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Protein

3-isopropylmalate dehydrogenase

Gene

leuB

Organism
Bacillus coagulans
Status
Reviewed-Annotation score: Annotation score: 4 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.

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-isopropylmalate synthase (B4099_2192), 2-isopropylmalate synthase (HMPREF3213_02514), 2-isopropylmalate synthase (B4098_1922)
  2. 3-isopropylmalate dehydratase (B4098_1925), 3-isopropylmalate dehydratase small subunit (leuD), 3-isopropylmalate dehydratase large subunit (HMPREF3213_02512), 3-isopropylmalate dehydratase large subunit (leuC), 3-isopropylmalate dehydratase large subunit (B4099_2195), 3-isopropylmalate dehydratase large subunit (B4100_2213), 3-isopropylmalate dehydratase large subunit (B4098_1924), 3-isopropylmalate dehydratase (B4099_2196)
  3. 3-isopropylmalate dehydrogenase (B4100_2212), 3-isopropylmalate dehydrogenase (B4098_1923), 3-isopropylmalate dehydrogenase (leuB), 3-isopropylmalate dehydrogenase (B4099_2193), 3-isopropylmalate dehydrogenase (leuB)
  4. Branched-chain-amino-acid aminotransferase (B4099_1554), Branched-chain-amino-acid aminotransferase (SB48_HM08orf00177), Branched-chain-amino-acid aminotransferase (HMPREF3213_01889), Branched-chain-amino-acid aminotransferase (B4098_1286), Branched-chain-amino-acid aminotransferase (B4100_1472)
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 sitei96 – 961SubstrateBy similarity
Binding sitei106 – 1061SubstrateBy similarity
Binding sitei134 – 1341SubstrateBy similarity
Sitei141 – 1411Important for catalysisBy similarity
Sitei190 – 1901Important for catalysisBy similarity
Metal bindingi222 – 2221Magnesium or manganeseBy similarity
Binding sitei222 – 2221SubstrateBy similarity
Metal bindingi246 – 2461Magnesium or manganeseBy similarity
Metal bindingi250 – 2501Magnesium or manganeseBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi76 – 8914NADBy similarityAdd
BLAST
Nucleotide bindingi280 – 29213NADBy similarityAdd
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, Manganese, Metal-binding, NAD

Enzyme and pathway databases

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
OrganismiBacillus coagulans
Taxonomic identifieri1398 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 3663663-isopropylmalate dehydrogenasePRO_0000083638Add
BLAST

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi345219.Bcoa_2059.

Structurei

Secondary structure

1
366
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 119Combined sources
Helixi14 – 2916Combined sources
Turni30 – 334Combined sources
Beta strandi36 – 405Combined sources
Helixi45 – 517Combined sources
Beta strandi52 – 554Combined sources
Helixi57 – 648Combined sources
Beta strandi66 – 738Combined sources
Helixi77 – 793Combined sources
Beta strandi80 – 823Combined sources
Helixi84 – 863Combined sources
Helixi88 – 9912Combined sources
Beta strandi103 – 1097Combined sources
Helixi112 – 1143Combined sources
Turni115 – 1173Combined sources
Beta strandi118 – 1203Combined sources
Helixi122 – 1254Combined sources
Beta strandi129 – 1357Combined sources
Beta strandi137 – 1393Combined sources
Turni140 – 1423Combined sources
Beta strandi146 – 1516Combined sources
Beta strandi155 – 1639Combined sources
Helixi164 – 18017Combined sources
Beta strandi183 – 1897Combined sources
Turni191 – 1933Combined sources
Helixi195 – 20814Combined sources
Beta strandi214 – 2207Combined sources
Helixi221 – 23010Combined sources
Helixi232 – 2343Combined sources
Beta strandi236 – 2405Combined sources
Helixi242 – 25211Combined sources
Turni253 – 2564Combined sources
Helixi259 – 2613Combined sources
Beta strandi263 – 2675Combined sources
Beta strandi269 – 2713Combined sources
Beta strandi273 – 2797Combined sources
Helixi283 – 2853Combined sources
Turni286 – 2894Combined sources
Helixi294 – 30815Combined sources
Helixi311 – 32616Combined sources
Beta strandi329 – 3346Combined sources
Helixi344 – 35411Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1V53X-ray2.85A/B1-366[»]
1V5BX-ray2.95A/B/C/D/E/F/G/H1-366[»]
2AYQX-ray3.00A/B1-366[»]
ProteinModelPortaliP12010.
SMRiP12010. Positions 1-357.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP12010.

Family & Domainsi

Sequence similaritiesi

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.

P12010-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKMKLAVLPG DGIGPEVMDA AIRVLKTVLD NDGHEAVFEN ALIGGAAIDE
60 70 80 90 100
AGTPLPEETL DICRRSDAIL LGAVGGPKWD HNPASLRPEK GLLGLRKEMG
110 120 130 140 150
LFANLRPVKA YATLLNASPL KRERVENVDL VIVRELTGGL YFGRPSERRG
160 170 180 190 200
PGENEVVDTL AYTREEIERI IEKAFQLAQI RRKKLASVDK ANVLESSRMW
210 220 230 240 250
REIAEETAKK YPDVELSHML VDSTSMQLIA NPGQFDVIVT ENMFGDILSD
260 270 280 290 300
EASVITGSLG MLPSASLRSD RFGMYEPVHG SAPDIAGQGK ANPLGTVLSA
310 320 330 340 350
ALMLRYSFGL EKEAAAIEKA VDDVLQDGYC TGDLQVANGK VVSTIELTDR
360
LIEKLNNSAA RPRIFQ
Length:366
Mass (Da):39,809
Last modified:October 1, 1989 - v1
Checksum:i05958B786718408E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M33099 Genomic DNA. Translation: AAA22554.1. Sequence problems.
PIRiA24537. DEBSIC.
RefSeqiWP_029141661.1. NZ_LQYJ01000066.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M33099 Genomic DNA. Translation: AAA22554.1. Sequence problems.
PIRiA24537. DEBSIC.
RefSeqiWP_029141661.1. NZ_LQYJ01000066.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1V53X-ray2.85A/B1-366[»]
1V5BX-ray2.95A/B/C/D/E/F/G/H1-366[»]
2AYQX-ray3.00A/B1-366[»]
ProteinModelPortaliP12010.
SMRiP12010. Positions 1-357.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi345219.Bcoa_2059.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4105C0C. Bacteria.
COG0473. LUCA.

Enzyme and pathway databases

UniPathwayiUPA00048; UER00072.

Miscellaneous databases

EvolutionaryTraceiP12010.

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. "DNA and amino-acid sequences of 3-isopropylmalate dehydrogenase of Bacillus coagulans. Comparison with the enzymes of Saccharomyces cerevisiae and Thermus thermophilus."
    Sekiguchi T., Ortega-Cesena J., Nosoh Y., Ohashi S., Tsuda K., Kanaya S.
    Biochim. Biophys. Acta 867:36-44(1986)
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Crystal structure of 3-isopropylmalate dehydrogenase from the moderate facultative thermophile, Bacillus coagulans: two strategies for thermostabilization of protein structures."
    Tsuchiya D., Sekiguchi T., Takenaka A.
    J. Biochem. 122:1092-1104(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS), SUBUNIT.

Entry informationi

Entry nameiLEU3_BACCO
AccessioniPrimary (citable) accession number: P12010
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1989
Last sequence update: October 1, 1989
Last modified: July 6, 2016
This is version 109 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.