5DSL

Structure of CO2 released holo-form of human carbonic anhydrase II with 10 min warming


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.102 
  • R-Value Observed: 0.104 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Tracking solvent and protein movement during CO2 release in carbonic anhydrase II crystals

Kim, C.U.Song, H.Avvaru, B.S.Gruner, S.M.Park, S.McKenna, R.

(2016) Proc Natl Acad Sci U S A 113: 5257-5262

  • DOI: https://doi.org/10.1073/pnas.1520786113
  • Primary Citation of Related Structures:  
    5DSK, 5DSL, 5DSM, 5DSO, 5DSP, 5DSQ, 5DSR, 5YUI, 5YUJ, 5YUK

  • PubMed Abstract: 

    Carbonic anhydrases are mostly zinc metalloenzymes that catalyze the reversible hydration/dehydration of CO2/HCO3 (-) Previously, the X-ray crystal structures of CO2-bound holo (zinc-bound) and apo (zinc-free) human carbonic anhydrase IIs (hCA IIs) were captured at high resolution. Here, we present sequential timeframe structures of holo- [T = 0 s (CO2-bound), 50 s, 3 min, 10 min, 25 min, and 1 h] and apo-hCA IIs [T = 0 s, 50 s, 3 min, and 10 min] during the "slow" release of CO2 Two active site waters, WDW (deep water) and WDW' (this study), replace the vacated space created on CO2 release, and another water, WI (intermediate water), is seen to translocate to the proton wire position W1. In addition, on the rim of the active site pocket, a water W2' (this study), in close proximity to residue His64 and W2, gradually exits the active site, whereas His64 concurrently rotates from pointing away ("out") to pointing toward ("in") active site rotameric conformation. This study provides for the first time, to our knowledge, structural "snapshots" of hCA II intermediate states during the formation of the His64-mediated proton wire that is induced as CO2 is released. Comparison of the holo- and apo-hCA II structures shows that the solvent network rearrangements require the presence of the zinc ion.


  • Organizational Affiliation

    Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY 14853; Department of Physics, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea; cukim@unist.ac.kr psy@ssu.ac.kr rmckenna@ufl.edu.


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
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: 1.45 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.102 
  • R-Value Observed: 0.104 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.228α = 90
b = 41.245β = 104.22
c = 72.048γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2018-10-17
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description