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Protein

3-isopropylmalate dehydrogenase

Gene

leuB

Organism
Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)
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+1 Publication, Mn2+1 PublicationNote: Binds 1 Mg2+ or Mn2+ ion per subunit.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.
Proteins known to be involved in the 4 steps of the subpathway in this organism are:
  1. Probable 2-isopropylmalate synthase (leuA)
  2. 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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei86 – 861SubstrateBy similarity
Binding sitei96 – 961SubstrateBy similarity
Binding sitei117 – 1171SubstrateBy similarity
Sitei124 – 1241Important for catalysisBy similarity
Sitei170 – 1701Important for catalysisBy similarity
Metal bindingi201 – 2011Magnesium or manganeseBy similarity
Binding sitei201 – 2011SubstrateBy similarity
Metal bindingi225 – 2251Magnesium or manganeseBy similarity
Metal bindingi229 – 2291Magnesium or manganeseBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi258 – 27013NADBy 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

BioCyciSTOK273063:GJC7-504-MONOMER.
BRENDAi1.1.1.85. 6166.
UniPathwayiUPA00048; UER00072.

Names & Taxonomyi

Protein namesi
Recommended name:
3-isopropylmalate dehydrogenase (EC:1.1.1.85)
Short name:
3-IPM-DH
Short name:
IMDH
Alternative name(s):
Beta-IPM dehydrogenase
Gene namesi
Name:leuB
Ordered Locus Names:STK_04330
OrganismiSulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)
Taxonomic identifieri273063 [NCBI]
Taxonomic lineageiArchaeaCrenarchaeotaThermoproteiSulfolobalesSulfolobaceaeSulfolobus
Proteomesi
  • UP000001015 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved1 Publication
Chaini2 – 3373363-isopropylmalate dehydrogenasePRO_0000083812Add
BLAST

Interactioni

Subunit structurei

Homotetramer.2 Publications

Protein-protein interaction databases

STRINGi273063.ST0433.

Structurei

Secondary structure

1
337
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 86Combined sources
Helixi14 – 3118Combined sources
Beta strandi36 – 416Combined sources
Helixi45 – 506Combined sources
Beta strandi51 – 555Combined sources
Helixi57 – 648Combined sources
Beta strandi67 – 715Combined sources
Helixi78 – 8710Combined sources
Turni88 – 903Combined sources
Beta strandi93 – 997Combined sources
Turni102 – 1043Combined sources
Beta strandi112 – 1187Combined sources
Beta strandi120 – 1223Combined sources
Turni123 – 1253Combined sources
Beta strandi128 – 1325Combined sources
Beta strandi135 – 1439Combined sources
Helixi144 – 15916Combined sources
Turni160 – 1623Combined sources
Beta strandi163 – 1697Combined sources
Turni171 – 1733Combined sources
Helixi177 – 18913Combined sources
Turni190 – 1923Combined sources
Beta strandi193 – 1997Combined sources
Helixi200 – 20910Combined sources
Helixi211 – 2133Combined sources
Beta strandi215 – 2195Combined sources
Helixi221 – 23515Combined sources
Helixi238 – 2403Combined sources
Beta strandi242 – 2465Combined sources
Beta strandi251 – 2577Combined sources
Turni261 – 2655Combined sources
Helixi272 – 28716Combined sources
Helixi293 – 31119Combined sources
Helixi317 – 3193Combined sources
Helixi325 – 33410Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WPWX-ray2.80A/B2-337[»]
ProteinModelPortaliP50455.
SMRiP50455. Positions 2-337.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP50455.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiarCOG01163. Archaea.
COG0473. LUCA.
HOGENOMiHOG000021113.
KOiK00052.
OMAiCREIASK.

Family and domain databases

Gene3Di3.40.718.10. 1 hit.
InterProiIPR019818. IsoCit/isopropylmalate_DH_CS.
IPR001804. Isocitrate/isopropylmalate_DH.
IPR024084. IsoPropMal-DH-like_dom.
IPR011828. LEU3_arc.
[Graphical view]
PANTHERiPTHR11835. PTHR11835. 1 hit.
PfamiPF00180. Iso_dh. 1 hit.
[Graphical view]
SMARTiSM01329. Iso_dh. 1 hit.
[Graphical view]
TIGRFAMsiTIGR02088. LEU3_arch. 1 hit.
PROSITEiPS00470. IDH_IMDH. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P50455-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGFTVALIQG DGIGPEIVSK SKRILAKINE LYSLPIEYIE VEAGDRALAR
60 70 80 90 100
YGEALPKDSL KIIDKADIIL KGPVGESAAD VVVKLRQIYD MYANIRPAKS
110 120 130 140 150
IPGIDTKYGN VDILIVRENT EDLYKGFEHI VSDGVAVGMK IITRFASERI
160 170 180 190 200
AKVGLNFALR RRKKVTCVHK ANVMRITDGL FAEACRSVLK GKVEYSEMYV
210 220 230 240 250
DAAAANLVRN PQMFDVIVTE NVYGDILSDE ASQIAGSLGI APSANIGDKK
260 270 280 290 300
ALFEPVHGAA FDIAGKNIGN PTAFLLSVSM MYERMYELSN DDRYIKASRA
310 320 330
LENAIYLVYK ERKALTPDVG GNATTDDLIN EIYNKLG
Length:337
Mass (Da):36,964
Last modified:January 23, 2007 - v3
Checksum:i1B44CB9A0CD70313
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D86857 Genomic DNA. Translation: BAA13178.1.
BA000023 Genomic DNA. Translation: BAK54281.1.
RefSeqiWP_010978405.1. NC_003106.2.

Genome annotation databases

EnsemblBacteriaiBAK54281; BAK54281; STK_04330.
GeneIDi1458369.
KEGGisto:STK_04330.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D86857 Genomic DNA. Translation: BAA13178.1.
BA000023 Genomic DNA. Translation: BAK54281.1.
RefSeqiWP_010978405.1. NC_003106.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WPWX-ray2.80A/B2-337[»]
ProteinModelPortaliP50455.
SMRiP50455. Positions 2-337.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi273063.ST0433.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAK54281; BAK54281; STK_04330.
GeneIDi1458369.
KEGGisto:STK_04330.

Phylogenomic databases

eggNOGiarCOG01163. Archaea.
COG0473. LUCA.
HOGENOMiHOG000021113.
KOiK00052.
OMAiCREIASK.

Enzyme and pathway databases

UniPathwayiUPA00048; UER00072.
BioCyciSTOK273063:GJC7-504-MONOMER.
BRENDAi1.1.1.85. 6166.

Miscellaneous databases

EvolutionaryTraceiP50455.

Family and domain databases

Gene3Di3.40.718.10. 1 hit.
InterProiIPR019818. IsoCit/isopropylmalate_DH_CS.
IPR001804. Isocitrate/isopropylmalate_DH.
IPR024084. IsoPropMal-DH-like_dom.
IPR011828. LEU3_arc.
[Graphical view]
PANTHERiPTHR11835. PTHR11835. 1 hit.
PfamiPF00180. Iso_dh. 1 hit.
[Graphical view]
SMARTiSM01329. Iso_dh. 1 hit.
[Graphical view]
TIGRFAMsiTIGR02088. LEU3_arch. 1 hit.
PROSITEiPS00470. IDH_IMDH. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Molecular and phylogenetic characterization of isopropylmalate dehydrogenase of a thermoacidophilic archaeon, Sulfolobus sp. strain 7."
    Suzuki T., Inoki Y., Yamagishi A., Iwasaki T., Wakagi T., Oshima T.
    J. Bacteriol. 179:1174-1179(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7.
  3. "Purification and characterization of 3-isopropylmalate dehydrogenase from a thermoacidophilic archaebacterium Sulfolobus sp. strain 7."
    Yoda E., Anraku Y., Kirino H., Wakagi T., Oshima T.
    FEMS Microbiol. Lett. 131:243-247(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-16, SUBUNIT, COFACTOR, CHARACTERIZATION.
    Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7.
  4. "Crystal structure of IPMDH from Sulfolobus tokodaii."
    Hirose R., Sakurai M., Suzuki T., Moriyama H., Sato T., Yamagishi A., Oshima T., Tanaka N.
    Submitted (OCT-2004) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS), SUBUNIT.

Entry informationi

Entry nameiLEU3_SULTO
AccessioniPrimary (citable) accession number: P50455
Secondary accession number(s): F9VMY4, O05169
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: January 23, 2007
Last modified: May 11, 2016
This is version 118 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, 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.