Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

3-isopropylmalate dehydrogenase

Gene

leuB

Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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.

Catalytic activityi

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

Cofactori

Mg2+, Mn2+Note: Binds 1 Mg2+ or Mn2+ ion per subunit.

Kineticsi

  1. KM=1.26 µM for 3-isopropylmalate (at pH 8 and 60 degrees Celsius)
  2. KM=40.9 µM for NAD

    Pathwayi: L-leucine biosynthesis

    This protein is involved in step 3 of the subpathway that synthesizes L-leucine from 3-methyl-2-oxobutanoate.
    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 large subunit (leuC), 3-isopropylmalate dehydratase small subunit (leuD), 3-isopropylmalate dehydratase large subunit (leuC), 3-isopropylmalate dehydratase small subunit (leuD)
    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)DescriptionActionsGraphical viewLength
    Binding sitei94SubstrateBy similarity1
    Binding sitei104SubstrateBy similarity1
    Binding sitei132SubstrateBy similarity1
    Sitei139Important for catalysis1
    Sitei185Important for catalysisBy similarity1
    Metal bindingi217Magnesium or manganeseBy similarity1
    Binding sitei217SubstrateBy similarity1
    Metal bindingi241Magnesium or manganeseBy similarity1
    Metal bindingi245Magnesium or manganeseBy similarity1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi74 – 87NAD1 PublicationAdd BLAST14
    Nucleotide bindingi274 – 286NAD1 PublicationAdd 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, Manganese, Metal-binding, NAD

    Enzyme and pathway databases

    BRENDAi1.1.1.85. 2305.
    UniPathwayiUPA00048; UER00072.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    3-isopropylmalate dehydrogenase (EC:1.1.1.85)
    Alternative name(s):
    3-IPM-DH
    Beta-IPM dehydrogenase
    Short name:
    IMDH
    Gene namesi
    Name:leuB
    Ordered Locus Names:TTHA1230
    OrganismiThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
    Taxonomic identifieri300852 [NCBI]
    Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
    Proteomesi
    • UP000000532 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi139Y → F: Large decrease in activity and a small decrease in substrate affinity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000837751 – 3453-isopropylmalate dehydrogenaseAdd BLAST345

    Interactioni

    Subunit structurei

    Homodimer.4 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    itself2EBI-9699580,EBI-9699580

    Protein-protein interaction databases

    STRINGi300852.TTHA1230.

    Structurei

    Secondary structure

    1345
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi1 – 6Combined sources6
    Helixi12 – 30Combined sources19
    Beta strandi34 – 38Combined sources5
    Helixi43 – 49Combined sources7
    Beta strandi50 – 53Combined sources4
    Helixi55 – 63Combined sources9
    Beta strandi64 – 69Combined sources6
    Helixi75 – 77Combined sources3
    Beta strandi78 – 80Combined sources3
    Helixi82 – 84Combined sources3
    Helixi86 – 96Combined sources11
    Beta strandi99 – 107Combined sources9
    Helixi113 – 115Combined sources3
    Beta strandi116 – 118Combined sources3
    Helixi120 – 123Combined sources4
    Beta strandi127 – 133Combined sources7
    Beta strandi135 – 137Combined sources3
    Turni138 – 140Combined sources3
    Beta strandi144 – 146Combined sources3
    Beta strandi148 – 158Combined sources11
    Helixi159 – 174Combined sources16
    Turni175 – 177Combined sources3
    Beta strandi178 – 184Combined sources7
    Turni186 – 188Combined sources3
    Helixi190 – 203Combined sources14
    Beta strandi209 – 215Combined sources7
    Helixi216 – 225Combined sources10
    Helixi227 – 229Combined sources3
    Beta strandi231 – 235Combined sources5
    Helixi237 – 248Combined sources12
    Turni249 – 251Combined sources3
    Helixi254 – 256Combined sources3
    Beta strandi258 – 265Combined sources8
    Beta strandi268 – 273Combined sources6
    Helixi277 – 279Combined sources3
    Turni280 – 282Combined sources3
    Helixi288 – 300Combined sources13
    Helixi305 – 321Combined sources17
    Helixi325 – 327Combined sources3
    Helixi333 – 345Combined sources13

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1DPZX-ray2.80A/B1-345[»]
    1DR0X-ray2.20A/B1-345[»]
    1DR8X-ray2.70A/B1-344[»]
    1G2UX-ray2.10A1-345[»]
    1GC8X-ray2.50A/B1-345[»]
    1GC9X-ray2.30A1-345[»]
    1HEXX-ray2.50A1-345[»]
    1IDMX-ray2.20A1-345[»]
    1IPDX-ray2.20A1-345[»]
    1OSIX-ray3.00A/B/C/D1-345[»]
    1OSJX-ray2.35A/B1-345[»]
    1XAAX-ray2.10A1-345[»]
    1XABX-ray2.10A1-345[»]
    1XACX-ray2.10A1-345[»]
    1XADX-ray2.10A1-345[»]
    2Y3ZX-ray1.83A1-345[»]
    2Y40X-ray2.50A/B1-345[»]
    2Y41X-ray2.20A/B1-345[»]
    2Y42X-ray2.50A/B/C/D1-345[»]
    2ZTWX-ray2.79A1-345[»]
    4F7IX-ray2.00A/B/C/D1-345[»]
    4WUOX-ray2.05A/B1-345[»]
    ProteinModelPortaliQ5SIY4.
    SMRiQ5SIY4.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ5SIY4.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105C0C. Bacteria.
    COG0473. LUCA.
    HOGENOMiHOG000021112.
    KOiK00052.
    OMAiHCGPEVV.
    PhylomeDBiQ5SIY4.

    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.

    Q5SIY4-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKVAVLPGDG IGPEVTEAAL KVLRALDEAE GLGLAYEVFP FGGAAIDAFG
    60 70 80 90 100
    EPFPEPTRKG VEEAEAVLLG SVGGPKWDGL PRKIRPETGL LSLRKSQDLF
    110 120 130 140 150
    ANLRPAKVFP GLERLSPLKE EIARGVDVLI VRELTGGIYF GEPRGMSEAE
    160 170 180 190 200
    AWNTERYSKP EVERVARVAF EAARKRRKHV VSVDKANVLE VGEFWRKTVE
    210 220 230 240 250
    EVGRGYPDVA LEHQYVDAMA MHLVRSPARF DVVVTGNIFG DILSDLASVL
    260 270 280 290 300
    PGSLGLLPSA SLGRGTPVFE PVHGSAPDIA GKGIANPTAA ILSAAMMLEH
    310 320 330 340
    AFGLVELARK VEDAVAKALL ETPPPDLGGS AGTEAFTATV LRHLA
    Length:345
    Mass (Da):36,780
    Last modified:December 21, 2004 - v1
    Checksum:i3EFF8736312E2785
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti85R → S in AAA16706 (PubMed:6321488).Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    K01444 Genomic DNA. Translation: AAA16706.1.
    AP008226 Genomic DNA. Translation: BAD71053.1.
    PIRiS41223. DETWIT.
    RefSeqiWP_011228534.1. NC_006461.1.
    YP_144496.1. NC_006461.1.

    Genome annotation databases

    EnsemblBacteriaiBAD71053; BAD71053; BAD71053.
    GeneIDi3168996.
    KEGGittj:TTHA1230.
    PATRICi23957423. VBITheThe93045_1209.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    K01444 Genomic DNA. Translation: AAA16706.1.
    AP008226 Genomic DNA. Translation: BAD71053.1.
    PIRiS41223. DETWIT.
    RefSeqiWP_011228534.1. NC_006461.1.
    YP_144496.1. NC_006461.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1DPZX-ray2.80A/B1-345[»]
    1DR0X-ray2.20A/B1-345[»]
    1DR8X-ray2.70A/B1-344[»]
    1G2UX-ray2.10A1-345[»]
    1GC8X-ray2.50A/B1-345[»]
    1GC9X-ray2.30A1-345[»]
    1HEXX-ray2.50A1-345[»]
    1IDMX-ray2.20A1-345[»]
    1IPDX-ray2.20A1-345[»]
    1OSIX-ray3.00A/B/C/D1-345[»]
    1OSJX-ray2.35A/B1-345[»]
    1XAAX-ray2.10A1-345[»]
    1XABX-ray2.10A1-345[»]
    1XACX-ray2.10A1-345[»]
    1XADX-ray2.10A1-345[»]
    2Y3ZX-ray1.83A1-345[»]
    2Y40X-ray2.50A/B1-345[»]
    2Y41X-ray2.20A/B1-345[»]
    2Y42X-ray2.50A/B/C/D1-345[»]
    2ZTWX-ray2.79A1-345[»]
    4F7IX-ray2.00A/B/C/D1-345[»]
    4WUOX-ray2.05A/B1-345[»]
    ProteinModelPortaliQ5SIY4.
    SMRiQ5SIY4.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi300852.TTHA1230.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiBAD71053; BAD71053; BAD71053.
    GeneIDi3168996.
    KEGGittj:TTHA1230.
    PATRICi23957423. VBITheThe93045_1209.

    Phylogenomic databases

    eggNOGiENOG4105C0C. Bacteria.
    COG0473. LUCA.
    HOGENOMiHOG000021112.
    KOiK00052.
    OMAiHCGPEVV.
    PhylomeDBiQ5SIY4.

    Enzyme and pathway databases

    UniPathwayiUPA00048; UER00072.
    BRENDAi1.1.1.85. 2305.

    Miscellaneous databases

    EvolutionaryTraceiQ5SIY4.

    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_THET8
    AccessioniPrimary (citable) accession number: Q5SIY4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 24, 2005
    Last sequence update: December 21, 2004
    Last modified: November 2, 2016
    This is version 99 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, Complete proteome, Reference proteome

    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.