5DSM

Structure of CO2 released holo-form of human carbonic anhydrase II with 25 min warming


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.112 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1073/pnas.1520786113
  • Primary Citation of Related Structures:  
  • Also Cited By: 5YUK, 5YUJ, 5YUI

  • 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) w ...

    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

    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;,Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610; cukim@unist.ac.kr psy@ssu.ac.kr rmckenna@ufl.edu.,School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea; cukim@unist.ac.kr psy@ssu.ac.kr rmckenna@ufl.edu.,Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY 14853; Department of Physics, Cornell University, Ithaca, NY 14853.,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: 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 2 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.112 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.211α = 90.00
b = 41.260β = 104.22
c = 72.066γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2018-10-17
    Type: Data collection, Database references, Derived calculations