Reviewed, UniProtKB/Swiss-Prot P37412 (LEU3_SALTY)

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
Ordered Locus Names:	STM0112

Organism

Salmonella typhimurium [Complete proteome] [HAMAP]

Taxonomic identifier

90371 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Salmonella

Protein attributes

Sequence length	363 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. 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. Ref.4
Pathway	Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine from 3-methyl-2-oxobutanoate: step 3/4. HAMAP MF_01033
Subunit structure	Homodimer. Ref.4 Ref.5
Subcellular location	Cytoplasm. HAMAP MF_01033
Sequence similarities	Belongs to the isocitrate and isopropylmalate dehydrogenases family. LeuB type 1 subfamily.
biophysicochemical properties	Kinetic parameters: KM=19 µM for beta-isopropylmalate Ref.4 KM=0.1 mM for NAD pH dependence: Optimum pH is 9.0.

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
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 – 363

363

3-isopropylmalate dehydrogenase HAMAP MF_01033

PRO_0000083743

Regions

Nucleotide binding

78 – 91

14

NAD By similarity

Nucleotide binding

285 – 297

13

NAD By similarity

Sites

Metal binding

227

1

Magnesium or manganese HAMAP MF_01033

Metal binding

251

1

Magnesium or manganese HAMAP MF_01033

Metal binding

255

1

Magnesium or manganese HAMAP MF_01033

Binding site

99

1

Substrate By similarity

Binding site

109

1

Substrate By similarity

Binding site

138

1

Substrate By similarity

Binding site

227

1

Substrate By similarity

Site

145

1

Important for catalysis By similarity

Site

195

1

Important for catalysis By similarity

Experimental info

Sequence conflict

32 – 40

9

SRFDMRITT → VLICVYH in CAA37456. Ref.1

Sequence conflict

52 – 55

4

NHGH → SSGI in CAA37456. Ref.1

Sequence conflict

81 – 94

14

WENLP…PERGA → MGKFAPGKPAGARR Ref.1

Sequence conflict

188

1

R → C in CAA37456. Ref.1

Sequence conflict

311 – 313

3

YSL → TA in CAA37456. Ref.1

Sequence conflict

345

1

Missing in CAA37456. Ref.1

Secondary structure

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363

Helix Strand Turn

Details...

Beta strand

5 – 13

9

Helix

16 – 34

19

Beta strand

38 – 42

5

Helix

47 – 53

7

Beta strand

54 – 57

4

Helix

59 – 66

8

Beta strand

68 – 75

8

Helix

79 – 81

3

Helix

86 – 88

3

Helix

92 – 102

11

Beta strand

106 – 112

7

Helix

118 – 120

3

Helix

125 – 130

6

Beta strand

133 – 139

7

Helix

143 – 145

3

Beta strand

151 – 153

3

Helix

156 – 158

3

Beta strand

160 – 168

9

Helix

169 – 184

16

Turn

185 – 187

3

Beta strand

188 – 194

7

Turn

196 – 198

3

Helix

200 – 213

14

Beta strand

219 – 225

7

Helix

226 – 235

10

Helix

237 – 239

3

Beta strand

241 – 245

5

Helix

247 – 261

15

Helix

264 – 266

3

Beta strand

268 – 272

5

Beta strand

278 – 284

7

Helix

288 – 290

3

Turn

291 – 294

4

Helix

299 – 312

14

Helix

316 – 331

16

Turn

337 – 344

8

Helix

348 – 360

13

Sequences

	Sequence		Length	Mass (Da)
	P37412-1 [UniParc]. Last modified November 1, 1995. Version 2. Checksum: 3AEEED0A4BAB7FB4	FASTA	363	39,513
	10 20 30 40 50 60 MSKNYHIAVL PGDGIGPEVM AQALKVMDAV RSRFDMRITT SHYDVGGIAI DNHGHPLPKA 70 80 90 100 110 120 TVEGCEQADA ILFGSVGGPK WENLPPESQP ERGALLPLRK HFKLFSNLRP AKLYQGLEAF 130 140 150 160 170 180 CPLRADIAAN GFDILCVREL TGGIYFGQPK GREGSGQYEK AFDTEVYHRF EIERIARIAF 190 200 210 220 230 240 ESARKRRRKV TSIDKANVLQ SSILWREIVN DVAKTYPDVE LAHMYIDNAT MQLIKDPSQF 250 260 270 280 290 300 DVLLCSNLFG DILSDECAMI TGSMGMLPSA SLNEQGFGLY EPAGGSAPDI AGKNIANPIA 310 320 330 340 350 360 QILSLALLLR YSLDANDAAT AIEQAINRAL EEGVRTGDLA RGAAAVSTDE MGDIIARYVA EGV

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The nucleotide sequence of leuB from Salmonella typhimurium." Andreadis A., Rosenthal E.R. Biochim. Biophys. Acta 1129:228-230(1992) [PubMed: 1730062] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: LT2.
[2]	"Revision of the amino-acid sequence of 3-isopropylmalate dehydrogenase from Salmonella typhimurium by means of X-ray crystallography." Kryger G., Wallon G., Lovett S.T., Ringe D., Petsko G.A. Gene 164:85-87(1995) [PubMed: 7590327] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], SEQUENCE REVISION. Strain: LT2.
[3]	"Complete genome sequence of Salmonella enterica serovar Typhimurium LT2." McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P., Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D., Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E. , Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R., Wilson R.K. Nature 413:852-856(2001) [PubMed: 11677609] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: LT2 / SGSC1412 / ATCC 700720.
[4]	"Purification and properties of beta-isopropylmalate dehydrogenase." Parsons S.J., Burns R.O. J. Biol. Chem. 244:996-1003(1969) [PubMed: 4889950] [Abstract] Cited for: KINETIC PARAMETERS, SUBUNIT, COFACTOR.
[5]	"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 (2.06 ANGSTROMS) IN COMPLEX WITH MANGANESE IONS, SUBUNIT.

Cross-references

Sequence databases

EMBLGenBankDDBJ

X53376 Genomic DNA. Translation: CAA37456.1.
U20795 Genomic DNA. Translation: AAB60185.1.
AE008699 Genomic DNA. Translation: AAL19076.1.

PIR

S20606.

RefSeq

NP_459117.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1CNZ	X-ray	1.76	A/B	1-363	[»]

ModBase

Search...

Genome annotation databases

GeneID

1251630.

GenomeReviews

Gene locus STM0112 in contig AE006468_GR.

KEGG

stm:STM0112.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

P37412.

OMA

P37412. EAFDTMR.

Enzyme and pathway databases

BioCyc

STYP99287:STM0112-MON.

BRENDA

1.1.1.85. 2.

Family and domain databases

HAMAP

MF_01033.
[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_SALTY

Accession

Primary (citable) accession number: P37412

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1994
Last sequence update:	November 1, 1995
Last modified:	June 16, 2009
This is version 79 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)