2W4D

Acylphosphatase variant G91A from Pyrococcus horikoshii

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

A Rigidifying Salt-Bridge Favors the Activity of Thermophilic Enzyme at High Temperatures at the Expense of Low-Temperature Activity.

Lam, S.Y., Yeung, R.C.Y., Yu, T., Sze, K., Wong, K.B.

(2011) PLoS Biol 9: 1027

  • DOI: https://doi.org/10.1371/journal.pbio.1001027
  • Primary Citation of Related Structures:  
    2VH7, 2W4C, 2W4D, 2W4P

  • PubMed Abstract: 

    Thermophilic enzymes are often less active than their mesophilic homologues at low temperatures. One hypothesis to explain this observation is that the extra stabilizing interactions increase the rigidity of thermophilic enzymes and hence reduce their activity. Here we employed a thermophilic acylphosphatase from Pyrococcus horikoshii and its homologous mesophilic acylphosphatase from human as a model to study how local rigidity of an active-site residue affects the enzymatic activity.

    • Organizational Affiliation: 

    School of Life Sciences, Centre for Protein Science and Crystallography, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ACYLPHOSPHATASE
A, B, C, D, E
A, B, C, D, E, F
90Pyrococcus horikoshiiMutation(s): 1 
EC: 3.6.1.7
UniProt
Find proteins for P84142 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore P84142 
Go to UniProtKB:  P84142
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84142
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4
Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
L [auth B]
N [auth C]
P [auth D]
I [auth A],
J [auth A],
L [auth B],
N [auth C],
P [auth D],
Q [auth E],
S [auth F]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
K
Query on K
Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
K [auth B]
M [auth C]
O [auth D]
G [auth A],
H [auth A],
K [auth B],
M [auth C],
O [auth D],
R [auth F]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.375α = 90
b = 153.526β = 90
c = 46.041γ = 90
Software Package:
Software NamePurpose
CNSrefinement
d*TREKdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2012-02-01
    Changes: Database references, Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Source and taxonomy
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description