Reviewed, UniProtKB/Swiss-Prot P12010 (LEU3_BACCO)

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

Bacillus coagulans

Taxonomic identifier

1398 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Bacillaceae › Bacillus

Protein attributes

Sequence length	366 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
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 + CO(2) + NADH.
Cofactor	Binds 1 magnesium or manganese ion per subunit.
Pathway	Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 3/4.
Subunit structure	Homodimer.
Subcellular location	Cytoplasm.
Sequence similarities	Belongs to the isocitrate and isopropylmalate dehydrogenases family. LeuB type 1 subfamily.

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: HAMAP
Molecular function	3-isopropylmalate dehydrogenase activity Inferred from electronic annotation. Source: HAMAP 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 – 366

366

3-isopropylmalate dehydrogenase

PRO_0000083638

Regions

Nucleotide binding

76 – 89

14

NAD By similarity

Nucleotide binding

280 – 292

13

NAD By similarity

Sites

Metal binding

222

1

Magnesium or manganese By similarity

Metal binding

246

1

Magnesium or manganese By similarity

Metal binding

250

1

Magnesium or manganese By similarity

Binding site

96

1

Substrate By similarity

Binding site

106

1

Substrate By similarity

Binding site

134

1

Substrate By similarity

Binding site

222

1

Substrate By similarity

Site

141

1

Important for catalysis By similarity

Site

190

1

Important for catalysis By similarity

Secondary structure

1

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366

Helix Strand Turn

Details...

Beta strand

3 – 11

9

Helix

14 – 29

16

Beta strand

36 – 40

5

Helix

45 – 51

7

Beta strand

52 – 55

4

Helix

57 – 64

8

Beta strand

66 – 73

8

Helix

77 – 79

3

Beta strand

80 – 82

3

Helix

84 – 86

3

Helix

88 – 99

12

Beta strand

103 – 109

7

Helix

112 – 114

3

Turn

115 – 117

3

Beta strand

118 – 120

3

Helix

122 – 125

4

Beta strand

129 – 135

7

Beta strand

137 – 139

3

Turn

140 – 142

3

Beta strand

146 – 151

6

Beta strand

155 – 163

9

Helix

164 – 180

17

Beta strand

183 – 189

7

Turn

191 – 193

3

Helix

195 – 208

14

Beta strand

214 – 220

7

Helix

221 – 230

10

Helix

232 – 234

3

Beta strand

236 – 240

5

Helix

242 – 252

11

Turn

253 – 256

4

Beta strand

263 – 267

5

Beta strand

269 – 271

3

Beta strand

273 – 279

7

Helix

283 – 285

3

Helix

294 – 308

15

Helix

311 – 326

16

Beta strand

329 – 334

6

Helix

344 – 354

11

Sequences

	Sequence		Length	Mass (Da)
	P12010-1 [UniParc]. Last modified October 1, 1989. Version 1. Checksum: 05958B786718408E	FASTA	366	39,809
	10 20 30 40 50 60 MKMKLAVLPG DGIGPEVMDA AIRVLKTVLD NDGHEAVFEN ALIGGAAIDE AGTPLPEETL 70 80 90 100 110 120 DICRRSDAIL LGAVGGPKWD HNPASLRPEK GLLGLRKEMG LFANLRPVKA YATLLNASPL 130 140 150 160 170 180 KRERVENVDL VIVRELTGGL YFGRPSERRG PGENEVVDTL AYTREEIERI IEKAFQLAQI 190 200 210 220 230 240 RRKKLASVDK ANVLESSRMW REIAEETAKK YPDVELSHML VDSTSMQLIA NPGQFDVIVT 250 260 270 280 290 300 ENMFGDILSD EASVITGSLG MLPSASLRSD RFGMYEPVHG SAPDIAGQGK ANPLGTVLSA 310 320 330 340 350 360 ALMLRYSFGL EKEAAAIEKA VDDVLQDGYC TGDLQVANGK VVSTIELTDR LIEKLNNSAA RPRIFQ

References

[1]	"DNA and amino-acid sequences of 3-isopropylmalate dehydrogenase of Bacillus coagulans. Comparison with the enzymes of Saccharomyces cerevisiae and Thermus thermophilus." Sekiguchi T., Ortega-Cesena J., Nosoh Y., Ohashi S., Tsuda K., Kanaya S. Biochim. Biophys. Acta 867:36-44(1986) Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Crystal structure of 3-isopropylmalate dehydrogenase from the moderate facultative thermophile, Bacillus coagulans: two strategies for thermostabilization of protein structures." Tsuchiya D., Sekiguchi T., Takenaka A. J. Biochem. 122:1092-1104(1997) [PubMed: 9498551] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS), SUBUNIT.

Cross-references

Sequence databases

EMBLGenBankDDBJ

M33099 Genomic DNA. Translation: AAA22554.1. Sequence problems.

PIR

DEBSIC. A24537.

3D structure databases

PDBMSD

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1V53	X-ray	2.85	A/B	1-366	[»]
1V5B	X-ray	2.95	A/B/C/D/E/F/G/H	1-366	[»]
2AYQ	X-ray	3.00	A/B	1-366	[»]

ModBase

Search...

Family and domain databases

HAMAP

MF_01033.
[Tree]

InterPro

IPR004429. 3-isopropylmalate_DHase.
IPR001804. IsoCit_IM_DHase.
[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...

Other Resources

LinkHub

P12010.

Entry information

Entry name

LEU3_BACCO

Accession

Primary (citable) accession number: P12010

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1989
Last sequence update:	October 1, 1989
Last modified:	November 4, 2008
This is version 72 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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