Reviewed, UniProtKB/Swiss-Prot P30125 (LEU3_ECOLI)

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:	b0073, JW5807

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	363 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. 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. Ref.7
Subcellular location	Cytoplasm. HAMAP MF_01033
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 Complete proteome Direct protein sequencing
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

Initiator methionine

1

1

Removed Ref.5

Chain

2 – 363

362

3-isopropylmalate dehydrogenase HAMAP MF_01033

PRO_0000083691

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 By similarity

Metal binding

251

1

Magnesium or manganese By similarity

Metal binding

255

1

Magnesium or manganese By similarity

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

Secondary structure

1

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363

Helix Strand Turn

Details...

Beta strand

3 – 13

11

Helix

16 – 34

19

Beta strand

37 – 42

6

Helix

47 – 53

7

Beta strand

54 – 57

4

Helix

59 – 66

8

Beta strand

68 – 75

8

Beta strand

86 – 89

4

Helix

90 – 101

12

Beta strand

106 – 112

7

Turn

118 – 120

3

Beta strand

121 – 123

3

Helix

125 – 128

4

Beta strand

133 – 139

7

Helix

143 – 145

3

Beta strand

148 – 153

6

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 – 212

13

Helix

213 – 215

3

Beta strand

219 – 225

7

Helix

226 – 235

10

Helix

237 – 239

3

Beta strand

241 – 245

5

Helix

247 – 261

15

Beta strand

268 – 272

5

Beta strand

278 – 284

7

Helix

288 – 290

3

Helix

299 – 311

13

Helix

316 – 331

16

Beta strand

336 – 338

3

Helix

348 – 359

12

Sequences

	Sequence		Length	Mass (Da)
	P30125-1 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 125EC1034FE1A3B5	FASTA	363	39,517
	10 20 30 40 50 60 MSKNYHIAVL PGDGIGPEVM TQALKVLDAV RNRFAMRITT SHYDVGGAAI DNHGQPLPPA 70 80 90 100 110 120 TVEGCEQADA VLFGSVGGPK WEHLPPDQQP ERGALLPLRK HFKLFSNLRP AKLYQGLEAF 130 140 150 160 170 180 CPLRADIAAN GFDILCVREL TGGIYFGQPK GREGSGQYEK AFDTEVYHRF EIERIARIAF 190 200 210 220 230 240 ESARKRRHKV TSIDKANVLQ SSILWREIVN EIATEYPDVE LAHMYIDNAT MQLIKDPSQF 250 260 270 280 290 300 DVLLCSNLFG DILSDECAMI TGSMGMLPSA SLNEQGFGLY EPAGGSAPDI AGKNIANPIA 310 320 330 340 350 360 QILSLALLLR YSLDADDAAC AIERAINRAL EEGIRTGDLA RGAAAVSTDE MGDIIARYVA EGV

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Hydrophobic interaction at the subunit interface contributes to the thermostability of 3-isopropylmalate dehydrogenase from an extreme thermophile, Thermus thermophilus." Kirino H., Aoki M., Aoshima M., Hayashi Y., Ohba M., Yamagishi A., Wakagi T., Oshima T. Eur. J. Biochem. 220:275-281(1994) [PubMed: 8119295] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 min region." Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K., Mizobuchi K., Nakata A. Nucleic Acids Res. 20:3305-3308(1992) [PubMed: 1630901] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Link A.J., Robison K., Church G.M. Electrophoresis 18:1259-1313(1997) [PubMed: 9298646] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-13. Strain: K12 / EMG2.
[6]	"Relationship between thermal stability and 3-D structure in a homology model of 3-isopropylmalate dehydrogenase from Escherichia coli." Magyar C., Szilagyi A., Zavodszy P. Protein Eng. 9:663-670(1996) [PubMed: 8875643] [Abstract] Cited for: 3D-STRUCTURE MODELING.
[7]	"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), SUBUNIT.

Cross-references

Sequence databases

EMBLGenBankDDBJ

D17631 Genomic DNA. Translation: BAA04537.1.
U00096 Genomic DNA. Translation: AAC73184.1. Different initiation.
AP009048 Genomic DNA. Translation: BAB96642.1.

PIR

A64729.

RefSeq

AP_000737.1.
NP_414615.4.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1CM7	X-ray	2.06	A/B	1-363	[»]

ModBase

Search...

Genome annotation databases

GeneID

944798.

GenomeReviews

Gene locus JW5807 in contig AP009048_GR.
Gene locus b0073 in contig U00096_GR.

KEGG

ecj:JW5807.
eco:b0073.

Organism-specific databases

EchoBASE

EB1537.

EcoGene

EG11577. leuB.

CMR

Search...

Phylogenomic databases

HOGENOM

P30125.

OMA

P30125. EAFDTMR.

Enzyme and pathway databases

BioCyc

EcoCyc:3-ISOPROPYLMALDEHYDROG-MON.
MetaCyc:3-ISOPROPYLMALDEHYDROG-MON.

BRENDA

1.1.1.85. 246.

Family and domain databases

HAMAP

MF_01033.
[Tree]

InterPro

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

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_ECOLI

Accession

Primary (citable) accession number: P30125
Secondary accession number(s): P78043

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1993
Last sequence update:	January 23, 2007
Last modified:	June 16, 2009
This is version 88 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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