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PDBsum entry 1gxs

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protein ligands Protein-protein interface(s) links
Lyase PDB id
1gxs
Jmol
Contents
Protein chains
267 a.a. *
158 a.a. *
Ligands
BEZ ×2
DKA ×2
NAG-NAG-FUL ×2
NAG ×2
Waters ×331
* Residue conservation analysis
PDB id:
1gxs
Name: Lyase
Title: Crystal structure of hydroxynitrile lyase from sorghum bicolor in complex with inhibitor benzoic acid: a novel cyanogenic enzyme
Structure: P-(s)-hydroxymandelonitrile lyase chain a. Chain: a, c. Synonym: hnl, hydroxynitrile lyase. Other_details: isoenzyme ii. P-(s)-hydroxymandelonitrile lyase chain b. Chain: b, d. Synonym: hnl, hydroxynitrile lyase. Other_details: isoenzyme ii
Source: Sorghum bicolor. Sorghum. Organism_taxid: 4558. Tissue: primary leaves of seedlings. Tissue: primary leaves of seedlings
Biol. unit: Tetramer (from PDB file)
Resolution:
2.30Å     R-factor:   0.165     R-free:   0.222
Authors: H.Lauble,B.Miehlich,S.Foerster,H.Wajant,F.Effenberger
Key ref:
H.Lauble et al. (2002). Crystal structure of hydroxynitrile lyase from Sorghum bicolor in complex with the inhibitor benzoic acid: a novel cyanogenic enzyme. Biochemistry, 41, 12043-12050. PubMed id: 12356304 DOI: 10.1021/bi020300o
Date:
11-Apr-02     Release date:   01-Oct-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P52708  (HNLS_SORBI) -  P-(S)-hydroxymandelonitrile lyase
Seq:
Struc:
510 a.a.
267 a.a.*
Protein chains
Pfam   ArchSchema ?
P52708  (HNLS_SORBI) -  P-(S)-hydroxymandelonitrile lyase
Seq:
Struc:
510 a.a.
158 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 7 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: E.C.4.1.2.11  - Hydroxymandelonitrile lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (S)-4-hydroxymandelonitrile = cyanide + 4-hydroxybenzaldehyde
(S)-4-hydroxymandelonitrile
= cyanide
+
4-hydroxybenzaldehyde
Bound ligand (Het Group name = BEZ)
matches with 80.00% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     serine-type carboxypeptidase activity     1 term  

 

 
    reference    
 
 
DOI no: 10.1021/bi020300o Biochemistry 41:12043-12050 (2002)
PubMed id: 12356304  
 
 
Crystal structure of hydroxynitrile lyase from Sorghum bicolor in complex with the inhibitor benzoic acid: a novel cyanogenic enzyme.
H.Lauble, B.Miehlich, S.Förster, H.Wajant, F.Effenberger.
 
  ABSTRACT  
 
The crystal structure of the hydroxynitrile lyase from Sorghum bicolor (SbHNL) in complex with the inhibitor benzoic acid has been determined at 2.3 A resolution and refined to a crystallographic R-factor of 16.5%. The SbHNL sequence places the enzyme in the alpha/beta hydrolase family where the active site nucleophile is predicted to be organized in a characteristic pentapeptide motif which is part of the active site strand-turn-helix motif. In SbHNL, however, a unique two-amino acid deletion is next to the putative active site Ser158, removing thereby the putative oxyanion hole-forming Tyr residue. The presented X-ray structure shows that the overall folding pattern of SbHNL is similar to that of the closely related wheat serine carboxypeptidase (CPD-WII); however, the deletion in SbHNL is forcing the putative active site residues away from the expected hydrolase binding site toward a small hydrophobic cleft, which also contains the inhibitor benzoic acid, defining thereby a completely different SbHNL active site architecture where the traditional view of a classic triad is not given any more. Rather, we propose a mechanism involving general base catalysis by the carboxy-terminal Trp270 carboxyl group and proton transfer toward the leaving nitrile group by an active site water molecule. The unexpected interactions of the inhibitor with the new SbHNL active site also reveal the structural basis for the enzyme's limited substrate specificity. The implications of this structure on the evolution of catalysis in the hydroxynitrile lyase superfamily are discussed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19256550 I.Dreveny, A.S.Andryushkova, A.Glieder, K.Gruber, and C.Kratky (2009).
Substrate binding in the FAD-dependent hydroxynitrile lyase from almond provides insight into the mechanism of cyanohydrin formation and explains the absence of dehydrogenation activity.
  Biochemistry, 48, 3370-3377.
PDB codes: 3gdn 3gdp
19716614 J.N.Andexer, J.V.Langermann, U.Kragl, and M.Pohl (2009).
How to overcome limitations in biotechnological processes - examples from hydroxynitrile lyase applications.
  Trends Biotechnol, 27, 599-607.  
17607575 T.Purkarthofer, W.Skranc, C.Schuster, and H.Griengl (2007).
Potential and capabilities of hydroxynitrile lyases as biocatalysts in the chemical industry.
  Appl Microbiol Biotechnol, 76, 309-320.  
17031431 J.Andexer, J.K.Guterl, M.Pohl, and T.Eggert (2006).
A high-throughput screening assay for hydroxynitrile lyase activity.
  Chem Commun (Camb), (), 4201-4203.  
16115872 J.Ren, M.Kotaka, M.Lockyer, H.K.Lamb, A.R.Hawkins, and D.K.Stammers (2005).
GTP cyclohydrolase II structure and mechanism.
  J Biol Chem, 280, 36912-36919.
PDB codes: 2bz0 2bz1
14662384 M.Breuer, and B.Hauer (2003).
Carbon-carbon coupling in biotransformation.
  Curr Opin Biotechnol, 14, 570-576.  
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. Where a reference describes a PDB structure, the PDB codes are shown on the right.