3-isopropylmalate/3-methylmalate dehydrogenase - Methanocaldococcus jannaschii

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Reviewed, UniProtKB/Swiss-Prot Q58130 (LEU3_METJA)

Last modified November 3, 2009. Version 63. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    3-isopropylmalate/3-methylmalate dehydrogenase
    EC=1.1.1.85
    EC=1.1.1.n5
Alternative name(s):
    3-isopropylmalate dehydrogenase
      Short name=3-IPM-DH
      Short name=IPMDH
      Short name=IMDH
    Beta-IPM dehydrogenase
    D-malate dehydrogenase [decarboxylating]
    EC=1.1.1.83

Gene names

Name:	leuB
Ordered Locus Names:	MJ0720

Organism

Methanocaldococcus jannaschii (Methanococcus jannaschii) [Complete proteome] [HAMAP]

Taxonomic identifier

2190 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Methanococci › Methanococcales › Methanocaldococcaceae › Methanocaldococcus

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Protein attributes

Sequence length	333 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Catalyzes the oxidation of 3-carboxy-2-hydroxy-4-methylpentanoate (3-isopropylmalate) to 3-carboxy-4-methyl-2-oxopentanoate, which decarboxylates to 4-methyl-2-oxopentanoate (2-oxoisocaproate). Also catalyzes the oxidative decarboxylation of 3-methylmalate to 2-oxobutyrate, and that of D-malate to pyruvate. Can not use NADP⁺ instead of NAD⁺. Can not catalyze the oxidation of L-malate, L-tartrate, D-tartrate, DL-isocitrate, or DL-lactate. Ref.3
Catalytic activity	(2R,3S)-3-isopropylmalate + NAD⁺ = 4-methyl-2-oxopentanoate + CO₂ + NADH. Ref.3 (2R,3S)-3-methylmalate + NAD⁺ = 2-oxobutanoate + CO₂ + NADH. Ref.3 (R)-malate + NAD⁺ = pyruvate + CO₂ + NADH. Ref.3
Cofactor	Binds 1 magnesium or manganese ion per subunit By similarity.
Pathway	Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 3/4. Amino-acid biosynthesis; L-isoleucine biosynthesis; 2-oxobutanoate from pyruvate: step 3/3.
Subunit structure	Homotetramer. Ref.3
Subcellular location	Cytoplasm Probable.
Sequence similarities	Belongs to the isocitrate and isopropylmalate dehydrogenases family.
Biophysicochemical properties	Kinetic parameters: K_M=24 µM for 3-isopropylmalate Ref.3 K_M=410 µM for D-malate Temperature dependence: Loses 50% of its activity after heating at 80 degrees Celsius for 10 min.

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Ontologies

Keywords
Biological process	Amino-acid biosynthesis Branched-chain amino acid biosynthesis Isoleucine biosynthesis Leucine biosynthesis
Cellular component	Cytoplasm
Ligand	Magnesium Manganese Metal-binding NAD
Molecular function	Oxidoreductase
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	isoleucine biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW leucine biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	3-isopropylmalate dehydrogenase activity Inferred from electronic annotation. Source: EC D-malate dehydrogenase (decarboxylating) activity Inferred from electronic annotation. Source: EC NAD or NADH binding Inferred from electronic annotation. Source: InterPro magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW manganese ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 333

333

3-isopropylmalate/3-methylmalate dehydrogenase

PRO_0000083809

Regions

Nucleotide binding

260 – 272

NAD By similarity

Sites

Metal binding

203

Magnesium or manganese By similarity

Metal binding

227

Magnesium or manganese By similarity

Metal binding

231

Magnesium or manganese By similarity

Binding site

Substrate By similarity

Binding site

Substrate By similarity

Binding site

112

Substrate By similarity

Binding site

203

Substrate By similarity

Site

119

Important for catalysis By similarity

Site

170

Important for catalysis By similarity

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Sequences

Sequence

Length

Mass (Da)

Tools

Q58130-1 [UniParc].

Last modified December 15, 1998. Version 2.
Checksum: 0618F119A4E682F0
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FASTA

333

36,330

        10         20         30         40         50         60 
MHKICVIEGD GIGKEVVPAT IQVLEATGLP FEFVYAEAGD EVYKRTGKAL PEETIETALD 

        70         80         90        100        110        120 
CDAVLFGAAG ETAADVIVKL RHILDTYANI RPVKAYKGVK CLRPDIDYVI VRENTEGLYK 

       130        140        150        160        170        180 
GIEAEIDEGI TIATRVITEK ACERIFRFAF NLARERKKMG KEGKVTCAHK ANVLKLTDGL 

       190        200        210        220        230        240 
FKKIFYKVAE EYDDIKAEDY YIDAMNMYII TKPQVFDVVV TSNLFGDILS DGAAGTVGGL 

       250        260        270        280        290        300 
GLAPSANIGD EHGLFEPVHG SAPDIAGKKI ANPTATILSA VLMLRYLGEY EAADKVEKAL 

       310        320        330 
EEVLALGLTT PDLGGNLNTF EMAEEVAKRV REE

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii." Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G., Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R., Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R., Kirkness E.F., Weinstock K.G. Venter J.C. Science 273:1058-1073(1996) [PubMed: 8688087] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.
[2]	"Identification of enzymes homologous to isocitrate dehydrogenase that are involved in coenzyme B and leucine biosynthesis in methanoarchaea." Howell D.M., Graupner M., Xu H., White R.H. J. Bacteriol. 182:5013-5016(2000) [PubMed: 10940051] [Abstract] Cited for: CHARACTERIZATION.
[3]	"Enzymology and evolution of the pyruvate pathway to 2-oxobutyrate in Methanocaldococcus jannaschii." Drevland R.M., Waheed A., Graham D.E. J. Bacteriol. 189:4391-4400(2007) [PubMed: 17449626] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, KINETIC PARAMETERS, SUBUNIT. Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.

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Cross-references

Sequence databases
	L77117 Genomic DNA. Translation: AAB98716.1.
RefSeq	NP_247705.1.
3D structure databases
HSSP	HSSP built from PDB template 1OSJ based on UniProtKB P00351.
ModBase	Search...
Genome annotation databases
GeneID	1451597.
GenomeReviews	Gene locus MJ0720 in contig L77117_GR.
KEGG	mja:MJ0720.
NMPDR	fig\|243232.1.peg.742.
TIGR	MJ0720.
Phylogenomic databases
HOGENOM	Q58130.
OMA	TCAHKAN.
Enzyme and pathway databases
BioCyc	MetaCyc:MON-13649. MJAN243232:MJ_0720-MON.
BRENDA	1.1.1.85. 256362.
Family and domain databases
InterPro	IPR019818. IsoCit/isopropylmalate_DH_CS. IPR001804. Isocitrate/isopropylmalate_DH. IPR011828. LEU3_arc. [Graphical view]
Gene3D	G3DSA:3.40.718.10. IDH_IMDH. 1 hit.
PANTHER	PTHR11835. IDH_IMDH_dimeric. 1 hit.
Pfam	PF00180. Iso_dh. 1 hit. [Graphical view]
TIGRFAMs	TIGR02088. LEU3_arch. 1 hit.
PROSITE	PS00470. IDH_IMDH. 1 hit. [Graphical view]
ProtoNet	Search...

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Entry information

Entry name

LEU3_METJA

Accession

Primary (citable) accession number: Q58130

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	December 15, 1998
Last modified:	November 3, 2009
This is version 63 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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Relevant documents

Methanococcus jannaschii

Methanococcus jannaschii: entries and gene names

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Genome annotation databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents