3GZ0

Apo-human carbonic anhydrase II revisited: Implications of the loss of a metal in protein structure, stability and solvent network


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.140 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Apo-Human Carbonic Anhydrase II Revisited: Implications of the Loss of a Metal in Protein Structure, Stability, and Solvent Network .

Avvaru, B.S.Busby, S.A.Chalmers, M.J.Griffin, P.R.Venkatakrishnan, B.Agbandje-McKenna, M.Silverman, D.N.McKenna, R.

(2009) Biochemistry 48: 7365-7372

  • DOI: 10.1021/bi9007512
  • Primary Citation of Related Structures:  
    3GZ0

  • PubMed Abstract: 
  • Human carbonic anhydrase II (HCA II) is a monomeric zinc-containing metalloenzyme that catalyzes the hydration of CO(2) to form bicarbonate and a proton. The properties of the zinc have been extensively elucidated in catalysis but less well studied as a contributor to structure and stability ...

    Human carbonic anhydrase II (HCA II) is a monomeric zinc-containing metalloenzyme that catalyzes the hydration of CO(2) to form bicarbonate and a proton. The properties of the zinc have been extensively elucidated in catalysis but less well studied as a contributor to structure and stability. Apo-HCA II (without zinc) was prepared and compared to holo-HCA II: in crystallographic structural features, in backbone amide H/D exchange, and in thermal stability. The removal of zinc from the active site has no effect on either the topological fold of the enzyme or the ordered water network in the active site. However, the removal of the zinc alters the collective electrostatics of the apo-HCA II that result in the following differences from that of the holoenzyme: (1) the main thermal unfolding transition of the apo-HCA II is lowered by 8 degrees C, (2) the relative increase in thermal mobility of atoms of the apo-HCA II was not observed in the vicinity of the active site but manifested on the surface of the enzyme, and (3) the side chain of His 64, the proton shuttle residue that sits on the rim of the active site, is oriented outward and is associated with additional ordered "external" waters, as opposed to a near equal inward and outward orientation in the holo-HCA II.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbonic anhydrase 2A259Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens)
Explore P00918 
Go to UniProtKB:  P00918
PHAROS:  P00918
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.140 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.737α = 90
b = 41.623β = 104.59
c = 72.821γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance