PDBsum entry 1sqm

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Hydrolase PDB id
Protein chain
610 a.a. *
Waters ×598
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Structure of [r563a] leukotriene a4 hydrolase
Structure: Leukotriene a-4 hydrolase. Chain: a. Synonym: lta-4 hydrolase. Leukotriene a(4) hydrolase. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: lta4h, lta4. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.30Å     R-factor:   0.190     R-free:   0.230
Authors: F.O.T.Tholander,P.C.Rudberg,M.M.G.M.Thunnissen, J.Z.Haeggstrom
Key ref:
P.C.Rudberg et al. (2004). Leukotriene A4 hydrolase: identification of a common carboxylate recognition site for the epoxide hydrolase and aminopeptidase substrates. J Biol Chem, 279, 27376-27382. PubMed id: 15078870 DOI: 10.1074/jbc.M401031200
19-Mar-04     Release date:   03-Aug-04    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P09960  (LKHA4_HUMAN) -  Leukotriene A-4 hydrolase
611 a.a.
610 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Leukotriene-A(4) hydrolase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (7E,9E,11Z,14Z)-(5S,6S)-5,6-epoxyicosa-7,9,11,14-tetraenoate + H2O = (6Z,8E,10E,14Z)-(5S,12R)-5,12-dihydroxyicosa-6,8,10,14-tetraenoate
+ H(2)O
= (6Z,8E,10E,14Z)-(5S,12R)-5,12-dihydroxyicosa-6,8,10,14-tetraenoate
      Cofactor: Zn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   4 terms 
  Biological process     small molecule metabolic process   7 terms 
  Biochemical function     hydrolase activity     9 terms  


    Key reference    
DOI no: 10.1074/jbc.M401031200 J Biol Chem 279:27376-27382 (2004)
PubMed id: 15078870  
Leukotriene A4 hydrolase: identification of a common carboxylate recognition site for the epoxide hydrolase and aminopeptidase substrates.
P.C.Rudberg, F.Tholander, M.Andberg, M.M.Thunnissen, J.Z.Haeggström.
Leukotriene (LT) A(4) hydrolase is a bifunctional zinc metalloenzyme, which converts LTA(4) into the neutrophil chemoattractant LTB(4) and also exhibits an anion-dependent aminopeptidase activity. In the x-ray crystal structure of LTA(4) hydrolase, Arg(563) and Lys(565) are found at the entrance of the active center. Here we report that replacement of Arg(563), but not Lys(565), leads to complete abrogation of the epoxide hydrolase activity. However, mutations of Arg(563) do not seem to affect substrate binding strength, because values of K(i) for LTA(4) are almost identical for wild type and (R563K)LTA(4) hydrolase. These results are supported by the 2.3-A crystal structure of (R563A)LTA(4) hydrolase, which does not reveal structural changes that can explain the complete loss of enzyme function. For the aminopeptidase reaction, mutations of Arg(563) reduce the catalytic activity (V(max) = 0.3-20%), whereas mutations of Lys(565) have limited effect on catalysis (V(max) = 58-108%). However, in (K565A)- and (K565M)LTA(4) hydrolase, i.e. mutants lacking a positive charge, values of the Michaelis constant for alanine-p-nitroanilide increase significantly (K(m) = 480-640%). Together, our data indicate that Arg(563) plays an unexpected, critical role in the epoxide hydrolase reaction, presumably in the positioning of the carboxylate tail to ensure perfect substrate alignment along the catalytic elements of the active site. In the aminopeptidase reaction, Arg(563) and Lys(565) seem to cooperate to provide sufficient binding strength and productive alignment of the substrate. In conclusion, Arg(563) and Lys(565) possess distinct roles as carboxylate recognition sites for two chemically different substrates, each of which is turned over in separate enzymatic reactions catalyzed by LTA(4) hydrolase.
  Selected figure(s)  
Figure 2.
FIG. 2. Stereo view of loop 562-566 of the (R563A)LTA4H in F[obs]-F[calc] electron density. For the calculation of F[calc] and [calc], the atoms of loop 562-566 were excluded from the calculations. The density was contoured at the 3 level. The picture was made using Molscript (59), Glr (L. Esser and J. Deisenhofer, personal communications), and POV-Ray (available at
Figure 3.
FIG. 3. Models for the catalytic mechanisms in LTA4H. A, in the epoxide hydrolase reaction a water molecule is polarized by Glu271 and the catalytic zinc (25), to promote an acid-induced opening of the epoxide. This reaction yields a carbocation intermediate and finally a nucleophilic attack, guided by Asp375, occurs at C-12 (20). In this reaction Arg563 serves in carboxylate recognition and substrate alignment. Dotted lines indicate interactions between important groups. B, in the aminopeptidase reaction, Glu271 is involved in N-terminal recognition (25), Glu296 and the catalytic zinc act as base catalyst, and Tyr383 functions as proton donor (60, 61). Here, Arg563 and Lys565 serve together in carboxylate recognition. Dotted lines indicate interactions between important groups. See text for further details.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 27376-27382) copyright 2004.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18157165 B.J.Whittle, C.Varga, A.Berko, K.Horvath, A.Posa, J.P.Riley, K.A.Lundeen, A.M.Fourie, and P.J.Dunford (2008).
Attenuation of inflammation and cytokine production in rat colitis by a novel selective inhibitor of leukotriene A4 hydrolase.
  Br J Pharmacol, 153, 983-991.  
15748653 J.W.Newman, C.Morisseau, and B.D.Hammock (2005).
Epoxide hydrolases: their roles and interactions with lipid metabolism.
  Prog Lipid Res, 44, 1.  
16286653 S.C.Chang, F.Momburg, N.Bhutani, and A.L.Goldberg (2005).
The ER aminopeptidase, ERAP1, trims precursors to lengths of MHC class I peptides by a "molecular ruler" mechanism.
  Proc Natl Acad Sci U S A, 102, 17107-17112.  
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