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Protein

3-isopropylmalate dehydrogenase

Gene

leuB

Organism
Bacillus coagulans
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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 activityi

(2R,3S)-3-isopropylmalate + NAD+ = 4-methyl-2-oxopentanoate + CO2 + NADH.

Cofactori

Mg2+, Mn2+Note: Binds 1 Mg2+ or Mn2+ ion per subunit.

Pathwayi: L-leucine biosynthesis

This protein is involved in step 3 of the subpathway that synthesizes L-leucine from 3-methyl-2-oxobutanoate.
Proteins known to be involved in the 4 steps of the subpathway in this organism are:
  1. 2-isopropylmalate synthase (leuA), 2-isopropylmalate synthase (leuA), 2-isopropylmalate synthase (leuA), 2-isopropylmalate synthase (leuA)
  2. 3-isopropylmalate dehydratase small subunit (leuD), 3-isopropylmalate dehydratase small subunit (leuD), 3-isopropylmalate dehydratase large subunit (leuC), 3-isopropylmalate dehydratase large subunit (leuC), 3-isopropylmalate dehydratase large subunit (leuC), 3-isopropylmalate dehydratase large subunit (leuC), 3-isopropylmalate dehydratase large subunit (leuC), 3-isopropylmalate dehydratase small subunit (leuD)
  3. 3-isopropylmalate dehydrogenase (leuB), 3-isopropylmalate dehydrogenase (leuB), 3-isopropylmalate dehydrogenase (leuB), 3-isopropylmalate dehydrogenase (leuB), 3-isopropylmalate dehydrogenase (leuB)
  4. Branched-chain-amino-acid aminotransferase (B4099_1554), Branched-chain-amino-acid aminotransferase (SB48_HM08orf00177), Branched-chain-amino-acid aminotransferase (HMPREF3213_01889), Branched-chain-amino-acid aminotransferase (B4098_1286), Branched-chain-amino-acid aminotransferase (B4100_1472)
This subpathway is part of the pathway L-leucine biosynthesis, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-leucine from 3-methyl-2-oxobutanoate, the pathway L-leucine biosynthesis and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei96SubstrateBy similarity1
Binding sitei106SubstrateBy similarity1
Binding sitei134SubstrateBy similarity1
Sitei141Important for catalysisBy similarity1
Sitei190Important for catalysisBy similarity1
Metal bindingi222Magnesium or manganeseBy similarity1
Binding sitei222SubstrateBy similarity1
Metal bindingi246Magnesium or manganeseBy similarity1
Metal bindingi250Magnesium or manganeseBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi76 – 89NADBy similarityAdd BLAST14
Nucleotide bindingi280 – 292NADBy similarityAdd BLAST13

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Amino-acid biosynthesis, Branched-chain amino acid biosynthesis, Leucine biosynthesis

Keywords - Ligandi

Magnesium, Manganese, Metal-binding, NAD

Enzyme and pathway databases

UniPathwayiUPA00048; UER00072.

Names & Taxonomyi

Protein namesi
Recommended name:
3-isopropylmalate dehydrogenase (EC:1.1.1.85)
Alternative name(s):
3-IPM-DH
Beta-IPM dehydrogenase
Short name:
IMDH
Gene namesi
Name:leuB
OrganismiBacillus coagulans
Taxonomic identifieri1398 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000836381 – 3663-isopropylmalate dehydrogenaseAdd BLAST366

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi345219.Bcoa_2059.

Structurei

Secondary structure

1366
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 11Combined sources9
Helixi14 – 29Combined sources16
Turni30 – 33Combined sources4
Beta strandi36 – 40Combined sources5
Helixi45 – 51Combined sources7
Beta strandi52 – 55Combined sources4
Helixi57 – 64Combined sources8
Beta strandi66 – 73Combined sources8
Helixi77 – 79Combined sources3
Beta strandi80 – 82Combined sources3
Helixi84 – 86Combined sources3
Helixi88 – 99Combined sources12
Beta strandi103 – 109Combined sources7
Helixi112 – 114Combined sources3
Turni115 – 117Combined sources3
Beta strandi118 – 120Combined sources3
Helixi122 – 125Combined sources4
Beta strandi129 – 135Combined sources7
Beta strandi137 – 139Combined sources3
Turni140 – 142Combined sources3
Beta strandi146 – 151Combined sources6
Beta strandi155 – 163Combined sources9
Helixi164 – 180Combined sources17
Beta strandi183 – 189Combined sources7
Turni191 – 193Combined sources3
Helixi195 – 208Combined sources14
Beta strandi214 – 220Combined sources7
Helixi221 – 230Combined sources10
Helixi232 – 234Combined sources3
Beta strandi236 – 240Combined sources5
Helixi242 – 252Combined sources11
Turni253 – 256Combined sources4
Helixi259 – 261Combined sources3
Beta strandi263 – 267Combined sources5
Beta strandi269 – 271Combined sources3
Beta strandi273 – 279Combined sources7
Helixi283 – 285Combined sources3
Turni286 – 289Combined sources4
Helixi294 – 308Combined sources15
Helixi311 – 326Combined sources16
Beta strandi329 – 334Combined sources6
Helixi344 – 354Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1V53X-ray2.85A/B1-366[»]
1V5BX-ray2.95A/B/C/D/E/F/G/H1-366[»]
2AYQX-ray3.00A/B1-366[»]
ProteinModelPortaliP12010.
SMRiP12010.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP12010.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105C0C. Bacteria.
COG0473. LUCA.

Family and domain databases

Gene3Di3.40.718.10. 1 hit.
HAMAPiMF_01033. LeuB_type1. 1 hit.
InterProiIPR019818. IsoCit/isopropylmalate_DH_CS.
IPR001804. Isocitrate/isopropylmalate_DH.
IPR024084. IsoPropMal-DH-like_dom.
IPR004429. Isopropylmalate_DH.
[Graphical view]
PANTHERiPTHR11835. PTHR11835. 1 hit.
PfamiPF00180. Iso_dh. 1 hit.
[Graphical view]
SMARTiSM01329. Iso_dh. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00169. leuB. 1 hit.
PROSITEiPS00470. IDH_IMDH. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P12010-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKMKLAVLPG DGIGPEVMDA AIRVLKTVLD NDGHEAVFEN ALIGGAAIDE
60 70 80 90 100
AGTPLPEETL DICRRSDAIL LGAVGGPKWD HNPASLRPEK GLLGLRKEMG
110 120 130 140 150
LFANLRPVKA YATLLNASPL KRERVENVDL VIVRELTGGL YFGRPSERRG
160 170 180 190 200
PGENEVVDTL AYTREEIERI IEKAFQLAQI RRKKLASVDK ANVLESSRMW
210 220 230 240 250
REIAEETAKK YPDVELSHML VDSTSMQLIA NPGQFDVIVT ENMFGDILSD
260 270 280 290 300
EASVITGSLG MLPSASLRSD RFGMYEPVHG SAPDIAGQGK ANPLGTVLSA
310 320 330 340 350
ALMLRYSFGL EKEAAAIEKA VDDVLQDGYC TGDLQVANGK VVSTIELTDR
360
LIEKLNNSAA RPRIFQ
Length:366
Mass (Da):39,809
Last modified:October 1, 1989 - v1
Checksum:i05958B786718408E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M33099 Genomic DNA. Translation: AAA22554.1. Sequence problems.
PIRiA24537. DEBSIC.
RefSeqiWP_029141661.1. NZ_LQYJ01000066.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M33099 Genomic DNA. Translation: AAA22554.1. Sequence problems.
PIRiA24537. DEBSIC.
RefSeqiWP_029141661.1. NZ_LQYJ01000066.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1V53X-ray2.85A/B1-366[»]
1V5BX-ray2.95A/B/C/D/E/F/G/H1-366[»]
2AYQX-ray3.00A/B1-366[»]
ProteinModelPortaliP12010.
SMRiP12010.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi345219.Bcoa_2059.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4105C0C. Bacteria.
COG0473. LUCA.

Enzyme and pathway databases

UniPathwayiUPA00048; UER00072.

Miscellaneous databases

EvolutionaryTraceiP12010.

Family and domain databases

Gene3Di3.40.718.10. 1 hit.
HAMAPiMF_01033. LeuB_type1. 1 hit.
InterProiIPR019818. IsoCit/isopropylmalate_DH_CS.
IPR001804. Isocitrate/isopropylmalate_DH.
IPR024084. IsoPropMal-DH-like_dom.
IPR004429. Isopropylmalate_DH.
[Graphical view]
PANTHERiPTHR11835. PTHR11835. 1 hit.
PfamiPF00180. Iso_dh. 1 hit.
[Graphical view]
SMARTiSM01329. Iso_dh. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00169. leuB. 1 hit.
PROSITEiPS00470. IDH_IMDH. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiLEU3_BACCO
AccessioniPrimary (citable) accession number: P12010
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1989
Last sequence update: October 1, 1989
Last modified: November 2, 2016
This is version 111 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.