Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Isopropylmalate/citramalate isomerase small subunit

Gene

leuD

Organism
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Enzyme with broad specificity that catalyzes reversible hydroxyacid isomerizations via dehydration/hydration reactions. Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate, a step involved in leucine biosynthesis. Catalyzes the isomerization between 2-methylmalate and 3-methylmalate, via the formation of 2-methylmaleate (citraconate), a step involved in isoleucine biosynthesis. Also displays malease activity, i.e. catalyzes the hydration of maleate to form (R)-malate.1 Publication

Catalytic activityi

(2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate.1 Publication
(R)-2-methylmalate = 2-methylmaleate + H2O.1 Publication
2-methylmaleate + H2O = (2R,3S)-3-methylmalate.1 Publication
(R)-malate = maleate + H2O.1 Publication

Kineticsi

  1. KM=80 µM for 2-methylmaleate1 Publication
  2. KM=810 µM for (R)-2-methylmalate1 Publication
  3. KM=1900 µM for racemic 2-isopropylmalate1 Publication
  4. KM=39 µM for racemic 3-isopropylmalate1 Publication
  5. KM=400 µM for maleate1 Publication
  1. Vmax=15 µmol/min/mg enzyme for 2-methylmaleate hydration reaction1 Publication
  2. Vmax=1.5 µmol/min/mg enzyme for (R)-2-methylmalate dehydration reaction1 Publication
  3. Vmax=4.2 µmol/min/mg enzyme for 2-isopropylmalate dehydration reaction1 Publication
  4. Vmax=1.8 µmol/min/mg enzyme for 3-isopropylmalate dehydration reaction1 Publication
  5. Vmax=34 µmol/min/mg enzyme for maleate hydration reaction1 Publication

pH dependencei

Optimum pH is 7.5.1 Publication

Temperature dependencei

Optimum temperature is 70 degrees Celsius.1 Publication

Pathwayi: L-leucine biosynthesis

This protein is involved in step 2 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/citramalate isomerase small subunit (leuD), Isopropylmalate/citramalate isomerase large subunit (leuC)
  3. 3-isopropylmalate/3-methylmalate dehydrogenase (leuB)
  4. Putative branched-chain-amino-acid aminotransferase (ilvE)
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.

Pathwayi: L-isoleucine biosynthesis

This protein is involved in step 2 of the subpathway that synthesizes 2-oxobutanoate from pyruvate.
Proteins known to be involved in the 3 steps of the subpathway in this organism are:
  1. (R)-citramalate synthase CimA (cimA)
  2. Isopropylmalate/citramalate isomerase small subunit (leuD), Isopropylmalate/citramalate isomerase large subunit (leuC)
  3. 3-isopropylmalate/3-methylmalate dehydrogenase (leuB)
This subpathway is part of the pathway L-isoleucine 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 2-oxobutanoate from pyruvate, the pathway L-isoleucine biosynthesis and in Amino-acid biosynthesis.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

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

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-13648.
SABIO-RKQ58673.
UniPathwayiUPA00047; UER00067.
UPA00048; UER00071.

Names & Taxonomyi

Protein namesi
Recommended name:
Isopropylmalate/citramalate isomerase small subunit (EC:4.2.1.33, EC:4.2.1.35)
Alternative name(s):
(R)-2-methylmalate dehydratase
(R)-citramalate dehydratase
3-isopropylmalate dehydratase
Alpha-isopropylmalate dehydratase
Citraconate hydratase
Isopropylmalate isomerase
Short name:
IPMI
Maleate hydratase (EC:4.2.1.31)
Short name:
Malease
Gene namesi
Name:leuD
Ordered Locus Names:MJ1277
OrganismiMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Taxonomic identifieri243232 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanococciMethanococcalesMethanocaldococcaceaeMethanocaldococcus
Proteomesi
  • UP000000805 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001419371 – 168Isopropylmalate/citramalate isomerase small subunitAdd BLAST168

Interactioni

Subunit structurei

Heterotetramer of 2 LeuC and 2 LeuD. The heterotetramer that can be formed in vitro between HacA and LeuD is inactive.1 Publication

Protein-protein interaction databases

STRINGi243232.MJ_1277.

Structurei

Secondary structure

1168
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 11Combined sources9
Helixi18 – 21Combined sources4
Helixi24 – 26Combined sources3
Helixi32 – 35Combined sources4
Helixi36 – 38Combined sources3
Turni39 – 43Combined sources5
Helixi47 – 50Combined sources4
Beta strandi56 – 59Combined sources4
Beta strandi65 – 67Combined sources3
Helixi71 – 78Combined sources8
Beta strandi83 – 87Combined sources5
Helixi91 – 99Combined sources9
Beta strandi104 – 106Combined sources3
Helixi110 – 113Combined sources4
Beta strandi119 – 123Combined sources5
Turni124 – 126Combined sources3
Beta strandi128 – 131Combined sources4
Turni132 – 134Combined sources3
Beta strandi137 – 139Combined sources3
Helixi145 – 153Combined sources9
Helixi156 – 165Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3VBAX-ray2.00A/B/C/D/E/F1-168[»]
ProteinModelPortaliQ58673.
SMRiQ58673.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the LeuD family.Curated

Phylogenomic databases

eggNOGiarCOG02230. Archaea.
COG0066. LUCA.
InParanoidiQ58673.
KOiK01704.
OMAiPFLRFNS.
PhylomeDBiQ58673.

Family and domain databases

CDDicd01577. IPMI_Swivel. 1 hit.
Gene3Di3.20.19.10. 1 hit.
HAMAPiMF_01032. LeuD_type2. 1 hit.
InterProiIPR015937. Acoase/IPM_deHydtase.
IPR015928. Aconitase/3IPM_dehydase_swvl.
IPR000573. AconitaseA/IPMdHydase_ssu_swvl.
IPR033940. IPMI_Swivel.
IPR011827. LeuD_type2/HacB/DmdB.
[Graphical view]
PANTHERiPTHR11670. PTHR11670. 1 hit.
PfamiPF00694. Aconitase_C. 1 hit.
[Graphical view]
SUPFAMiSSF52016. SSF52016. 1 hit.
TIGRFAMsiTIGR02087. LEUD_arch. 1 hit.

Sequencei

Sequence statusi: Complete.

Q58673-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRSIIKGRVW KFGNNVDTDA ILPARYLVYT KPEELAQFVM TGADPDFPKK
60 70 80 90 100
VKPGDIIVGG KNFGCGSSRE HAPLGLKGAG ISCVIAESFA RIFYRNAINV
110 120 130 140 150
GLPLIECKGI SEKVNEGDEL EVNLETGEIK NLTTGEVLKG QKLPEFMMEI
160
LEAGGLMPYL KKKMAESQ
Length:168
Mass (Da):18,377
Last modified:November 1, 1996 - v1
Checksum:iA53C2CA883B6CCD7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA. Translation: AAB99283.1.
PIRiD64459.

Genome annotation databases

EnsemblBacteriaiAAB99283; AAB99283; MJ_1277.
KEGGimja:MJ_1277.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA. Translation: AAB99283.1.
PIRiD64459.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3VBAX-ray2.00A/B/C/D/E/F1-168[»]
ProteinModelPortaliQ58673.
SMRiQ58673.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243232.MJ_1277.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB99283; AAB99283; MJ_1277.
KEGGimja:MJ_1277.

Phylogenomic databases

eggNOGiarCOG02230. Archaea.
COG0066. LUCA.
InParanoidiQ58673.
KOiK01704.
OMAiPFLRFNS.
PhylomeDBiQ58673.

Enzyme and pathway databases

UniPathwayiUPA00047; UER00067.
UPA00048; UER00071.
BioCyciMetaCyc:MONOMER-13648.
SABIO-RKQ58673.

Family and domain databases

CDDicd01577. IPMI_Swivel. 1 hit.
Gene3Di3.20.19.10. 1 hit.
HAMAPiMF_01032. LeuD_type2. 1 hit.
InterProiIPR015937. Acoase/IPM_deHydtase.
IPR015928. Aconitase/3IPM_dehydase_swvl.
IPR000573. AconitaseA/IPMdHydase_ssu_swvl.
IPR033940. IPMI_Swivel.
IPR011827. LeuD_type2/HacB/DmdB.
[Graphical view]
PANTHERiPTHR11670. PTHR11670. 1 hit.
PfamiPF00694. Aconitase_C. 1 hit.
[Graphical view]
SUPFAMiSSF52016. SSF52016. 1 hit.
TIGRFAMsiTIGR02087. LEUD_arch. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiLEUD_METJA
AccessioniPrimary (citable) accession number: Q58673
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: November 1, 1996
Last modified: November 30, 2016
This is version 109 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, Complete proteome, Reference proteome

Documents

  1. Methanococcus jannaschii
    Methanococcus jannaschii: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.