PDBsum entry 3vba

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protein Protein-protein interface(s) links
Lyase PDB id
Protein chains
(+ 0 more) 169 a.a.
Waters ×721
PDB id:
Name: Lyase
Title: Crystal structure of methanogen 3-isopropylmalate isomerase subunit
Structure: Isopropylmalate/citramalate isomerase small subun chain: a, b, c, d, e, f. Synonym: (r)-2-methylmalate dehydratase, (r)-citramalate de 3-isopropylmalate dehydratase, alpha-isopropylmalate dehydr citraconate hydratase, isopropylmalate isomerase, ipmi, mal hydratase, malease. Engineered: yes
Source: Methanocaldococcus jannaschii. Organism_taxid: 243232. Strain: dsm 2661. Gene: leud, mj1277. Expressed in: escherichia coli. Expression_system_taxid: 562
2.00Å     R-factor:   0.199     R-free:   0.244
Authors: K.Y.Hwang,E.H.Lee
Key ref: E.H.Lee et al. (2012). Crystal structure of LeuD from Methanococcus jannaschii. Biochem Biophys Res Commun, 419, 160-164. PubMed id: 22326391 DOI: 10.1016/j.bbrc.2012.01.125
02-Jan-12     Release date:   14-Nov-12    
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Protein chains
Pfam   ArchSchema ?
Q58673  (LEUD_METJA) -  Isopropylmalate/citramalate isomerase small subunit
168 a.a.
169 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: E.C.  - Maleate hydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (R)-malate = maleate + H2O
= maleate
+ H(2)O
   Enzyme class 3: E.C.  - 3-isopropylmalate dehydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Reaction: (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate
= (2S)-2-isopropylmalate
      Cofactor: Iron-sulfur
   Enzyme class 4: E.C.  - (R)-2-methylmalate dehydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (R)-2-methylmalate = 2-methylmaleate + H2O
= 2-methylmaleate
+ H(2)O
      Cofactor: Fe cation
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     3-isopropylmalate dehydratase complex   1 term 
  Biological process     metabolic process   5 terms 
  Biochemical function     lyase activity     4 terms  


DOI no: 10.1016/j.bbrc.2012.01.125 Biochem Biophys Res Commun 419:160-164 (2012)
PubMed id: 22326391  
Crystal structure of LeuD from Methanococcus jannaschii.
E.H.Lee, Y.W.Cho, K.Y.Hwang.
3-Isopropylmalate/citramalate (IPM) isomerase catalyzes the second step in the leucine biosynthesis pathway. IPM isomerase from Methanococcus jannaschii is a complex protein consisting of a large (MjLeuC) and a small subunit (MjLeuD). It has broad substrate specificity, unlike other bacterial IPM isomerases. In order to understand the reasons for this broad substrate specificity, we determined the crystal structure of MjLeuD at a resolution of 2.0 Å. The asymmetric unit contained 6 molecules of LeuD, including three homodimers. The overall structure had a β/β/α sandwich-fold consisting of 8 α-helices and 7 β-strands. The C-terminal helix, which is important in homodimer formation, showed conformational differences between two homodimer forms of MjLeuD. In addition, we identified a hydrophobic residue (Val28) near the substrate recognition region that may explain the broad substrate specificity of IPM isomerase. Therefore, we suggest that LeuD proteins can be divided into 2 subfamilies, LeuD subfamilies 1 and 2, which show differences in overall structure and in the substrate recognition region.