4Q49

Room temperature neutron crystal structure of apo human carbonic anhydrase at pH 7.5


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.6 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

    Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge TN 37831; and.,Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545;,Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich GmbH, 85747 Garching, Germany;,Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545; zoe.fisher@esss.se.,Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universität München, 85748 Garching, Germany;,Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase 2
A
260Homo 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: 1.8 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.187 
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
nCNSrefinement
CNSrefinement
DENZOdata reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-25
    Type: Initial release
  • Version 1.1: 2015-04-22
    Type: Database references
  • Version 1.2: 2015-05-06
    Type: Database references
  • Version 1.3: 2015-05-20
    Type: Database references
  • Version 1.4: 2017-11-22
    Type: Refinement description
  • Version 1.5: 2018-04-25
    Type: Data collection
  • Version 1.6: 2018-06-13
    Type: Data collection