4Y0J

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


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.00 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 U S A 112: 5673-5678

  • DOI: 10.1073/pnas.1502255112
  • Primary Citation of Related Structures:  
    4Q49, 4Y0J

  • 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 residues ...

    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; zoe.fisher@esss.se.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbonic anhydrase 2A258Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00918
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: NEUTRON DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.263 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.75α = 90
b = 41.68β = 104.67
c = 72.95γ = 90
Software Package:
Software NamePurpose
d*TREKdata reduction
CNSrefinement
Cootmodel building
CNSphasing
SCALAdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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