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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. 2-isopropylmalate synthase (leuA), 2-isopropylmalate synthase (leuA)
    2. 3-isopropylmalate dehydratase large subunit (leuC), 3-isopropylmalate dehydratase small subunit (leuD)
    3. 3-isopropylmalate dehydrogenase (leuB), 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)DescriptionActionsGraphical viewLength
    Binding sitei95SubstrateUniRule annotation1 Publication1
    Binding sitei105SubstrateUniRule annotation1 Publication1
    Binding sitei133SubstrateUniRule annotation1 Publication1
    Sitei140Important for catalysisUniRule annotation1 Publication1
    Sitei190Important for catalysisUniRule annotation1 Publication1
    Metal bindingi222Magnesium1 Publication1
    Binding sitei222SubstrateUniRule annotation1 Publication1
    Metal bindingi246Magnesium1 Publication1
    Metal bindingi250MagnesiumBy similarity1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi75 – 88NADUniRule annotationAdd BLAST14
    Nucleotide bindingi279 – 291NADUniRule annotationAdd BLAST13

    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)DescriptionActionsGraphical viewLength
    ChainiPRO_00000837771 – 3583-isopropylmalate dehydrogenaseAdd BLAST358

    Interactioni

    Subunit structurei

    Homodimer.UniRule annotation2 Publications

    Protein-protein interaction databases

    STRINGi380394.Lferr_1732.

    Structurei

    Secondary structure

    1358
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi3 – 10Combined sources8
    Helixi13 – 31Combined sources19
    Beta strandi36 – 39Combined sources4
    Helixi43 – 50Combined sources8
    Beta strandi51 – 54Combined sources4
    Helixi56 – 64Combined sources9
    Beta strandi66 – 72Combined sources7
    Helixi76 – 78Combined sources3
    Helixi83 – 85Combined sources3
    Helixi87 – 98Combined sources12
    Beta strandi102 – 108Combined sources7
    Helixi114 – 116Combined sources3
    Helixi121 – 124Combined sources4
    Beta strandi128 – 134Combined sources7
    Beta strandi136 – 138Combined sources3
    Turni139 – 141Combined sources3
    Beta strandi146 – 150Combined sources5
    Beta strandi153 – 163Combined sources11
    Helixi164 – 179Combined sources16
    Turni180 – 182Combined sources3
    Beta strandi183 – 189Combined sources7
    Turni191 – 193Combined sources3
    Helixi195 – 207Combined sources13
    Helixi208 – 210Combined sources3
    Beta strandi214 – 220Combined sources7
    Helixi221 – 230Combined sources10
    Helixi232 – 234Combined sources3
    Beta strandi236 – 240Combined sources5
    Helixi242 – 254Combined sources13
    Helixi259 – 261Combined sources3
    Beta strandi263 – 267Combined sources5
    Beta strandi272 – 278Combined sources7
    Helixi282 – 284Combined sources3
    Turni285 – 288Combined sources4
    Helixi293 – 305Combined sources13
    Helixi310 – 325Combined sources16
    Helixi331 – 333Combined sources3
    Helixi343 – 352Combined sources10
    Turni353 – 355Combined sources3

    3D structure databases

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

    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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1A05X-ray2.00A/B1-358[»]
    ProteinModelPortaliQ56268.
    SMRiQ56268.
    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. 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_ACIFR
    AccessioniPrimary (citable) accession number: Q56268
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: November 1, 1997
    Last modified: November 2, 2016
    This is version 107 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.