2ESF

Identification of a Novel Non-Catalytic Bicarbonate Binding Site in Eubacterial beta-Carbonic Anhydrase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Identification of a Novel Noncatalytic Bicarbonate Binding Site in Eubacterial beta-Carbonic Anhydrase.

Cronk, J.D.Rowlett, R.S.Zhang, K.Y.J.Tu, C.Endrizzi, J.A.Lee, J.Gareiss, P.C.Preiss, J.R.

(2006) Biochemistry 45: 4351-4361

  • DOI: 10.1021/bi052272q
  • Primary Citation of Related Structures:  2A8C, 2A8D

  • PubMed Abstract: 
  • The structures of beta class carbonic anhydrases (beta-CAs) determined so far fall into two distinct subclasses based on the observed coordination of the catalytic zinc (Zn2+) ion. The subclass of beta-CAs that coordinate Zn2+ tetrahedrally with four ...

    The structures of beta class carbonic anhydrases (beta-CAs) determined so far fall into two distinct subclasses based on the observed coordination of the catalytic zinc (Zn2+) ion. The subclass of beta-CAs that coordinate Zn2+ tetrahedrally with four protein-derived ligands is represented by the structures of orthologues from Porphyridium purpureum, Escherichia coli, and Mycobacterium tuberculosis. Here we present the structure of an additional member of that subclass, that from Haemophilus influenzae, as well as detailed kinetic analysis, revealing the correspondence between structural classification and kinetic profile for this subclass. In addition, we identify a unique, noncatalytic binding mode for the substrate bicarbonate that occurs in both the H. influenzae and E. coli enzymes. The kinetic and structural analysis indicates that binding of bicarbonate in this site of the enzyme may modulate its activity by influencing a pH-dependent, cooperative transition between active and inactive forms. We hypothesize that the two structural subclasses of beta-CAs may provide models for the proposed active and inactive forms of the H. influenzae and E. coli enzymes.


    Organizational Affiliation

    Department of Chemistry, Gonzaga University, 502 East Boone Avenue, Spokane, Washington 99258, USA. cronk@gonzaga.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase 2
A, B
220Escherichia coli (strain K12)Gene Names: can (cynT2, yadF)
EC: 4.2.1.1
Find proteins for P61517 (Escherichia coli (strain K12))
Go to UniProtKB:  P61517
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

Download SDF File 
Download CCD File 
A, B
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.198 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 82.866α = 90.00
b = 82.866β = 90.00
c = 162.213γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
SCALAdata scaling
CNSphasing
CNSrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-04-18
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance