3RLD | pdb_00003rld

Crystal structure of the Y7I mutant of human carbonic anhydrase II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.211 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

Kinetic and crystallographic studies of the role of tyrosine 7 in the active site of human carbonic anhydrase II.

Mikulski, R.Avvaru, B.S.Tu, C.Case, N.McKenna, R.Silverman, D.N.

(2011) Arch Biochem Biophys 506: 181-187

  • DOI: https://doi.org/10.1016/j.abb.2010.12.004
  • Primary Citation Related Structures: 
    3RLD

  • PubMed Abstract: 

    The rate limiting step in catalysis of bicarbonate dehydration by human carbonic anhydrase II (HCA II) is an intramolecular proton transfer from His64 to the zinc-bound hydroxide. We have examined the role of Tyr7 using site-specific mutagenesis and measuring catalysis by the ¹⁸O exchange method using membrane inlet mass spectrometry. The side chain of Tyr7 in HCA II extends into the active-site cavity about 7 Å from the catalytic zinc atom. Replacement of Tyr7 with eight other amino acids had no effect on the interconversion of bicarbonate and CO₂, but in some cases caused enhancements in the rate constant of proton transfer by nearly 10-fold. The variant Y7I HCA II enhanced intramolecular proton transfer approximately twofold; its structure was determined by X-ray crystallography at 1.5 Å resolution. No changes were observed in the ordered solvent structure in the active-site cavity or in the conformation of the side chain of the proton shuttle His64. However, the first 11 residues of the amino-terminal chain in Y7I HCA II assumed an alternate conformation compared with the wild type. Differential scanning calorimetry showed variants at position 7 had a melting temperature approximately 8 °C lower than that of the wild type.


  • Organizational Affiliation
    • Department of Pharmacology, University of Florida, Gainesville, FL 32610, USA.

Macromolecule Content 

  • Total Structure Weight: 29.59 kDa 
  • Atom Count: 2,261 
  • Modeled Residue Count: 257 
  • Deposited Residue Count: 260 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2260Homo sapiensMutation(s): 1 
Gene Names: CA2
EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens)
Explore P00918 
Go to UniProtKB:  P00918
PHAROS:  P00918
GTEx:  ENSG00000104267 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00918
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.211 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.789α = 90
b = 41.598β = 104.83
c = 73.195γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction
CNSphasing
SHELXLrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2012-03-14
    Changes: Other
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description