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PDBsum entry 1sqm

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protein ligands metals links
Hydrolase PDB id
1sqm
Jmol
Contents
Protein chain
610 a.a. *
Ligands
IMD
ACY
Metals
_ZN
_YB
Waters ×598
* Residue conservation analysis
PDB id:
1sqm
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.
Resolution:
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
Date:
19-Mar-04     Release date:   03-Aug-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P09960  (LKHA4_HUMAN) -  Leukotriene A-4 hydrolase
Seq:
Struc:
 
Seq:
Struc:
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.3.3.2.6  - 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
(7E,9E,11Z,14Z)-(5S,6S)-5,6-epoxyicosa-7,9,11,14-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.
 
  ABSTRACT  
 
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 www.povray.org).
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.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.