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Protein

3-isopropylmalate dehydrogenase

Gene

leuB

Organism
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
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 (leuA)
  2. 3-isopropylmalate dehydratase small subunit (leuD), 3-isopropylmalate dehydratase large subunit 2 (leuC2), 3-isopropylmalate dehydratase small subunit 2 (leuD2), 3-isopropylmalate dehydratase large subunit (leuC), 3-isopropylmalate dehydratase large subunit 1 (leuC1), 3-isopropylmalate dehydratase small subunit 1 (leuD1), 3-isopropylmalate dehydratase large subunit (leuC), 3-isopropylmalate dehydratase small subunit (leuD)
  3. 3-isopropylmalate dehydrogenase (leuB), 3-isopropylmalate dehydrogenase (leuB)
  4. Probable 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 sitei95SubstrateBy similarity1
Binding sitei105SubstrateBy similarity1
Binding sitei134SubstrateBy similarity1
Sitei141Important for catalysisBy similarity1
Sitei187Important for catalysisBy similarity1
Metal bindingi219Magnesium or manganeseBy similarity1
Binding sitei219SubstrateBy similarity1
Metal bindingi243Magnesium or manganeseBy similarity1
Metal bindingi247Magnesium or manganeseBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi74 – 87NADBy similarityAdd BLAST14
Nucleotide bindingi275 – 287NADBy similarityAdd 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

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:TM_0556
OrganismiThermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Taxonomic identifieri243274 [NCBI]
Taxonomic lineageiBacteriaThermotogaeThermotogalesThermotogaceaeThermotoga
Proteomesi
  • UP000008183 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000837711 – 3543-isopropylmalate dehydrogenaseAdd BLAST354

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi243274.TM0556.

Structurei

Secondary structure

1354
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi1 – 9Combined sources9
Helixi11 – 30Combined sources20
Beta strandi33 – 38Combined sources6
Helixi43 – 49Combined sources7
Beta strandi50 – 53Combined sources4
Helixi55 – 63Combined sources9
Beta strandi64 – 71Combined sources8
Helixi75 – 77Combined sources3
Helixi86 – 89Combined sources4
Helixi91 – 97Combined sources7
Beta strandi102 – 108Combined sources7
Helixi111 – 116Combined sources6
Beta strandi117 – 119Combined sources3
Helixi121 – 124Combined sources4
Beta strandi129 – 135Combined sources7
Helixi139 – 141Combined sources3
Beta strandi143 – 148Combined sources6
Beta strandi153 – 156Combined sources4
Helixi161 – 176Combined sources16
Turni177 – 179Combined sources3
Beta strandi180 – 186Combined sources7
Turni188 – 190Combined sources3
Helixi192 – 205Combined sources14
Beta strandi211 – 217Combined sources7
Helixi218 – 227Combined sources10
Helixi229 – 231Combined sources3
Beta strandi233 – 237Combined sources5
Helixi239 – 249Combined sources11
Beta strandi252 – 254Combined sources3
Helixi256 – 258Combined sources3
Beta strandi260 – 274Combined sources15
Turni278 – 284Combined sources7
Helixi289 – 303Combined sources15
Helixi306 – 321Combined sources16
Helixi327 – 329Combined sources3
Helixi333 – 335Combined sources3
Helixi339 – 353Combined sources15

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1VLCX-ray1.90A1-354[»]
ProteinModelPortaliQ9WZ26.
SMRiQ9WZ26.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9WZ26.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105C0C. Bacteria.
COG0473. LUCA.
InParanoidiQ9WZ26.
KOiK00052.
OMAiRRPKQFD.

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.

Q9WZ26-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKIAVLPGDG IGPEVVREAL KVLEVVEKKT GKTFEKVFGH IGGDAIDRFG
60 70 80 90 100
EPLPEETKKI CLEADAIFLG SVGGPKWDDL PPEKRPEIGG LLALRKMLNL
110 120 130 140 150
YANIRPIKVY RSLVHVSPLK EKVIGSGVDL VTVRELSYGV YYGQPRGLDE
160 170 180 190 200
EKGFDTMIYD RKTVERIART AFEIAKNRRK KVTSVDKANV LYSSMLWRKV
210 220 230 240 250
VNEVAREYPD VELTHIYVDN AAMQLILKPS QFDVILTTNM FGDILSDESA
260 270 280 290 300
ALPGSLGLLP SASFGDKNLY EPAGGSAPDI AGKNIANPIA QILSLAMMLE
310 320 330 340 350
HSFGMVEEAR KIERAVELVI EEGYRTRDIA EDPEKAVSTS QMGDLICKKL

EEIW
Length:354
Mass (Da):39,190
Last modified:November 1, 1999 - v1
Checksum:i2C93ACBF888A0D38
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000512 Genomic DNA. Translation: AAD35641.1.
PIRiB72363.
RefSeqiNP_228366.1. NC_000853.1.
WP_004081326.1. NZ_CP011107.1.

Genome annotation databases

EnsemblBacteriaiAAD35641; AAD35641; TM_0556.
GeneIDi897614.
KEGGitma:TM0556.
PATRICi23936019. VBITheMar51294_0564.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000512 Genomic DNA. Translation: AAD35641.1.
PIRiB72363.
RefSeqiNP_228366.1. NC_000853.1.
WP_004081326.1. NZ_CP011107.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1VLCX-ray1.90A1-354[»]
ProteinModelPortaliQ9WZ26.
SMRiQ9WZ26.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243274.TM0556.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAD35641; AAD35641; TM_0556.
GeneIDi897614.
KEGGitma:TM0556.
PATRICi23936019. VBITheMar51294_0564.

Phylogenomic databases

eggNOGiENOG4105C0C. Bacteria.
COG0473. LUCA.
InParanoidiQ9WZ26.
KOiK00052.
OMAiRRPKQFD.

Enzyme and pathway databases

UniPathwayiUPA00048; UER00072.

Miscellaneous databases

EvolutionaryTraceiQ9WZ26.

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_THEMA
AccessioniPrimary (citable) accession number: Q9WZ26
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: November 1, 1999
Last modified: November 30, 2016
This is version 127 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.