulose 5-phosphate reductoisomerasePRO_1000098532Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Structurei

Secondary structure

1
398
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 87Combined sources
Helixi12 – 2312Combined sources
Turni25 – 273Combined sources
Beta strandi28 – 347Combined sources
Helixi39 – 4911Combined sources
Beta strandi52 – 587Combined sources
Helixi59 – 7113Combined sources
Beta strandi77 – 815Combined sources
Helixi82 – 887Combined sources
Beta strandi96 – 994Combined sources
Helixi104 – 1063Combined sources
Helixi107 – 1159Combined sources
Beta strandi119 – 1224Combined sources
Helixi126 – 14217Combined sources
Beta strandi145 – 1484Combined sources
Helixi151 – 1588Combined sources
Helixi162 – 1665Combined sources
Turni167 – 1693Combined sources
Helixi174 – 1763Combined sources
Beta strandi178 – 1858Combined sources
Beta strandi191 – 1933Combined sources
Helixi195 – 2006Combined sources
Turni203 – 2053Combined sources
Helixi217 – 2237Combined sources
Helixi226 – 23914Combined sources
Helixi243 – 2453Combined sources
Beta strandi246 – 2505Combined sources
Beta strandi256 – 2627Combined sources
Beta strandi267 – 2715Combined sources
Helixi277 – 2859Combined sources
Turni312 – 3143Combined sources
Helixi316 – 32712Combined sources
Helixi329 – 34719Combined sources
Helixi355 – 36511Combined sources
Helixi375 – 39420Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3IIEX-ray2.21A/B1-398[»]
ProteinModelPortaliB1JQG4.
SMRiB1JQG4. Positions 1-396.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiB1JQG4.

Family & Domainsi

Sequence similaritiesi

Belongs to the DXR family.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000007221.
KOiK00099.
OMAiGFCPLSE.
OrthoDBiEOG6R2H04.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_00183. DXP_reductoisom.
InterProiIPR003821. DXP_reductoisomerase.
IPR013644. DXP_reductoisomerase_C.
IPR013512. DXP_reductoisomerase_N.
IPR026877. DXPR_C.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PANTHERiPTHR30525. PTHR30525. 1 hit.
PfamiPF08436. DXP_redisom_C. 1 hit.
PF02670. DXP_reductoisom. 1 hit.
PF13288. DXPR_C. 1 hit.
[Graphical view]
PIRSFiPIRSF006205. Dxp_reductismrs. 1 hit.
SUPFAMiSSF51735. SSF51735. 1 hit.
SSF69055. SSF69055. 1 hit.
TIGRFAMsiTIGR00243. Dxr. 1 hit.

Sequencei

Sequence statusi: Complete.

B1JQG4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKQLTILGST GSIGNSTLSV VRANPELFKV TALVAGRNVR EMAQQCLEFS
60 70 80 90 100
PRYAAMSDEH SAKSLRLLLA EQGSDTEVYS GETAACELAA LDDVDQVMAA
110 120 130 140 150
IVGIAGLPST LAAIRAGKQV LLANKESLIT CGKLFMDEVK RSRAQLLPID
160 170 180 190 200
SEHNAIFQSL PERIQRQLGY SSLNENGVSR IILTGSGGPF RETPLSQFSD
210 220 230 240 250
VTPDQACAHP NWSMGRKISV DSATMMNKGL EYIEARWLFN ASAEQIEVVL
260 270 280 290 300
HPQSVIHSMV RYHDGSILAQ MGTPDMRTPI AHAMAYPMRV SSGVAPLDFC
310 320 330 340 350
KVGALTFTTP DYQRYPCLKL AIDACNAGQA ATTALNAANE ISVMAFLDSK
360 370 380 390
IRFTDIEVIN RTVVEGLLLS EPTSVEEVLV IDRKARDVAA QVIAKLNN
Length:398
Mass (Da):43,115
Last modified:April 29, 2008 - v1
Checksum:iC9B1FC9E0166D057
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000950 Genomic DNA. Translation: ACA67371.1.
RefSeqiWP_002212135.1. NZ_CP009792.1.

Genome annotation databases

EnsemblBacteriaiACA67371; ACA67371; YPK_1070.
KEGGiypy:YPK_1070.
PATRICi18659292. VBIYerPse127545_1147.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000950 Genomic DNA. Translation: ACA67371.1.
RefSeqiWP_002212135.1. NZ_CP009792.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3IIEX-ray2.21A/B1-398[»]
ProteinModelPortaliB1JQG4.
SMRiB1JQG4. Positions 1-396.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACA67371; ACA67371; YPK_1070.
KEGGiypy:YPK_1070.
PATRICi18659292. VBIYerPse127545_1147.

Phylogenomic databases

HOGENOMiHOG000007221.
KOiK00099.
OMAiGFCPLSE.
OrthoDBiEOG6R2H04.

Enzyme and pathway databases

UniPathwayiUPA00056; UER00092.
BioCyciYPSE502800:GH0W-1083-MONOMER.

Miscellaneous databases

EvolutionaryTraceiB1JQG4.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_00183. DXP_reductoisom.
InterProiIPR003821. DXP_reductoisomerase.
IPR013644. DXP_reductoisomerase_C.
IPR013512. DXP_reductoisomerase_N.
IPR026877. DXPR_C.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PANTHERiPTHR30525. PTHR30525. 1 hit.
PfamiPF08436. DXP_redisom_C. 1 hit.
PF02670. DXP_reductoisom. 1 hit.
PF13288. DXPR_C. 1 hit.
[Graphical view]
PIRSFiPIRSF006205. Dxp_reductismrs. 1 hit.
SUPFAMiSSF51735. SSF51735. 1 hit.
SSF69055. SSF69055. 1 hit.
TIGRFAMsiTIGR00243. Dxr. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: YPIII.

Entry informationi

Entry nameiDXR_YERPY
AccessioniPrimary (citable) accession number: B1JQG4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: April 29, 2008
Last modified: December 9, 2015
This is version 59 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.