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Protein

3-isopropylmalate dehydrogenase

Gene

leuB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the oxidation of 3-carboxy-2-hydroxy-4-methylpentanoate (3-isopropylmalate) to 3-carboxy-4-methyl-2-oxopentanoate. The product decarboxylates to 4-methyl-2 oxopentanoate.UniRule annotation1 Publication

Catalytic activityi

(2R,3S)-3-isopropylmalate + NAD+ = 4-methyl-2-oxopentanoate + CO2 + NADH.UniRule annotation1 Publication

Cofactori

Mg2+UniRule annotation1 Publication, Mn2+UniRule annotation1 PublicationNote: Binds 1 Mg2+ or Mn2+ ion per subunit.UniRule annotation

Enzyme regulationi

Requires K+ ions for optimum activity.1 Publication

Kineticsi

kcat is 69 sec(-1).1 Publication

Manual assertion based on experiment ini

  1. KM=105 µM for 3-isopropylmalate (at 40 degrees Celsius)1 Publication
  2. KM=321 µM for NAD (at 40 degrees Celsius)1 Publication

    pH dependencei

    Optimum pH is 7.6.1 Publication

    Temperature dependencei

    Optimum temperature is 70 degrees Celsius.1 Publication

    Pathwayi: L-leucine biosynthesis

    This protein is involved in step 3 of the subpathway that synthesizes L-leucine from 3-methyl-2-oxobutanoate.UniRule annotation1 Publication
    Proteins known to be involved in the 4 steps of the subpathway in this organism are:
    1. 2-isopropylmalate synthase (leuA)
    2. 3-isopropylmalate dehydratase small subunit (leuD), 3-isopropylmalate dehydratase large subunit (leuC)
    3. 3-isopropylmalate dehydrogenase (leuB)
    4. Branched-chain-amino-acid aminotransferase (ilvE)
    This subpathway is part of the pathway L-leucine biosynthesis, which is itself part of Amino-acid biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-leucine from 3-methyl-2-oxobutanoate, the pathway L-leucine biosynthesis and in Amino-acid biosynthesis.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei99SubstrateUniRule annotation1
    Binding sitei109SubstrateUniRule annotation1
    Binding sitei138SubstrateUniRule annotation1
    Sitei145Important for catalysisUniRule annotation1
    Sitei195Important for catalysisUniRule annotation1
    Metal bindingi227Magnesium or manganeseUniRule annotation1
    Binding sitei227SubstrateUniRule annotation1
    Metal bindingi251Magnesium or manganeseUniRule annotation1
    Metal bindingi255Magnesium or manganeseUniRule annotation1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi78 – 91NADUniRule annotationAdd BLAST14
    Nucleotide bindingi285 – 297NADUniRule annotationAdd BLAST13

    GO - Molecular functioni

    • 3-isopropylmalate dehydrogenase activity Source: EcoCyc
    • magnesium ion binding Source: EcoCyc
    • manganese ion binding Source: EcoCyc
    • metal ion binding Source: EcoCyc
    • NAD binding Source: InterPro

    GO - Biological processi

    • branched-chain amino acid biosynthetic process Source: UniProtKB-KW
    • cellular response to amino acid starvation Source: EcoliWiki
    • leucine biosynthetic process Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Amino-acid biosynthesis, Branched-chain amino acid biosynthesis, Leucine biosynthesis

    Keywords - Ligandi

    Magnesium, Manganese, Metal-binding, NAD

    Enzyme and pathway databases

    BioCyciEcoCyc:3-ISOPROPYLMALDEHYDROG-MONOMER.
    ECOL316407:JW5807-MONOMER.
    MetaCyc:3-ISOPROPYLMALDEHYDROG-MONOMER.
    BRENDAi1.1.1.85. 2026.
    UniPathwayiUPA00048; UER00072.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    3-isopropylmalate dehydrogenase1 PublicationUniRule annotation (EC:1.1.1.85UniRule annotation1 Publication)
    Alternative name(s):
    3-IPM-DHUniRule annotation
    Beta-IPM dehydrogenaseUniRule annotation
    Short name:
    IMDHUniRule annotation
    Gene namesi
    Name:leuBUniRule annotation
    Ordered Locus Names:b0073, JW5807
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11577. leuB.

    Subcellular locationi

    • Cytoplasm UniRule annotation

    GO - Cellular componenti

    • cytosol Source: EcoCyc
    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemoved2 Publications
    ChainiPRO_00000836912 – 3633-isopropylmalate dehydrogenaseAdd BLAST362

    Proteomic databases

    EPDiP30125.
    PaxDbiP30125.
    PRIDEiP30125.

    Interactioni

    Subunit structurei

    Homodimer.UniRule annotation1 Publication

    Protein-protein interaction databases

    BioGridi4259727. 8 interactors.
    IntActiP30125. 2 interactors.
    STRINGi511145.b0073.

    Structurei

    Secondary structure

    1363
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi3 – 13Combined sources11
    Helixi16 – 34Combined sources19
    Beta strandi37 – 42Combined sources6
    Helixi47 – 53Combined sources7
    Beta strandi54 – 57Combined sources4
    Helixi59 – 66Combined sources8
    Beta strandi68 – 75Combined sources8
    Beta strandi86 – 89Combined sources4
    Helixi90 – 101Combined sources12
    Beta strandi106 – 112Combined sources7
    Turni118 – 120Combined sources3
    Beta strandi121 – 123Combined sources3
    Helixi125 – 128Combined sources4
    Beta strandi133 – 139Combined sources7
    Helixi143 – 145Combined sources3
    Beta strandi148 – 153Combined sources6
    Helixi156 – 158Combined sources3
    Beta strandi160 – 168Combined sources9
    Helixi169 – 184Combined sources16
    Turni185 – 187Combined sources3
    Beta strandi188 – 194Combined sources7
    Turni196 – 198Combined sources3
    Helixi200 – 212Combined sources13
    Helixi213 – 215Combined sources3
    Beta strandi219 – 225Combined sources7
    Helixi226 – 235Combined sources10
    Helixi237 – 239Combined sources3
    Beta strandi241 – 245Combined sources5
    Helixi247 – 261Combined sources15
    Beta strandi268 – 272Combined sources5
    Beta strandi278 – 284Combined sources7
    Helixi288 – 290Combined sources3
    Helixi299 – 311Combined sources13
    Helixi316 – 331Combined sources16
    Beta strandi336 – 338Combined sources3
    Helixi348 – 359Combined sources12

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1CM7X-ray2.06A/B1-363[»]
    ProteinModelPortaliP30125.
    SMRiP30125.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP30125.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the isocitrate and isopropylmalate dehydrogenases family. LeuB type 1 subfamily.UniRule annotationCurated

    Phylogenomic databases

    eggNOGiENOG4105C0C. Bacteria.
    COG0473. LUCA.
    HOGENOMiHOG000021112.
    InParanoidiP30125.
    KOiK00052.
    OMAiRRPKQFD.
    PhylomeDBiP30125.

    Family and domain databases

    Gene3Di3.40.718.10. 1 hit.
    HAMAPiMF_01033. LeuB_type1. 1 hit.
    InterProiIPR019818. IsoCit/isopropylmalate_DH_CS.
    IPR001804. Isocitrate/isopropylmalate_DH.
    IPR024084. IsoPropMal-DH-like_dom.
    IPR004429. Isopropylmalate_DH.
    [Graphical view]
    PANTHERiPTHR11835. PTHR11835. 1 hit.
    PfamiPF00180. Iso_dh. 1 hit.
    [Graphical view]
    SMARTiSM01329. Iso_dh. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR00169. leuB. 1 hit.
    PROSITEiPS00470. IDH_IMDH. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P30125-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSKNYHIAVL PGDGIGPEVM TQALKVLDAV RNRFAMRITT SHYDVGGAAI
    60 70 80 90 100
    DNHGQPLPPA TVEGCEQADA VLFGSVGGPK WEHLPPDQQP ERGALLPLRK
    110 120 130 140 150
    HFKLFSNLRP AKLYQGLEAF CPLRADIAAN GFDILCVREL TGGIYFGQPK
    160 170 180 190 200
    GREGSGQYEK AFDTEVYHRF EIERIARIAF ESARKRRHKV TSIDKANVLQ
    210 220 230 240 250
    SSILWREIVN EIATEYPDVE LAHMYIDNAT MQLIKDPSQF DVLLCSNLFG
    260 270 280 290 300
    DILSDECAMI TGSMGMLPSA SLNEQGFGLY EPAGGSAPDI AGKNIANPIA
    310 320 330 340 350
    QILSLALLLR YSLDADDAAC AIERAINRAL EEGIRTGDLA RGAAAVSTDE
    360
    MGDIIARYVA EGV
    Length:363
    Mass (Da):39,517
    Last modified:January 23, 2007 - v3
    Checksum:i125EC1034FE1A3B5
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti2S → D AA sequence (PubMed:9003442).Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    D17631 Genomic DNA. Translation: BAA04537.1.
    U00096 Genomic DNA. Translation: AAC73184.2.
    AP009048 Genomic DNA. Translation: BAB96642.1.
    PIRiA64729.
    RefSeqiNP_414615.4. NC_000913.3.
    WP_000042353.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73184; AAC73184; b0073.
    BAB96642; BAB96642; BAB96642.
    GeneIDi944798.
    KEGGiecj:JW5807.
    eco:b0073.
    PATRICi32115249. VBIEscCol129921_0076.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    D17631 Genomic DNA. Translation: BAA04537.1.
    U00096 Genomic DNA. Translation: AAC73184.2.
    AP009048 Genomic DNA. Translation: BAB96642.1.
    PIRiA64729.
    RefSeqiNP_414615.4. NC_000913.3.
    WP_000042353.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1CM7X-ray2.06A/B1-363[»]
    ProteinModelPortaliP30125.
    SMRiP30125.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4259727. 8 interactors.
    IntActiP30125. 2 interactors.
    STRINGi511145.b0073.

    Proteomic databases

    EPDiP30125.
    PaxDbiP30125.
    PRIDEiP30125.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC73184; AAC73184; b0073.
    BAB96642; BAB96642; BAB96642.
    GeneIDi944798.
    KEGGiecj:JW5807.
    eco:b0073.
    PATRICi32115249. VBIEscCol129921_0076.

    Organism-specific databases

    EchoBASEiEB1537.
    EcoGeneiEG11577. leuB.

    Phylogenomic databases

    eggNOGiENOG4105C0C. Bacteria.
    COG0473. LUCA.
    HOGENOMiHOG000021112.
    InParanoidiP30125.
    KOiK00052.
    OMAiRRPKQFD.
    PhylomeDBiP30125.

    Enzyme and pathway databases

    UniPathwayiUPA00048; UER00072.
    BioCyciEcoCyc:3-ISOPROPYLMALDEHYDROG-MONOMER.
    ECOL316407:JW5807-MONOMER.
    MetaCyc:3-ISOPROPYLMALDEHYDROG-MONOMER.
    BRENDAi1.1.1.85. 2026.

    Miscellaneous databases

    EvolutionaryTraceiP30125.
    PROiP30125.

    Family and domain databases

    Gene3Di3.40.718.10. 1 hit.
    HAMAPiMF_01033. LeuB_type1. 1 hit.
    InterProiIPR019818. IsoCit/isopropylmalate_DH_CS.
    IPR001804. Isocitrate/isopropylmalate_DH.
    IPR024084. IsoPropMal-DH-like_dom.
    IPR004429. Isopropylmalate_DH.
    [Graphical view]
    PANTHERiPTHR11835. PTHR11835. 1 hit.
    PfamiPF00180. Iso_dh. 1 hit.
    [Graphical view]
    SMARTiSM01329. Iso_dh. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR00169. leuB. 1 hit.
    PROSITEiPS00470. IDH_IMDH. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiLEU3_ECOLI
    AccessioniPrimary (citable) accession number: P30125
    Secondary accession number(s): P78043
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 1, 1993
    Last sequence update: January 23, 2007
    Last modified: November 2, 2016
    This is version 150 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, 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.