2A8D

Haemophilus influenzae beta-carbonic anhydrase complexed with bicarbonate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1021/bi052272q
  • Primary Citation of Related Structures:  
    2A8C, 2A8D, 2ESF

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2
A, B, C, D, E
A, B, C, D, E, F
229Haemophilus influenzaeMutation(s): 0 
Gene Names: can
EC: 4.2.1.1
UniProt
Find proteins for P45148 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Explore P45148 
Go to UniProtKB:  P45148
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45148
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
K [auth B]
L [auth B]
O [auth C]
R [auth D]
U [auth E]
K [auth B],
L [auth B],
O [auth C],
R [auth D],
U [auth E],
V [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
M [auth C]
P [auth D]
S [auth E]
G [auth A],
I [auth B],
M [auth C],
P [auth D],
S [auth E],
W [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
BCT
Query on BCT

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
N [auth C]
Q [auth D]
T [auth E]
H [auth A],
J [auth B],
N [auth C],
Q [auth D],
T [auth E],
X [auth F]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 232.807α = 90
b = 144.602β = 94.1
c = 52.101γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-04-18
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description