2W4P

Human common-type acylphosphatase variant, A99G

• PDB DOI:  https://doi.org/10.2210/pdb2W4P/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-11-29 Released: 2009-12-29 
• Deposition Author(s): Lam, S.Y., Sze, K.H., Wong, K.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.241 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 

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.H., Wong, K.B.

(2011) PLoS Biol 9: 1027

• PubMed: 21423654 
• 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.

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Related Citations: 

• Crystallization and Preliminary Crystallographic Analysis of Human Common-Type Acylphosphatase.
  Yeung, R.C.Y., Lam, S.Y., Wong, K.
  (2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 80

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 11.3 kDa 
• Atom Count: 859 
• Modelled Residue Count: 96 
• Deposited Residue Count: 99 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACYLPHOSPHATASE-1	A	99	Homo sapiens	Mutation(s): 1  Gene Names: ACYP1, ACYPE EC: 3.6.1.7
UniProt & NIH Common Fund Data Resources
Find proteins for P07311 (Homo sapiens) Explore P07311  Go to UniProtKB:  P07311
PHAROS:  P07311

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.241 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.206	α = 90
b = 57.339	β = 90
c = 58.777	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-29 
Deposition Author(s): Lam, S.Y., Sze, K.H., Wong, K.B.

Revision History  

• Version 1.0: 2009-12-29
  Type: Initial release
  
• Version 1.1: 2012-02-01
  Changes: Database references, Derived calculations, Version format compliance