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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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei125 – 1251Substrate1 Publication
    Metal bindingi150 – 1501Divalent metal cation
    Metal bindingi152 – 1521Divalent metal cation
    Binding sitei152 – 1521Substrate1 Publication
    Binding sitei186 – 1861Substrate1 Publication
    Binding sitei209 – 2091Substrate1 Publication
    Metal bindingi231 – 2311Divalent metal cation
    Binding sitei231 – 2311Substrate1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi7 – 3630NADP2 PublicationsAdd
    BLAST

    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG12715. dxr.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi14 – 141G → D: Loss of solubility and activity. 1 Publication
    Mutagenesisi153 – 1531H → Q: Increase in KM for substrate. Reduces activity 35-fold. 1 Publication
    Mutagenesisi209 – 2091H → Q: Increase in KM for substrate. Reduces activity 5000-fold. 1 Publication
    Mutagenesisi231 – 2311E → K: No effect on KM for substrate. Reduces activity by over 99.9%. 1 Publication
    Mutagenesisi257 – 2571H → Q: Strong increase in KM for substrate. Loss of activity. 1 Publication

    Chemistry

    ChEMBLiCHEMBL4091.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 3983981-deoxy-D-xylulose 5-phosphate reductoisomerasePRO_0000163651Add
    BLAST

    Proteomic databases

    PaxDbiP45568.
    PRIDEiP45568.

    Interactioni

    Subunit structurei

    Homodimer.5 Publications

    GO - Molecular functioni

    • identical protein binding Source: EcoCyc

    Protein-protein interaction databases

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

    Chemistry

    BindingDBiP45568.

    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 – 3710Combined sources
    Helixi39 – 4911Combined sources
    Beta strandi52 – 587Combined sources
    Helixi59 – 7113Combined sources
    Beta strandi77 – 815Combined sources
    Helixi82 – 898Combined sources
    Beta strandi96 – 994Combined sources
    Helixi104 – 1063Combined sources
    Helixi107 – 1159Combined sources
    Beta strandi119 – 1224Combined sources
    Helixi125 – 1317Combined sources
    Helixi133 – 14210Combined sources
    Beta strandi145 – 1484Combined sources
    Helixi151 – 1588Combined sources
    Helixi162 – 1654Combined sources
    Turni166 – 1705Combined sources
    Helixi174 – 1763Combined sources
    Beta strandi178 – 1858Combined sources
    Turni189 – 1924Combined sources
    Helixi195 – 2006Combined sources
    Helixi203 – 2075Combined sources
    Beta strandi210 – 2123Combined sources
    Helixi216 – 2238Combined sources
    Helixi226 – 23914Combined sources
    Helixi243 – 2453Combined sources
    Beta strandi246 – 2505Combined sources
    Beta strandi256 – 2627Combined sources
    Beta strandi267 – 2715Combined sources
    Helixi277 – 2859Combined sources
    Turni299 – 3013Combined sources
    Turni312 – 3143Combined sources
    Helixi316 – 32712Combined sources
    Helixi329 – 34719Combined sources
    Helixi355 – 36612Combined sources
    Helixi375 – 39521Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    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. Positions 1-398.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP45568.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni222 – 2287Binding to substrate phosphate group

    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
    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. Positions 1-398.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

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

    Chemistry

    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: September 7, 2016
    This is version 143 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.