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PDBsum entry 1rql

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1rql
Jmol
Contents
Protein chains
257 a.a. *
Ligands
VSO
Metals
_MG ×2
Waters ×145
* Residue conservation analysis
PDB id:
1rql
Name: Hydrolase
Title: Crystal structure of phosponoacetaldehyde hydrolase complexed with magnesium and the inhibitor vinyl sulfonate
Structure: Phosphonoacetaldehyde hydrolase. Chain: a, b. Synonym: phosphonatase. Engineered: yes
Source: Bacillus cereus. Organism_taxid: 1396. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.40Å     R-factor:   0.227     R-free:   0.282
Authors: M.C.Morais,G.Zhang,W.Zhang,D.B.Olsen,D.Dunaway-Mariano, K.N.Allen
Key ref:
M.C.Morais et al. (2004). X-ray crystallographic and site-directed mutagenesis analysis of the mechanism of Schiff-base formation in phosphonoacetaldehyde hydrolase catalysis. J Biol Chem, 279, 9353-9361. PubMed id: 14670958 DOI: 10.1074/jbc.M312345200
Date:
05-Dec-03     Release date:   20-Apr-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O31156  (PHNX_BACCE) -  Phosphonoacetaldehyde hydrolase
Seq:
Struc:
264 a.a.
257 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.3.11.1.1  - Phosphonoacetaldehyde hydrolase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Phosphonoacetaldehyde + H2O = acetaldehyde + phosphate
Phosphonoacetaldehyde
+ H(2)O
= acetaldehyde
+ phosphate
      Cofactor: Mg(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M312345200 J Biol Chem 279:9353-9361 (2004)
PubMed id: 14670958  
 
 
X-ray crystallographic and site-directed mutagenesis analysis of the mechanism of Schiff-base formation in phosphonoacetaldehyde hydrolase catalysis.
M.C.Morais, G.Zhang, W.Zhang, D.B.Olsen, D.Dunaway-Mariano, K.N.Allen.
 
  ABSTRACT  
 
Phosphonoacetaldehyde hydrolase (phosphonatase) catalyzes the hydrolytic P-C bond cleavage of phosphonoacetaldehyde (Pald) to form orthophosphate and acetaldehyde. The reaction proceeds via a Schiff-base intermediate formed between Lys-53 and the Pald carbonyl. The x-ray crystal structures of the wild-type phosphonatase complexed with Mg(II) alone or with Mg(II) plus vinylsulfonate (a phosphonoethylenamine analog) were determined to 2.8 and 2.4 A, respectively. These structures were used to determine the identity and positions of active site residues surrounding the Lys-53 ammonium group and the Pald carbonyl. These include Cys-22, His-56, Tyr-128, and Met-49. Site-directed mutagenesis was then employed to determine whether or not these groups participate in catalysis. Based on rate contributions, Tyr-128 and Cys-22 were eliminated as potential catalytic groups. The Lys-53 epsilon-amino group, positioned for reaction with the Pald carbonyl, forms a hydrogen bond with water 120. Water 120 is also within hydrogen bond distance of an imidazole nitrogen of His-56 and the sulfur atom of Met-49. Kinetic constants for mutants indicated that His-56 (1000-fold reduction in k(cat)/K(m) upon Ala substitution) and Met-49 (17,000-fold reduction in k(cat)/K(m) upon Leu substitution) function in catalysis of Schiff-base formation. Based on these results, it is proposed that a network of hydrogen bonds among Lys-53, water 120, His-56, and Met-49 facilitate proton transfer from Lys-53 to the carbinolamine intermediate. Comparison of the vinylsulfonate complex versus unliganded structures indicated that association of the cap and core domains is essential for the positioning of the Lys-53 for attack at the Pald carbonyl and that substrate binding at the core domain stabilizes cap domain binding.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. The reaction pathway of phosphonatase-catalyzed hydrolytic P-C bond cleavage of Pald.
Figure 2.
FIG. 2. Mechanism of Schiff-base formation between an amine and a ketone in aqueous solution (12).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 9353-9361) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20859643 P.V.Attwood, P.G.Besant, and M.J.Piggott (2011).
Focus on phosphoaspartate and phosphoglutamate.
  Amino Acids, 40, 1035-1051.  
18802516 B.Szefczyk (2008).
Towards understanding phosphonoacetaldehyde hydrolase: an alternative mechanism involving proton transfer that triggers P-C bond cleavage.
  Chem Commun (Camb), (), 4162-4164.  
17803765 J.P.Quinn, A.N.Kulakova, N.A.Cooley, and J.W.McGrath (2007).
New ways to break an old bond: the bacterial carbon-phosphorus hydrolases and their role in biogeochemical phosphorus cycling.
  Environ Microbiol, 9, 2392-2400.  
17070898 S.D.Lahiri, G.Zhang, D.Dunaway-Mariano, and K.N.Allen (2006).
Diversification of function in the haloacid dehalogenase enzyme superfamily: The role of the cap domain in hydrolytic phosphoruscarbon bond cleavage.
  Bioorg Chem, 34, 394-409.
PDB codes: 2iof 2ioh
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.