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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)DescriptionActionsGraphical viewLength
Binding sitei125SubstrateUniRule annotation1
Metal bindingi150Divalent metal cationUniRule annotation1
Metal bindingi152Divalent metal cationUniRule annotation1
Binding sitei152SubstrateUniRule annotation1
Binding sitei186SubstrateUniRule annotation1
Binding sitei209SubstrateUniRule annotation1
Metal bindingi231Divalent metal cationUniRule annotation1
Binding sitei231SubstrateUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi7 – 36NADPUniRule annotationAdd BLAST30

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

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesYersiniaceaeYersinia
Proteomesi
  • UP000000721 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000985321 – 3981-deoxy-D-xylulose 5-phosphate reductoisomeraseAdd BLAST398

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Structurei

Secondary structure

1398
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 8Combined sources7
Helixi12 – 23Combined sources12
Turni25 – 27Combined sources3
Beta strandi28 – 34Combined sources7
Helixi39 – 49Combined sources11
Beta strandi52 – 58Combined sources7
Helixi59 – 71Combined sources13
Beta strandi77 – 81Combined sources5
Helixi82 – 88Combined sources7
Beta strandi96 – 99Combined sources4
Helixi104 – 106Combined sources3
Helixi107 – 115Combined sources9
Beta strandi119 – 122Combined sources4
Helixi126 – 142Combined sources17
Beta strandi145 – 148Combined sources4
Helixi151 – 158Combined sources8
Helixi162 – 166Combined sources5
Turni167 – 169Combined sources3
Helixi174 – 176Combined sources3
Beta strandi178 – 185Combined sources8
Beta strandi191 – 193Combined sources3
Helixi195 – 200Combined sources6
Turni203 – 205Combined sources3
Helixi217 – 223Combined sources7
Helixi226 – 239Combined sources14
Helixi243 – 245Combined sources3
Beta strandi246 – 250Combined sources5
Beta strandi256 – 262Combined sources7
Beta strandi267 – 271Combined sources5
Helixi277 – 285Combined sources9
Turni312 – 314Combined sources3
Helixi316 – 327Combined sources12
Helixi329 – 347Combined sources19
Helixi355 – 365Combined sources11
Helixi375 – 394Combined sources20

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiB1JQG4.

Family & Domainsi

Sequence similaritiesi

Belongs to the DXR family.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000007221.
KOiK00099.
OMAiGFCPLSE.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_00183. DXP_reductoisom. 1 hit.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3IIEX-ray2.21A/B1-398[»]
ProteinModelPortaliB1JQG4.
SMRiB1JQG4.
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.

Enzyme and pathway databases

UniPathwayiUPA00056; UER00092.

Miscellaneous databases

EvolutionaryTraceiB1JQG4.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_00183. DXP_reductoisom. 1 hit.
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...

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: November 2, 2016
This is version 62 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.