Reviewed, UniProtKB/Swiss-Prot P61495 (LEU3_THETH)

Names and origin

Protein names

Recommended name:
    3-isopropylmalate dehydrogenase
    EC=1.1.1.85
Alternative name(s):
    Beta-IPM dehydrogenase
      Short name=IMDH
    3-IPM-DH

Gene names

Name:

leuB

Organism

Thermus thermophilus

Taxonomic identifier

274 [NCBI]

Taxonomic lineage

Bacteria › Deinococcus-Thermus › Deinococci › Thermales › Thermaceae › Thermus

Protein attributes

Sequence length	345 AA.
Sequence status	Complete.
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. HAMAP MF_01033
Catalytic activity	(2R,3S)-3-isopropylmalate + NAD+ = 4-methyl-2-oxopentanoate + CO2 + NADH. HAMAP MF_01033
Cofactor	Binds 1 magnesium or manganese ion per subunit. HAMAP MF_01033
Pathway	Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 3/4. HAMAP MF_01033
Subunit structure	Homodimer. HAMAP MF_01033
Subcellular location	Cytoplasm HAMAP MF_01033.
Sequence similarities	Belongs to the isocitrate and isopropylmalate dehydrogenases family. LeuB type 1 subfamily.
Caution	The sequence shown here has been extracted from PDB entry 1WAL.

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
Gene Ontology (GO)
Biological process	leucine biosynthetic process Inferred from electronic annotation. Source: HAMAP 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: HAMAP 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...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 345

345

3-isopropylmalate dehydrogenase HAMAP MF_01033

PRO_0000083773

Regions

Nucleotide binding

74 – 87

14

NAD By similarity

Nucleotide binding

274 – 286

13

NAD By similarity

Sites

Metal binding

217

1

Magnesium or manganese By similarity

Metal binding

241

1

Magnesium or manganese By similarity

Metal binding

245

1

Magnesium or manganese By similarity

Binding site

94

1

Substrate By similarity

Binding site

104

1

Substrate By similarity

Binding site

132

1

Substrate By similarity

Binding site

217

1

Substrate By similarity

Site

139

1

Important for catalysis By similarity

Site

185

1

Important for catalysis By similarity

Secondary structure

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345

Helix Strand Turn

Details...

Beta strand

2 – 9

8

Helix

12 – 30

19

Beta strand

35 – 38

4

Helix

43 – 49

7

Beta strand

50 – 53

4

Helix

55 – 63

9

Beta strand

64 – 71

8

Helix

75 – 77

3

Helix

82 – 84

3

Helix

86 – 97

12

Beta strand

99 – 107

9

Helix

113 – 115

3

Beta strand

116 – 118

3

Helix

120 – 123

4

Beta strand

127 – 133

7

Helix

137 – 139

3

Beta strand

148 – 158

11

Helix

159 – 174

16

Turn

175 – 177

3

Beta strand

178 – 184

7

Turn

186 – 188

3

Helix

190 – 202

13

Helix

203 – 205

3

Beta strand

209 – 215

7

Helix

216 – 225

10

Helix

227 – 229

3

Beta strand

231 – 235

5

Helix

237 – 248

12

Turn

249 – 251

3

Helix

254 – 256

3

Beta strand

258 – 265

8

Beta strand

268 – 273

6

Helix

277 – 279

3

Helix

288 – 302

15

Helix

305 – 321

17

Helix

325 – 327

3

Helix

333 – 344

12

Sequences

	Sequence		Length	Mass (Da)
	P61495-1 [UniParc]. Last modified May 24, 2005. Version 2. Checksum: 3521F7363A0550C5	FASTA	345	36,651
	10 20 30 40 50 60 MKVAVLPGDG IGPEVTEAAL KVLRALDEAE GLGLAYEVFP FGGAAIDAFG EPFPEPTRKG 70 80 90 100 110 120 VEEAEAVLLG SVGGPKWDGL PRKISPETGL LSLRKSQDLF ANLRPAKVFP GLERLSPLKE 130 140 150 160 170 180 EIARGVDVLI VRELTGGIYF GEPRGMSEAE AWNTERYSKP EVERVARVAF EAARKRRKHV 190 200 210 220 230 240 VSVDKANVLE VGEFWRKTVE EVGRGYPDVA LEHQYVDAAA MHLVRSPARF DVVVTGNIFG 250 260 270 280 290 300 DILSDLASVL PGSLGLLPSA SLGRGTPVFE PVHGSAPDIA GKGIANPTAA ILSAAMMLEH 310 320 330 340 AFGLVELARK VEDAVAKALL ETPPPDLGGS AGTEAFTATV LRHLA

References

[1]

"Crystal structures of Escherichia coli and Salmonella typhimurium 3-isopropylmalate dehydrogenase and comparison with their thermophilic counterpart from Thermus thermophilus." Wallon G., Kryger G., Lovett S.T., Oshima T., Ringe D., Petsko G.A. J. Mol. Biol. 266:1016-1031(1997) [PubMed: 9086278] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.27 ANGSTROMS).

Cross-references

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1WAL	X-ray	2.27	A	1-345	[»]

ModBase

Search...

Enzyme and pathway databases

BRENDA

1.1.1.85. 245.

Family and domain databases

HAMAP

MF_01033. LeuB_type1.
[Tree]

InterPro

IPR019818. IsoCit/isopropylmalate_DH_CS.
IPR001804. Isocitrate/isopropylmalate_DH.
IPR004429. Isopropylmalate_DH.
[Graphical view]

Gene3D

G3DSA:3.40.718.10. IDH_IMDH. 1 hit.

PANTHER

PTHR11835. IDH_IMDH_dimeric. 1 hit.
PTHR11835:SF13. IPMDH. 1 hit.

Pfam

PF00180. Iso_dh. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00169. leuB. 1 hit.

PROSITE

PS00470. IDH_IMDH. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

LEU3_THETH

Accession

Primary (citable) accession number: P61495
Secondary accession number(s): P00351

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	May 24, 2005
Last modified:	February 9, 2010
This is version 45 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)