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Protein

3-isopropylmalate dehydrogenase

Gene

leuB

Organism
Acidithiobacillus ferrooxidans (Thiobacillus ferrooxidans)
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. Can also use D-malate and L-malate, with lower efficiency.1 Publication

Catalytic activityi

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

Cofactori

Mg2+UniRule annotation, Mn2+UniRule annotationNote: Binds 1 Mg2+ or Mn2+ ion per subunit.UniRule annotation

Enzyme regulationi

The presence of K+ or NH4+ is essential for activity.1 Publication

Kineticsi

  1. KM=26 µM for 3-isopropylmalate1 Publication
  2. KM=0.8 mM for NAD1 Publication
  3. KM=4 mM for D-malate1 Publication
  4. KM=12 mM for L-malate1 Publication

    pH dependencei

    Optimum pH is 9.0.1 Publication

    Temperature dependencei

    Optimum temperature is 60 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 annotation
    Proteins known to be involved in the 4 steps of the subpathway in this organism are:
    1. no protein annotated in this organism
    2. no protein annotated in this organism
    3. 3-isopropylmalate dehydrogenase (leuB)
    4. no protein annotated in this organism
    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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei95 – 951SubstrateUniRule annotation1 Publication
    Binding sitei105 – 1051SubstrateUniRule annotation1 Publication
    Binding sitei133 – 1331SubstrateUniRule annotation1 Publication
    Sitei140 – 1401Important for catalysisUniRule annotation1 Publication
    Sitei190 – 1901Important for catalysisUniRule annotation1 Publication
    Metal bindingi222 – 2221Magnesium1 Publication
    Binding sitei222 – 2221SubstrateUniRule annotation1 Publication
    Metal bindingi246 – 2461Magnesium1 Publication
    Metal bindingi250 – 2501MagnesiumBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi75 – 8814NADUniRule annotationAdd
    BLAST
    Nucleotide bindingi279 – 29113NADUniRule annotationAdd
    BLAST

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

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

    Keywords - Ligandi

    Magnesium, Metal-binding, NAD

    Enzyme and pathway databases

    BRENDAi1.1.1.85. 91.
    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:leuB1 PublicationUniRule annotation
    OrganismiAcidithiobacillus ferrooxidans (Thiobacillus ferrooxidans)
    Taxonomic identifieri920 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAcidithiobacilliaAcidithiobacillalesAcidithiobacillaceaeAcidithiobacillus

    Subcellular locationi

    • Cytoplasm UniRule annotation

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 3583583-isopropylmalate dehydrogenasePRO_0000083777Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer.UniRule annotation2 Publications

    Protein-protein interaction databases

    STRINGi380394.Lferr_1732.

    Structurei

    Secondary structure

    1
    358
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 108Combined sources
    Helixi13 – 3119Combined sources
    Beta strandi36 – 394Combined sources
    Helixi43 – 508Combined sources
    Beta strandi51 – 544Combined sources
    Helixi56 – 649Combined sources
    Beta strandi66 – 727Combined sources
    Helixi76 – 783Combined sources
    Helixi83 – 853Combined sources
    Helixi87 – 9812Combined sources
    Beta strandi102 – 1087Combined sources
    Helixi114 – 1163Combined sources
    Helixi121 – 1244Combined sources
    Beta strandi128 – 1347Combined sources
    Beta strandi136 – 1383Combined sources
    Turni139 – 1413Combined sources
    Beta strandi146 – 1505Combined sources
    Beta strandi153 – 16311Combined sources
    Helixi164 – 17916Combined sources
    Turni180 – 1823Combined sources
    Beta strandi183 – 1897Combined sources
    Turni191 – 1933Combined sources
    Helixi195 – 20713Combined sources
    Helixi208 – 2103Combined sources
    Beta strandi214 – 2207Combined sources
    Helixi221 – 23010Combined sources
    Helixi232 – 2343Combined sources
    Beta strandi236 – 2405Combined sources
    Helixi242 – 25413Combined sources
    Helixi259 – 2613Combined sources
    Beta strandi263 – 2675Combined sources
    Beta strandi272 – 2787Combined sources
    Helixi282 – 2843Combined sources
    Turni285 – 2884Combined sources
    Helixi293 – 30513Combined sources
    Helixi310 – 32516Combined sources
    Helixi331 – 3333Combined sources
    Helixi343 – 35210Combined sources
    Turni353 – 3553Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1A05X-ray2.00A/B1-358[»]
    ProteinModelPortaliQ56268.
    SMRiQ56268. Positions 1-357.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ56268.

    Family & Domainsi

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiENOG4105C0C. Bacteria.
    COG0473. LUCA.

    Family and domain databases

    Gene3Di3.40.718.10. 1 hit.
    HAMAPiMF_01033. LeuB_type1.
    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.

    Q56268-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKKIAIFAGD GIGPEIVAAA RQVLDAVDQA AHLGLRCTEG LVGGAALDAS
    60 70 80 90 100
    DDPLPAASLQ LAMAADAVIL GAVGGPRWDA YPPAKRPEQG LLRLRKGLDL
    110 120 130 140 150
    YANLRPAQIF PQLLDASPLR PELVRDVDIL VVRELTGDIY FGQPRGLEVI
    160 170 180 190 200
    DGKRRGFNTM VYDEDEIRRI AHVAFRAAQG RRKQLCSVDK ANVLETTRLW
    210 220 230 240 250
    REVVTEVARD YPDVRLSHMY VDNAAMQLIR APAQFDVLLT GNMFGDILSD
    260 270 280 290 300
    EASQLTGSIG MLPSASLGEG RAMYEPIHGS APDIAGQDKA NPLATILSVA
    310 320 330 340 350
    MMLRHSLNAE PWAQRVEAAV QRVLDQGLRT ADIAAPGTPV IGTKAMGAAV

    VNALNLKD
    Length:358
    Mass (Da):38,462
    Last modified:November 1, 1997 - v1
    Checksum:i139AFDC3E2CD2060
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    D14585 Genomic DNA. Translation: BAA03437.1.
    PIRiJX0286.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    D14585 Genomic DNA. Translation: BAA03437.1.
    PIRiJX0286.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1A05X-ray2.00A/B1-358[»]
    ProteinModelPortaliQ56268.
    SMRiQ56268. Positions 1-357.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi380394.Lferr_1732.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Phylogenomic databases

    eggNOGiENOG4105C0C. Bacteria.
    COG0473. LUCA.

    Enzyme and pathway databases

    UniPathwayiUPA00048; UER00072.
    BRENDAi1.1.1.85. 91.

    Miscellaneous databases

    EvolutionaryTraceiQ56268.

    Family and domain databases

    Gene3Di3.40.718.10. 1 hit.
    HAMAPiMF_01033. LeuB_type1.
    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...

    Publicationsi

    1. "3-isopropylmalate dehydrogenase from chemolithoautotroph Thiobacillus ferrooxidans: DNA sequence, enzyme purification, and characterization."
      Kawaguchi H., Inagaki K., Kuwata Y., Tanaka H., Tano T.
      J. Biochem. 114:370-377(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
      Strain: AP19-3.
    2. "Structure of 3-isopropylmalate dehydrogenase in complex with 3-isopropylmalate at 2.0-A resolution: the role of Glu88 in the unique substrate-recognition mechanism."
      Imada K., Inagaki K., Matsunami H., Kawaguchi H., Tanaka H., Tanaka N., Namba K.
      Structure 6:971-982(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND MAGNESIUM IONS, SUBUNIT.
      Strain: AP19-3.

    Entry informationi

    Entry nameiLEU3_ACIFR
    AccessioniPrimary (citable) accession number: Q56268
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: November 1, 1997
    Last modified: May 11, 2016
    This is version 105 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

    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.