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Protein

1-deoxy-D-xylulose 5-phosphate reductoisomerase

Gene

dxr

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 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).

Catalytic activityi

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

Cofactori

Mg2+, Mn2+, Co2+Note: Divalent cation. Prefers Mg2+, Mn2+ or Co2+.

Enzyme regulationi

Inhibited by fosmidomycin.

Kineticsi

Measured in the presence of manganese ions.

  1. KM=250 µM for DXP1 Publication

    pH dependencei

    Optimum pH is 7.0-8.5.1 Publication

    Temperature dependencei

    Optimum temperature is 40-60 degrees Celsius.1 Publication

    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.
    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 sitei125Substrate1 Publication1
    Metal bindingi150Divalent metal cation1
    Metal bindingi152Divalent metal cation1
    Binding sitei152Substrate1 Publication1
    Binding sitei186Substrate1 Publication1
    Binding sitei209Substrate1 Publication1
    Metal bindingi231Divalent metal cation1
    Binding sitei231Substrate1 Publication1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi7 – 36NADP2 PublicationsAdd BLAST30

    GO - Molecular functioni

    • 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity Source: EcoCyc
    • identical protein binding Source: EcoCyc
    • manganese ion binding Source: EcoCyc
    • NADPH binding Source: GO_Central

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Isoprene biosynthesis

    Keywords - Ligandi

    Cobalt, Magnesium, Manganese, Metal-binding, NADP

    Enzyme and pathway databases

    BioCyciEcoCyc:DXPREDISOM-MONOMER.
    ECOL316407:JW0168-MONOMER.
    MetaCyc:DXPREDISOM-MONOMER.
    BRENDAi1.1.1.267. 2026.
    SABIO-RKP45568.
    UniPathwayiUPA00056; UER00092.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC:1.1.1.267)
    Short name:
    DXP reductoisomerase
    Alternative name(s):
    1-deoxyxylulose-5-phosphate reductoisomerase
    2-C-methyl-D-erythritol 4-phosphate synthase
    Gene namesi
    Name:dxr
    Synonyms:ispC, yaeM
    Ordered Locus Names:b0173, JW0168
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG12715. dxr.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi14G → D: Loss of solubility and activity. 1 Publication1
    Mutagenesisi153H → Q: Increase in KM for substrate. Reduces activity 35-fold. 1 Publication1
    Mutagenesisi209H → Q: Increase in KM for substrate. Reduces activity 5000-fold. 1 Publication1
    Mutagenesisi231E → K: No effect on KM for substrate. Reduces activity by over 99.9%. 1 Publication1
    Mutagenesisi257H → Q: Strong increase in KM for substrate. Loss of activity. 1 Publication1

    Chemistry databases

    ChEMBLiCHEMBL4091.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001636511 – 3981-deoxy-D-xylulose 5-phosphate reductoisomeraseAdd BLAST398

    Proteomic databases

    PaxDbiP45568.
    PRIDEiP45568.

    Interactioni

    Subunit structurei

    Homodimer.5 Publications

    GO - Molecular functioni

    • identical protein binding Source: EcoCyc

    Protein-protein interaction databases

    BioGridi4259751. 202 interactors.
    DIPiDIP-9484N.
    IntActiP45568. 6 interactors.
    STRINGi511145.b0173.

    Chemistry databases

    BindingDBiP45568.

    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 – 37Combined sources10
    Helixi39 – 49Combined sources11
    Beta strandi52 – 58Combined sources7
    Helixi59 – 71Combined sources13
    Beta strandi77 – 81Combined sources5
    Helixi82 – 89Combined sources8
    Beta strandi96 – 99Combined sources4
    Helixi104 – 106Combined sources3
    Helixi107 – 115Combined sources9
    Beta strandi119 – 122Combined sources4
    Helixi125 – 131Combined sources7
    Helixi133 – 142Combined sources10
    Beta strandi145 – 148Combined sources4
    Helixi151 – 158Combined sources8
    Helixi162 – 165Combined sources4
    Turni166 – 170Combined sources5
    Helixi174 – 176Combined sources3
    Beta strandi178 – 185Combined sources8
    Turni189 – 192Combined sources4
    Helixi195 – 200Combined sources6
    Helixi203 – 207Combined sources5
    Beta strandi210 – 212Combined sources3
    Helixi216 – 223Combined sources8
    Helixi226 – 239Combined sources14
    Helixi243 – 245Combined sources3
    Beta strandi246 – 250Combined sources5
    Beta strandi256 – 262Combined sources7
    Beta strandi267 – 271Combined sources5
    Helixi277 – 285Combined sources9
    Turni299 – 301Combined sources3
    Turni312 – 314Combined sources3
    Helixi316 – 327Combined sources12
    Helixi329 – 347Combined sources19
    Helixi355 – 366Combined sources12
    Helixi375 – 395Combined sources21

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1JVSX-ray2.20A/B2-398[»]
    1K5HX-ray2.50A/B/C1-398[»]
    1ONNX-ray2.60A/B1-398[»]
    1ONOX-ray2.50A/B1-398[»]
    1ONPX-ray2.50A/B1-398[»]
    1Q0HX-ray2.20A1-398[»]
    1Q0LX-ray2.65A1-398[»]
    1Q0QX-ray1.90A/B1-398[»]
    1T1RX-ray2.30A/B2-398[»]
    1T1SX-ray2.40A/B2-398[»]
    2EGHX-ray2.20A/B2-398[»]
    3ANLX-ray2.10A/B2-398[»]
    3ANMX-ray2.00A/B2-398[»]
    3ANNX-ray2.00A/B2-398[»]
    3R0IX-ray2.10A/B1-398[»]
    ProteinModelPortaliP45568.
    SMRiP45568.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP45568.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni222 – 228Binding to substrate phosphate group7

    Sequence similaritiesi

    Belongs to the DXR family.Curated

    Phylogenomic databases

    eggNOGiENOG4105CEA. Bacteria.
    COG0743. LUCA.
    HOGENOMiHOG000007221.
    InParanoidiP45568.
    KOiK00099.
    OMAiGFCPLSE.
    PhylomeDBiP45568.

    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.

    P45568-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKQLTILGST GSIGCSTLDV VRHNPEHFRV VALVAGKNVT RMVEQCLEFS
    60 70 80 90 100
    PRYAVMDDEA SAKLLKTMLQ QQGSRTEVLS GQQAACDMAA LEDVDQVMAA
    110 120 130 140 150
    IVGAAGLLPT LAAIRAGKTI LLANKESLVT CGRLFMDAVK QSKAQLLPVD
    160 170 180 190 200
    SEHNAIFQSL PQPIQHNLGY ADLEQNGVVS ILLTGSGGPF RETPLRDLAT
    210 220 230 240 250
    MTPDQACRHP NWSMGRKISV DSATMMNKGL EYIEARWLFN ASASQMEVLI
    260 270 280 290 300
    HPQSVIHSMV RYQDGSVLAQ LGEPDMRTPI AHTMAWPNRV NSGVKPLDFC
    310 320 330 340 350
    KLSALTFAAP DYDRYPCLKL AMEAFEQGQA ATTALNAANE ITVAAFLAQQ
    360 370 380 390
    IRFTDIAALN LSVLEKMDMR EPQCVDDVLS VDANAREVAR KEVMRLAS
    Length:398
    Mass (Da):43,388
    Last modified:November 1, 1997 - v2
    Checksum:i8B532683A4FF1207
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB013300 Genomic DNA. Translation: BAA32426.1.
    U70214 Genomic DNA. Translation: AAB08602.1.
    U00096 Genomic DNA. Translation: AAC73284.1.
    AP009048 Genomic DNA. Translation: BAA77848.2.
    D13334 Genomic DNA. No translation available.
    PIRiE64741.
    RefSeqiNP_414715.1. NC_000913.3.
    WP_000811923.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73284; AAC73284; b0173.
    BAA77848; BAA77848; BAA77848.
    GeneIDi945019.
    KEGGiecj:JW0168.
    eco:b0173.
    PATRICi32115455. VBIEscCol129921_0179.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB013300 Genomic DNA. Translation: BAA32426.1.
    U70214 Genomic DNA. Translation: AAB08602.1.
    U00096 Genomic DNA. Translation: AAC73284.1.
    AP009048 Genomic DNA. Translation: BAA77848.2.
    D13334 Genomic DNA. No translation available.
    PIRiE64741.
    RefSeqiNP_414715.1. NC_000913.3.
    WP_000811923.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1JVSX-ray2.20A/B2-398[»]
    1K5HX-ray2.50A/B/C1-398[»]
    1ONNX-ray2.60A/B1-398[»]
    1ONOX-ray2.50A/B1-398[»]
    1ONPX-ray2.50A/B1-398[»]
    1Q0HX-ray2.20A1-398[»]
    1Q0LX-ray2.65A1-398[»]
    1Q0QX-ray1.90A/B1-398[»]
    1T1RX-ray2.30A/B2-398[»]
    1T1SX-ray2.40A/B2-398[»]
    2EGHX-ray2.20A/B2-398[»]
    3ANLX-ray2.10A/B2-398[»]
    3ANMX-ray2.00A/B2-398[»]
    3ANNX-ray2.00A/B2-398[»]
    3R0IX-ray2.10A/B1-398[»]
    ProteinModelPortaliP45568.
    SMRiP45568.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4259751. 202 interactors.
    DIPiDIP-9484N.
    IntActiP45568. 6 interactors.
    STRINGi511145.b0173.

    Chemistry databases

    BindingDBiP45568.
    ChEMBLiCHEMBL4091.

    Proteomic databases

    PaxDbiP45568.
    PRIDEiP45568.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC73284; AAC73284; b0173.
    BAA77848; BAA77848; BAA77848.
    GeneIDi945019.
    KEGGiecj:JW0168.
    eco:b0173.
    PATRICi32115455. VBIEscCol129921_0179.

    Organism-specific databases

    EchoBASEiEB2575.
    EcoGeneiEG12715. dxr.

    Phylogenomic databases

    eggNOGiENOG4105CEA. Bacteria.
    COG0743. LUCA.
    HOGENOMiHOG000007221.
    InParanoidiP45568.
    KOiK00099.
    OMAiGFCPLSE.
    PhylomeDBiP45568.

    Enzyme and pathway databases

    UniPathwayiUPA00056; UER00092.
    BioCyciEcoCyc:DXPREDISOM-MONOMER.
    ECOL316407:JW0168-MONOMER.
    MetaCyc:DXPREDISOM-MONOMER.
    BRENDAi1.1.1.267. 2026.
    SABIO-RKP45568.

    Miscellaneous databases

    EvolutionaryTraceiP45568.
    PROiP45568.

    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_ECOLI
    AccessioniPrimary (citable) accession number: P45568
    Secondary accession number(s): P77209, Q8KMY5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1995
    Last sequence update: November 1, 1997
    Last modified: November 2, 2016
    This is version 145 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. 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.