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PDBsum entry 1y6v

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1y6v
Jmol
Contents
Protein chains
449 a.a. *
Ligands
PO4 ×2
SO4 ×2
Metals
_CO ×6
Waters ×712
* Residue conservation analysis
PDB id:
1y6v
Name: Hydrolase
Title: Structure of e. Coli alkaline phosphatase in presence of cobalt at 1.60 a resolution
Structure: Alkaline phosphatase. Chain: a, b. Synonym: apase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: phoa. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.60Å     R-factor:   0.191     R-free:   0.212
Authors: J.Wang,K.Stieglitz,E.R.Kantrowitz
Key ref:
J.Wang et al. (2005). Metal specificity is correlated with two crucial active site residues in Escherichia coli alkaline phosphatase. Biochemistry, 44, 8378-8386. PubMed id: 15938627 DOI: 10.1021/bi050155p
Date:
07-Dec-04     Release date:   21-Jun-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00634  (PPB_ECOLI) -  Alkaline phosphatase
Seq:
Struc:
471 a.a.
449 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.3.1  - Alkaline phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: A phosphate monoester + H2O = an alcohol + phosphate
phosphate monoester
+ H(2)O
= alcohol
+
phosphate
Bound ligand (Het Group name = PO4)
corresponds exactly
      Cofactor: Magnesium; Zinc
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     periplasmic space   2 terms 
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     10 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi050155p Biochemistry 44:8378-8386 (2005)
PubMed id: 15938627  
 
 
Metal specificity is correlated with two crucial active site residues in Escherichia coli alkaline phosphatase.
J.Wang, K.A.Stieglitz, E.R.Kantrowitz.
 
  ABSTRACT  
 
Escherichia coli alkaline phosphatase exhibits maximal activity when Zn(2+) fills the M1 and M2 metal sites and Mg(2+) fills the M3 metal site. When other metals replace the zinc and magnesium, the catalytic efficiency is reduced by more than 5000-fold. Alkaline phosphatases from organisms such as Thermotoga maritima and Bacillus subtilis require cobalt for maximal activity and function poorly with zinc and magnesium. Previous studies have shown that the D153H alkaline phosphatase exhibited very little activity in the presence of cobalt, while the K328W and especially the D153H/K328W mutant enzymes can use cobalt for catalysis. To understand the structural basis for the altered metal specificity and the ability of the D153H/K328W enzyme to utilize cobalt for catalysis, we determined the structures of the inactive wild-type E. coli enzyme with cobalt (WT_Co) and the structure of the active D153H/K328W enzyme with cobalt (HW_Co). The structural data reveal differences in the metal coordination and in the strength of the interaction with the product phosphate (P(i)). Since release of P(i) is the slow step in the mechanism at alkaline pH, the enhanced binding of P(i) in the WT_Co structure explains the observed decrease in activity, while the weakened binding of P(i) in the HW_Co structure explains the observed increase in activity. These alterations in P(i) affinity are directly related to alterations in the coordination of the metals in the active site of the enzyme.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20926683 C.Maurer, S.Panahandeh, A.C.Jungkamp, M.Moser, and M.Müller (2010).
TatB functions as an oligomeric binding site for folded Tat precursor proteins.
  Mol Biol Cell, 21, 4151-4161.  
  19916164 D.Koutsioulis, A.Lyskowski, S.Mäki, E.Guthrie, G.Feller, V.Bouriotis, and P.Heikinheimo (2010).
Coordination sphere of the third metal site is essential to the activity and metal selectivity of alkaline phosphatases.
  Protein Sci, 19, 75-84.
PDB codes: 2w5v 2w5w 2w5x
17008720 J.Wang, and E.R.Kantrowitz (2006).
Trapping the tetrahedral intermediate in the alkaline phosphatase reaction by substitution of the active site serine with threonine.
  Protein Sci, 15, 2395-2401.
PDB codes: 2g9y 2ga3
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.