4Y0J

H/D exchanged human carbonic anhydrase II pH 6 room temperature neutron crystal structure.


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.263 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history

Literature

Joint neutron crystallographic and NMR solution studies of Tyr residue ionization and hydrogen bonding: Implications for enzyme-mediated proton transfer.

Michalczyk, R.Unkefer, C.J.Bacik, J.P.Schrader, T.E.Ostermann, A.Kovalevsky, A.Y.McKenna, R.Fisher, S.Z.

(2015) Proc.Natl.Acad.Sci.USA 112: 5673-5678

  • DOI: 10.1073/pnas.1502255112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human carbonic anhydrase II (HCA II) uses a Zn-bound OH(-)/H2O mechanism to catalyze the reversible hydration of CO2. This catalysis also involves a separate proton transfer step, mediated by an ordered solvent network coordinated by hydrophilic resi ...

    Human carbonic anhydrase II (HCA II) uses a Zn-bound OH(-)/H2O mechanism to catalyze the reversible hydration of CO2. This catalysis also involves a separate proton transfer step, mediated by an ordered solvent network coordinated by hydrophilic residues. One of these residues, Tyr7, was previously shown to be deprotonated in the neutron crystal structure at pH 10. This observation indicated that Tyr7 has a perturbed pKa compared with free tyrosine. To further probe the pKa of this residue, NMR spectroscopic measurements of [(13)C]Tyr-labeled holo HCA II (with active-site Zn present) were preformed to titrate all Tyr residues between pH 5.4-11.0. In addition, neutron studies of apo HCA II (with Zn removed from the active site) at pH 7.5 and holo HCA II at pH 6 were conducted. This detailed interrogation of tyrosines in HCA II by NMR and neutron crystallography revealed a significantly lowered pKa of Tyr7 and how pH and Tyr proximity to Zn affect hydrogen-bonding interactions.


    Organizational Affiliation

    Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase 2
A
258Homo sapiensMutation(s): 0 
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
DOD
Query on DOD

Download SDF File 
Download CCD File 
A
DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.263 
Software Package:
Software NamePurpose
CNSphasing
d*TREKdata reduction
Cootmodel building
CNSrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-02-06 
  • Released Date: 2015-04-22 
  • Deposition Author(s): Fisher, S.Z.

Revision History 

  • Version 1.0: 2015-04-22
    Type: Initial release
  • Version 1.1: 2015-05-06
    Type: Database references
  • Version 1.2: 2015-05-13
    Type: Database references
  • Version 2.0: 2018-04-04
    Type: Advisory, Atomic model, Data collection, Derived calculations
  • Version 2.1: 2018-11-14
    Type: Data collection