P50455 (LEU3_SULTO) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
3-isopropylmalate dehydrogenase
Short name=3-IPM-DH
Short name=IMDH
EC=1.1.1.85

Alternative name(s):
Beta-IPM dehydrogenase

Gene names

Name:	leuB
Ordered Locus Names:	STK_04330

Organism

Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) [Complete proteome] [HAMAP]

Taxonomic identifier

273063 [NCBI]

Taxonomic lineage

Archaea › Crenarchaeota › Thermoprotei › Sulfolobales › Sulfolobaceae › Sulfolobus

Protein attributes

Sequence length	337 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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 activity	(2R,3S)-3-isopropylmalate + NAD+ = 4-methyl-2-oxopentanoate + CO2 + NADH.
Cofactor	Binds 1 magnesium or manganese ion per subunit. Ref.3
Pathway	Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 3/4.
Subunit structure	Homotetramer. Ref.3 Ref.4
Subcellular location	Cytoplasm.
Sequence similarities	Belongs to the isocitrate and isopropylmalate dehydrogenases family.

Ontologies

Keywords
Biological process	Amino-acid biosynthesis Branched-chain amino acid biosynthesis Leucine biosynthesis
Cellular component	Cytoplasm
Ligand	Magnesium Manganese Metal-binding NAD
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	leucine biosynthetic process Inferred from electronic annotation. Source: InterPro
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	3-isopropylmalate dehydrogenase activity Inferred from electronic annotation. Source: EC NAD binding Inferred from electronic annotation. Source: InterPro homoisocitrate dehydrogenase activity Inferred from electronic annotation. Source: EC magnesium ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.3

Chain

2 – 337

336

3-isopropylmalate dehydrogenase

PRO_0000083812

Regions

Nucleotide binding

258 – 270

13

NAD By similarity

Sites

Metal binding

201

1

Magnesium or manganese By similarity

Metal binding

225

1

Magnesium or manganese By similarity

Metal binding

229

1

Magnesium or manganese By similarity

Binding site

86

1

Substrate By similarity

Binding site

96

1

Substrate By similarity

Binding site

117

1

Substrate By similarity

Binding site

201

1

Substrate By similarity

Site

124

1

Important for catalysis By similarity

Site

170

1

Important for catalysis By similarity

Secondary structure

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337

Helix Strand Turn

Details...

Beta strand

3 – 8

6

Helix

14 – 31

18

Beta strand

36 – 41

6

Helix

45 – 50

6

Beta strand

51 – 55

5

Helix

57 – 64

8

Beta strand

67 – 71

5

Helix

78 – 87

10

Turn

88 – 90

3

Beta strand

93 – 99

7

Turn

102 – 104

3

Beta strand

112 – 118

7

Beta strand

120 – 122

3

Turn

123 – 125

3

Beta strand

128 – 132

5

Beta strand

135 – 143

9

Helix

144 – 159

16

Turn

160 – 162

3

Beta strand

163 – 169

7

Turn

171 – 173

3

Helix

177 – 189

13

Turn

190 – 192

3

Beta strand

193 – 199

7

Helix

200 – 209

10

Helix

211 – 213

3

Beta strand

215 – 219

5

Helix

221 – 235

15

Helix

238 – 240

3

Beta strand

242 – 246

5

Beta strand

251 – 257

7

Turn

261 – 265

5

Helix

272 – 287

16

Helix

293 – 311

19

Helix

317 – 319

3

Helix

325 – 334

10

Sequences

	Sequence		Length	Mass (Da)
	P50455 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 1B44CB9A0CD70313	FASTA	337	36,964
	10 20 30 40 50 60 MGFTVALIQG DGIGPEIVSK SKRILAKINE LYSLPIEYIE VEAGDRALAR YGEALPKDSL 70 80 90 100 110 120 KIIDKADIIL KGPVGESAAD VVVKLRQIYD MYANIRPAKS IPGIDTKYGN VDILIVRENT 130 140 150 160 170 180 EDLYKGFEHI VSDGVAVGMK IITRFASERI AKVGLNFALR RRKKVTCVHK ANVMRITDGL 190 200 210 220 230 240 FAEACRSVLK GKVEYSEMYV DAAAANLVRN PQMFDVIVTE NVYGDILSDE ASQIAGSLGI 250 260 270 280 290 300 APSANIGDKK ALFEPVHGAA FDIAGKNIGN PTAFLLSVSM MYERMYELSN DDRYIKASRA 310 320 330 LENAIYLVYK ERKALTPDVG GNATTDDLIN EIYNKLG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 9023199] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7.
[2]	"Complete genome sequence of an aerobic thermoacidophilic Crenarchaeon, Sulfolobus tokodaii strain7." Kawarabayasi Y., Hino Y., Horikawa H., Jin-no K., Takahashi M., Sekine M., Baba S., Ankai A., Kosugi H., Hosoyama A., Fukui S., Nagai Y., Nishijima K., Otsuka R., Nakazawa H., Takamiya M., Kato Y., Yoshizawa T. , Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Masuda S., Yanagii M., Nishimura M., Yamagishi A., Oshima T., Kikuchi H. DNA Res. 8:123-140(2001) [PubMed: 11572479] [Abstract] 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: 7557336] [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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

D86857 Genomic DNA. Translation: BAA13178.1.
BA000023 Genomic DNA. Translation: BAK54281.1.

RefSeq

NP_376313.1. NC_003106.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1WPW	X-ray	2.80	A/B	2-336	[»]

ProteinModelPortal

P50455.

SMR

P50455. Positions 2-337.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

1458369.

GenomeReviews

Gene locus ST0433 in contig BA000023_GR.

KEGG

sto:ST0433.

NMPDR

fig|273063.1.peg.481.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

HBG518924.

OMA

TCAHKAN.

PhylomeDB

P50455.

ProtClustDB

CLSK802842.

Enzyme and pathway databases

BioCyc

STOK273063:ST0433-MONOMER.

BRENDA

1.1.1.85. 6166.

Family and domain databases

InterPro

IPR019818. IsoCit/isopropylmalate_DH_CS.
IPR001804. Isocitrate/isopropylmalate_DH.
IPR024084. IsoPropMal-DH-like_dom.
IPR011828. LEU3_arc.
[Graphical view]

Gene3D

G3DSA:3.40.718.10. IDH_IMDH. 1 hit.

KO

K00052.

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...

Entry information

Entry name

LEU3_SULTO

Accession

Primary (citable) accession number: P50455
Secondary accession number(s): F9VMY4, O05169

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1996
Last sequence update:	January 23, 2007
Last modified:	January 25, 2012
This is version 88 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program