3RGE

Crystal structure of the W5H mutant of human carbonic anhydrase II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.096 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.141 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure and catalysis by carbonic anhydrase II: role of active-site tryptophan 5.

Mikulski, R.Domsic, J.F.Ling, G.Tu, C.Robbins, A.H.Silverman, D.N.McKenna, R.

(2011) Arch.Biochem.Biophys. 516: 97-102

  • DOI: 10.1016/j.abb.2011.09.011
  • Primary Citation of Related Structures:  3RG3, 3RG4

  • PubMed Abstract: 
  • The tryptophan residue Trp5, highly conserved in the α class of carbonic anhydrases including human carbonic anhydrase II (HCA II), is positioned at the entrance of the active site cavity and forms a π-stacking interaction with the imidazole ring of ...

    The tryptophan residue Trp5, highly conserved in the α class of carbonic anhydrases including human carbonic anhydrase II (HCA II), is positioned at the entrance of the active site cavity and forms a π-stacking interaction with the imidazole ring of the proton shuttle His64 in its outward orientation. We have observed that replacement of Trp5 in HCA II caused significant structural changes, as determined by X-ray diffraction, in the conformation of 11 residues at the N-terminus and in the orientation of the proton shuttle residue His64. Most significantly, two variants W5H and W5E HCA II had His64 predominantly outward in orientation, while W5F and wild type showed the superposition of both outward and inward orientations in crystal structures. Although Trp5 influences the orientation of the proton shuttle His64, this orientation had no significant effect on the rate constant for proton transfer near 1μs(-1), determined by exchange of (18)O between CO(2) and water measured by mass spectrometry. The apparent values of the pK(a) of the zinc-bound water and the proton shuttle residue suggest that different active-site conformations influence the two stages of catalysis, the proton transfer stage and the interconversion of CO(2) and bicarbonate.


    Organizational Affiliation

    Department of Pharmacology and Therapeutics, University of Florida, Gainesville, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase 2
A
260Homo sapiensGene 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 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.096 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.141 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.700α = 90.00
b = 41.510β = 104.32
c = 72.642γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHENIXphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
CrystalCleardata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-22
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Refinement description