3E28

H. influenzae beta-carbonic anhydrase, variant Y181F


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Allosteric site variants of Haemophilus influenzae beta-carbonic anhydrase.

Rowlett, R.S.Tu, C.Lee, J.Herman, A.G.Chapnick, D.A.Shah, S.H.Gareiss, P.C.

(2009) Biochemistry 48: 6146-6156

  • DOI: https://doi.org/10.1021/bi900663h
  • Primary Citation of Related Structures:  
    3E1V, 3E1W, 3E24, 3E28, 3E2A, 3E2W

  • PubMed Abstract: 

    Haemophilus influenzae beta-carbonic anhydrase (HICA) is hypothesized to be an allosteric protein that is regulated by the binding of bicarbonate ion to a non-catalytic (inhibitory) site that controls the ligation of Asp44 to the catalytically essential zinc ion. We report here the X-ray crystallographic structures of two variants (W39F and Y181F) involved in the binding of bicarbonate ion in the non-catalytic site and an active-site variant (D44N) that is incapable of forming a strong zinc ligand. The alteration of Trp39 to Phe increases the apparent K(i) for bicarbonate inhibition by 4.8-fold. While the structures of W39F and Y181F are very similar to the wild-type enzyme, the X-ray crystal structure of the D44N variant reveals that it has adopted an active-site conformation nearly identical to that of non-allosteric beta-carbonic anhydrases. We propose that the structure of the D44N variant is likely to be representative of the active conformation of the enzyme. These results lend additional support to the hypothesis that HICA is an allosteric enzyme that can adopt active and inactive conformations, the latter of which is stabilized by bicarbonate ion binding to a non-catalytic site.


  • Organizational Affiliation

    Department of Chemistry, Colgate University, 13 Oak Drive, Hamilton, New York 13346, USA. rrowlett@mail.colgate.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): 1 
Gene Names: canHI1301
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth F]
H [auth A]
I [auth A]
J [auth A]
AA [auth F],
BA [auth F],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
M [auth B],
N [auth B],
P [auth C],
Q [auth C],
R [auth C],
T [auth D],
U [auth D],
W [auth E],
X [auth E],
Y [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A]
L [auth B]
O [auth C]
S [auth D]
V [auth E]
G [auth A],
L [auth B],
O [auth C],
S [auth D],
V [auth E],
Z [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 230.193α = 90
b = 144.943β = 93.78
c = 52.714γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
EPMRphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Derived calculations, Refinement description, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-30
    Changes: Data collection, Refinement description