1YDA

STRUCTURAL BASIS OF INHIBITOR AFFINITY TO VARIANTS OF HUMAN CARBONIC ANHYDRASE II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Observed: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of inhibitor affinity to variants of human carbonic anhydrase II.

Nair, S.K.Krebs, J.F.Christianson, D.W.Fierke, C.A.

(1995) Biochemistry 34: 3981-3989

  • DOI: 10.1021/bi00012a016
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The activities and structures of certain L198 variants of human carbonic anhydrase II (CAII) have been reported recently [Krebs, J. F., Rana, F., Dluhy, R. A., & Fierke, C. A. (1993) Biochemistry 32, 4496-4505; Nair, S. K., & Christianson, D. W. (199 ...

    The activities and structures of certain L198 variants of human carbonic anhydrase II (CAII) have been reported recently [Krebs, J. F., Rana, F., Dluhy, R. A., & Fierke, C. A. (1993) Biochemistry 32, 4496-4505; Nair, S. K., & Christianson, D. W. (1993) Biochemistry 32, 4506-4514]. In order to understand the structural basis of enzyme-inhibitor affinity, we now report the dissociation rate and equilibrium constants for acetazolamide and dansylamide binding to 13 variants of CAII containing substituted amino acids at position 198. These data indicate that inhibitor affinity is modulated by the hydrophobicity and charge of the 198 side chain. Furthermore, we have determined crystal structures of L198R, L198E, and L198F CAIIs complexed with the transition state analog acetazolamide. The substituted benzyl side chain of L198F CAII does not occlude the substrate association pocket, and it is therefore not surprising that this substitution has minimal effects on catalytic properties and inhibitor binding. Nevertheless, the F198 side chain undergoes a significant conformation change in order to accommodate the binding of acetazolamide; the same behavior is observed for the engineered side chain of L198R CAII. In contrast, the engineered side chain of L198E CAII does not alter its conformation upon inhibitor binding. We conclude that the mobility and hydrophobicity or residue 198 side chains affect enzyme-inhibitor (and enzyme-substrate) affinity, and these structure-function relationships are important for understanding the behavior of carbonic anhydrase isozyme III, which bears a wild-type F198 side chain.(ABSTRACT TRUNCATED AT 250 WORDS)


    Organizational Affiliation

    Department of Chemistry, University of Pennsylvania, Philadelphia 19104-6323.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CARBONIC ANHYDRASE II
A
259Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens)
Go to UniProtKB:  P00918
NIH Common Fund Data Resources
PHAROS  P00918
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AZM
Query on AZM

Download CCD File 
A
5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE
C4 H6 N4 O3 S2
BZKPWHYZMXOIDC-UHFFFAOYSA-N
 Ligand Interaction
HG
Query on HG

Download CCD File 
A
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AZMIC50:  56.5   nM  BindingDB
AZMKi:  0.800000011920929   nM  BindingDB
AZMIC50:  68   nM  BindingDB
AZMKi:  25   nM  BindingDB
AZMIC50:  63   nM  BindingDB
AZMIC50:  36   nM  BindingDB
AZMIC50:  37   nM  BindingDB
AZMIC50:  38   nM  BindingDB
AZMKi:  61   nM  BindingDB
AZMIC50:  6.699999809265137   nM  BindingDB
AZMKi:  159   nM  BindingDB
AZMKi:  184   nM  BindingDB
AZMKi:  0.3400000035762787   nM  BindingDB
AZMIC50:  124   nM  BindingDB
AZMKi:  104   nM  BindingDB
AZMKd :  280   nM  PDBBind
AZMIC50:  92.5   nM  BindingDB
AZMIC50:  14   nM  BindingDB
AZMIC50:  13   nM  BindingDB
AZMKi:  370   nM  BindingDB
AZMKi:  374   nM  BindingDB
AZMIC50:  15   nM  BindingDB
AZMIC50:  10   nM  BindingDB
AZMKi:  250   nM  BindingDB
AZMIC50:  12   nM  BindingDB
AZMIC50:  110.27999877929688   nM  BindingDB
AZMIC50:  28   nM  BindingDB
AZMIC50:  29   nM  BindingDB
AZMIC50:  20   nM  BindingDB
AZMKi:  420   nM  BindingDB
AZMIC50:  18.5   nM  BindingDB
AZMIC50:  24   nM  BindingDB
AZMIC50:  25   nM  BindingDB
AZMIC50:  23   nM  BindingDB
AZMIC50:  0.47999998927116394   nM  BindingDB
AZMIC50:  47.599998474121094   nM  BindingDB
AZMIC50:  48.099998474121094   nM  BindingDB
AZMKi:  11   nM  BindingDB
AZMKi:  10   nM  BindingDB
AZMIC50:  69.69999694824219   nM  BindingDB
AZMIC50:  6   nM  BindingDB
AZMKi:  7   nM  BindingDB
AZMIC50:  53.099998474121094   nM  BindingDB
AZMKi:  18   nM  BindingDB
AZMKi:  10.100000381469727   nM  BindingDB
AZMKi:  22   nM  BindingDB
AZMKi:  12   nM  BindingDB
AZMKi:  15   nM  BindingDB
AZMKi:  33   nM  BindingDB
AZMIC50:  8.899999618530273   nM  BindingDB
AZMIC50:  89.9000015258789   nM  BindingDB
AZMKd:  0.05999999865889549   nM  BindingDB
AZMKi:  25   nM  BindingDB
AZMKd:  1.5   nM  BindingDB
AZMIC50:  34.29999923706055   nM  BindingDB
AZMKd:  10   nM  BindingDB
AZMIC50:  4100   nM  BindingDB
AZMKd:  18   nM  BindingDB
AZMIC50:  4300   nM  BindingDB
AZMIC50:  3800   nM  BindingDB
AZMIC50:  3900   nM  BindingDB
AZMKd:  2.5999999046325684   nM  BindingDB
AZMIC50:  4020   nM  BindingDB
AZMKd:  17   nM  BindingDB
AZMIC50:  2400   nM  BindingDB
AZMIC50:  2800   nM  BindingDB
AZMKd:  46   nM  BindingDB
AZMKi:  3.299999952316284   nM  BindingDB
AZMKd:  38   nM  BindingDB
AZMIC50:  48.29999923706055   nM  BindingDB
AZMIC50:  8.880000114440918   nM  BindingDB
AZMIC50:  4500   nM  BindingDB
AZMKd:  0.07000000029802322   nM  BindingDB
AZMIC50:  68.5999984741211   nM  BindingDB
AZMKi:  12.300000190734863   nM  BindingDB
AZMKi:  40.810001373291016   nM  BindingDB
AZMKd:  280   nM  Binding MOAD
AZMKd:  6.800000190734863   nM  BindingDB
AZMKi:  2100   nM  BindingDB
AZMKi:  2150   nM  BindingDB
AZMIC50:  16.200000762939453   nM  BindingDB
AZMKi:  2000   nM  BindingDB
AZMIC50:  220   nM  BindingDB
AZMKi:  3300   nM  BindingDB
AZMIC50:  98.30000305175781   nM  BindingDB
AZMIC50:  152   nM  BindingDB
AZMIC50:  77.80000305175781   nM  BindingDB
AZMKi:  4.900000095367432   nM  BindingDB
AZMIC50:  441   nM  BindingDB
AZMIC50:  60.400001525878906   nM  BindingDB
AZMIC50:  440   nM  BindingDB
AZMIC50:  283   nM  BindingDB
AZMIC50:  285   nM  BindingDB
AZMIC50:  48.900001525878906   nM  BindingDB
AZMIC50:  309   nM  BindingDB
AZMIC50:  351   nM  BindingDB
AZMIC50:  362   nM  BindingDB
AZMIC50:  370   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.7α = 90
b = 41.7β = 104.6
c = 73γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-02-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other