1KEQ

Crystal Structure of F65A/Y131C Carbonic Anhydrase V, covalently modified with 4-chloromethylimidazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Crystal structure of F65A/Y131C-methylimidazole carbonic anhydrase V reveals architectural features of an engineered proton shuttle.

Jude, K.M.Wright, S.K.Tu, C.Silverman, D.N.Viola, R.E.Christianson, D.W.

(2002) Biochemistry 41: 2485-2491

  • DOI: https://doi.org/10.1021/bi015808q
  • Primary Citation of Related Structures:  
    1KEQ

  • PubMed Abstract: 

    The crystal structure of F65A/Y131C murine alpha-carbonic anhydrase V (CAV), covalently modified at cysteine residues with 4-chloromethylimidazole, is reported at 1.88 A resolution. This modification introduces a methylimidazole (MI) group at residue C131 in the active site with important consequences. F65A/Y131C-MI CAV exhibits an up to 3-fold enhancement of catalytic activity over that of wild-type CAV [Earnhardt, J. N., Wright, S. K., Qian, M., Tu, C., Laipis, P. J., Viola, R. E., and Silverman, D. N. (1999) Arch. Biochem. Biophys. 361, 264-270]. In this modified CAV variant, C131-MI acts as a proton shuttle, facilitating the deprotonation of a zinc-bound water molecule to regenerate the nucleophilic zinc-bound hydroxide ion. A network of three hydrogen-bonded water molecules, across which proton transfer likely proceeds, bridges the zinc-bound water molecule and the C131-MI imidazole group. The structure of F65A/Y131C-MI CAV is compared to structures of Y64H/F65A murine CAV, wild-type human alpha-carbonic anhydrase II, and the gamma-carbonic anhydrase from Methanosarcina thermophilain an effort to outline common features of catalytic proton shuttles.


  • Organizational Affiliation

    Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
F65A/Y131C-MI Carbonic Anhydrase V
A, B
248Mus musculusMutation(s): 2 
Gene Names: MCA5C
EC: 4.2.1.1
UniProt
Find proteins for P23589 (Mus musculus)
Explore P23589 
Go to UniProtKB:  P23589
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23589
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4MZ
Query on 4MZ

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
K [auth B],
L [auth B]
4-METHYLIMIDAZOLE
C4 H6 N2
XLSZMDLNRCVEIJ-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACY
Query on ACY

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
M [auth B]
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
C [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.299α = 90
b = 66.703β = 105.7
c = 92.563γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-03-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-12-25
    Changes: Advisory, Derived calculations
  • Version 1.4: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-08-16
    Changes: Data collection, Refinement description