4HEY

Activity Enhancers of H64A Variant of Human Carbonic Anhydrase II Possess Multiple Binding Sites within and around the Enzyme Structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural insight into activity enhancement and inhibition of H64A carbonic anhydrase II by imidazoles.

Aggarwal, M.Kondeti, B.Tu, C.Maupin, C.M.Silverman, D.N.McKenna, R.

(2014) IUCrJ 1: 129-135

  • DOI: 10.1107/S2052252514004096
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human carbonic anhydrases (CAs) are zinc metalloenzymes that catalyze the hydration and dehydration of CO2 and HCO3 (-), respectively. The reaction follows a ping-pong mechanism, in which the rate-limiting step is the transfer of a proton from the zi ...

    Human carbonic anhydrases (CAs) are zinc metalloenzymes that catalyze the hydration and dehydration of CO2 and HCO3 (-), respectively. The reaction follows a ping-pong mechanism, in which the rate-limiting step is the transfer of a proton from the zinc-bound solvent (OH(-)/H2O) in/out of the active site via His64, which is widely believed to be the proton-shuttling residue. The decreased catalytic activity (∼20-fold lower with respect to the wild type) of a variant of CA II in which His64 is replaced with Ala (H64A CA II) can be enhanced by exogenous proton donors/acceptors, usually derivatives of imidazoles and pyridines, to almost the wild-type level. X-ray crystal structures of H64A CA II in complex with four imidazole derivatives (imidazole, 1--methylimidazole, 2--methylimidazole and 4-methylimidazole) have been determined and reveal multiple binding sites. Two of these imidazole binding sites have been identified that mimic the positions of the 'in' and 'out' rotamers of His64 in wild-type CA II, while another directly inhibits catalysis by displacing the zinc-bound solvent. The data presented here not only corroborate the importance of the imidazole side chain of His64 in proton transfer during CA catalysis, but also provide a complete structural understanding of the mechanism by which imidazoles enhance (and inhibit when used at higher concentrations) the activity of H64A CA II.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Florida , PO Box 100245, Gainesville, FL 32610, USA.,Department of Chemical and Biological Engineering, Colorado School of Mines , 1500 Illinois Street, Golden, CO 80401, USA.,Department of Pharmacology and Therapeutics, University of Florida , PO Box 100247, Gainesville, FL 32610, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase 2
A
260Homo sapiensMutation(s): 1 
Gene Names: CA2
EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens)
Go to Gene View: CA2
Go to UniProtKB:  P00918
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
4MZ
Query on 4MZ

Download SDF File 
Download CCD File 
A
4-METHYLIMIDAZOLE
C4 H6 N2
XLSZMDLNRCVEIJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.143 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.418α = 90.00
b = 41.334β = 104.44
c = 71.958γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PHENIXphasing
DENZOdata reduction
ADSCdata collection
HKL-2000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2014-03-12
    Type: Database references
  • Version 1.2: 2014-08-20
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description