6KM6

Human Carbonic Anhydrase II native 15 atm CO2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.105 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structural insights into the effect of active-site mutation on the catalytic mechanism of carbonic anhydrase.

Kim, J.K.Lee, C.Lim, S.W.Andring, J.T.Adhikari, A.McKenna, R.Kim, C.U.

(2020) IUCrJ 7: 985-994

  • DOI: https://doi.org/10.1107/S2052252520011008
  • Primary Citation of Related Structures:  
    6KLZ, 6KM0, 6KM1, 6KM2, 6KM3, 6KM4, 6KM5, 6KM6

  • PubMed Abstract: 

    Enzymes are catalysts of biological processes. Significant insight into their catalytic mechanisms has been obtained by relating site-directed mutagenesis studies to kinetic activity assays. However, revealing the detailed relationship between structural modifications and functional changes remains challenging owing to the lack of information on reaction intermediates and of a systematic way of connecting them to the measured kinetic parameters. Here, a systematic approach to investigate the effect of an active-site-residue mutation on a model enzyme, human carbonic anhydrase II (CA II), is described. Firstly, structural analysis is performed on the crystallographic intermediate states of native CA II and its V143I variant. The structural comparison shows that the binding affinities and configurations of the substrate (CO 2 ) and product (HCO 3 - ) are altered in the V143I variant and the water network in the water-replenishment pathway is restructured, while the proton-transfer pathway remains mostly unaffected. This structural information is then used to estimate the modifications of the reaction rate constants and the corresponding free-energy profiles of CA II catalysis. Finally, the obtained results are used to reveal the effect of the V143I mutation on the measured kinetic parameters ( k cat and k cat / K m ) at the atomic level. It is believed that the systematic approach outlined in this study may be used as a template to unravel the structure-function relationships of many other biologically important enzymes.


  • Organizational Affiliation

    Department of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2260Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens)
Explore P00918 
Go to UniProtKB:  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: 1.15 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.105 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.153α = 90
b = 41.308β = 104.088
c = 71.964γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic Of2019R1A2C1004274

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2020-11-11
    Changes: Database references
  • Version 1.2: 2020-12-02
    Changes: Database references
  • Version 1.3: 2021-03-03
    Changes: Database references
  • Version 1.4: 2023-11-22
    Changes: Data collection, Database references, Refinement description