1W2I

Crystal structuore of acylphosphatase from Pyrococcus horikoshii complexed with formate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of a Hyperthermophilic Archaeal Acylphosphatase from Pyrococcus Horikoshii-Structural Insights Into Enzymatic Catalysis, Thermostability, and Dimerization

Cheung, Y.Y.Lam, S.Y.Chu, W.K.Allen, M.D.Bycroft, M.Wong, K.B.

(2005) Biochemistry 44: 4601

  • DOI: 10.1021/bi047832k
  • Also Cited By: 2W4D

  • PubMed Abstract: 
  • Acylphosphatases catalyze the hydrolysis of the carboxyl-phosphate bond in acyl phosphates. Although acylphosphatase-like sequences are found in all three domains of life, no structure of acylphosphatase has been reported for bacteria and archaea so ...

    Acylphosphatases catalyze the hydrolysis of the carboxyl-phosphate bond in acyl phosphates. Although acylphosphatase-like sequences are found in all three domains of life, no structure of acylphosphatase has been reported for bacteria and archaea so far. Here, we report the characterization of enzymatic activities and crystal structure of an archaeal acylphosphatase. A putative acylphosphatase gene (PhAcP) was cloned from the genomic DNA of Pyrococcus horikoshii and was expressed in Escherichia coli. Enzymatic parameters of the recombinant PhAcP were measured using benzoyl phosphate as the substrate. Our data suggest that, while PhAcP is less efficient than other mammalian homologues at 25 degrees C, the thermophilic enzyme is fully active at the optimal growth temperature (98 degrees C) of P. horikoshii. PhAcP is extremely stable; its apparent melting temperature was 111.5 degrees C and free energy of unfolding at 25 degrees C was 54 kJ mol(-)(1). The 1.5 A crystal structure of PhAcP adopts an alpha/beta sandwich fold that is common to other acylphosphatases. PhAcP forms a dimer in the crystal structure via antiparallel association of strand 4. Structural comparison to mesophilic acylphosphatases reveals significant differences in the conformation of the L5 loop connecting strands 4 and 5. The extreme thermostability of PhAcP can be attributed to an extensive ion-pair network consisting of 13 charge residues on the beta sheet of the protein. The reduced catalytic efficiency of PhAcP at 25 degrees C may be due to a less flexible active-site residue, Arg20, which forms a salt bridge to the C-terminal carboxyl group. New insights into catalysis were gained by docking acetyl phosphate to the active site of PhAcP.


    Related Citations: 
    • Crystallization and Preliminary Crystallographic Analysis of an Acylphosphatase from the Hyperthermophilic Archaeon Pyrococcus Horikoshii
      Cheung, Y.Y.,Allen, M.D.,Bycroft, M.,Wong, K.B.
      (2004) Acta Crystallogr.,Sect.D 60: 1308


    Organizational Affiliation

    Department of Biochemistry, The Chinese University of Hong Kong, Hong Kong, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ACYLPHOSPHATASE
A, B
91Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)Gene Names: acyP
EC: 3.6.1.7
Find proteins for P84142 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Go to UniProtKB:  P84142
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
A, B
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.166 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 85.336α = 90.00
b = 85.336β = 90.00
c = 75.650γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-04
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance