5Y2R

2.5 atm CO2-pressurized human carbonic anhydrase II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.131 
  • R-Value Work: 0.114 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Active-site solvent replenishment observed during human carbonic anhydrase II catalysis.

Kim, J.K.Lomelino, C.L.Avvaru, B.S.Mahon, B.P.McKenna, R.Park, S.Kim, C.U.

(2018) IUCrJ 5: 93-102

  • DOI: 10.1107/S2052252517017626
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human carbonic anhydrase II (hCA II) is a zinc metalloenzyme that catalyzes the reversible hydration/dehydration of CO <sub>2 </sub>/HCO <sub>3 </sub> <sup>- </sup>. Although hCA II has been extensively studied to investigate the proton-transfer proc ...

    Human carbonic anhydrase II (hCA II) is a zinc metalloenzyme that catalyzes the reversible hydration/dehydration of CO 2 /HCO 3 - . Although hCA II has been extensively studied to investigate the proton-transfer process that occurs in the active site, its underlying mechanism is still not fully understood. Here, ultrahigh-resolution crystallographic structures of hCA II cryocooled under CO 2 pressures of 7.0 and 2.5 atm are presented. The structures reveal new intermediate solvent states of hCA II that provide crystallographic snapshots during the restoration of the proton-transfer water network in the active site. Specifically, a new intermediate water (W I ') is observed next to the previously observed intermediate water W I , and they are both stabilized by the five water molecules at the entrance to the active site (the entrance conduit). Based on these structures, a water network-restructuring mechanism is proposed, which takes place at the active site after the nucleophilic attack of OH - on CO 2 . This mechanism explains how the zinc-bound water (W Zn ) and W1 are replenished, which are directly responsible for the reconnection of the His64-mediated proton-transfer water network. This study provides the first 'physical' glimpse of how a water reservoir flows into the hCA II active site during its catalytic activity.


    Organizational Affiliation

    School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea.,Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA.,Department of Physics, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase 2
A
260Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens)
Go to Gene View: CA2
Go to UniProtKB:  P00918
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CO2
Query on CO2

Download SDF File 
Download CCD File 
A
CARBON DIOXIDE
C O2
CURLTUGMZLYLDI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.131 
  • R-Value Work: 0.114 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.279α = 90.00
b = 41.406β = 104.16
c = 72.109γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-07-27 
  • Released Date: 2018-02-14 
  • Deposition Author(s): Kim, C.U., Park, S.Y.

Funding OrganizationLocationGrant Number
National Research Foundation of KoreaKorea, Republic Of2014R1A2A1A11051254
National Research Foundation of KoreaKorea, Republic Of2016R1A5A1013277
National Research Foundation of KoreaKorea, Republic Of2016R1D1A1A09918187

Revision History 

  • Version 1.0: 2018-02-14
    Type: Initial release