9JWE | pdb_00009jwe

Native Carbonic Anhydrase II pH 7.8 0 atm CO2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 
    0.170 (Depositor), 0.170 (DCC) 
  • R-Value Work: 
    0.138 (Depositor), 0.138 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Conformational flexibility of His200 enables catalytic activity in the T200H mutant of carbonic anhydrase II.

Lim, S.W.Jeong, H.Kim, G.H.Min, D.Kim, J.K.Kim, C.U.

(2025) Mol Cells 48: 100226-100226

  • DOI: https://doi.org/10.1016/j.mocell.2025.100226
  • Primary Citation of Related Structures:  
    9JWE, 9JWU, 9JWW, 9U5B

  • PubMed Abstract: 

    Carbonic anhydrase II (CAII) is one of the most efficient enzymes known, catalyzing the reversible hydration of CO 2 to regulate pH and facilitate CO 2 transport in biological systems. Its exceptional catalytic rate depends on a highly ordered active site composed of a Zn 2+ ion and a hydrogen-bonded water network that supports substrate binding, proton transfer, and product release. Among the residues maintaining this network, Thr200 plays a crucial role by stabilizing key water molecules. To investigate the structural and functional consequences of perturbing this network, we examined the T200H mutant of CAII using high-pressure cryocooling and X-ray crystallography under CO 2 pressures of 0, 5, and 20 atm. The crystallographic snapshots captured the resting (T200H-0atm), substrate-bound (T200H-20atm), and product-bound (T200H-5atm) states of the T200H mutant. In the resting state, His200 disrupts the active site by displacing essential water molecules (W1 and W2), thereby impairing the proton transfer pathway. However, the substrate- and product-bound states reveal that His200 exhibits conformational flexibility, allowing partial restoration of the water network required for catalysis. These findings suggest that His200 functions as a dynamic gatekeeper, modulating access of water, substrate, and product to the active site. This structural plasticity explains how the T200H mutant retains partial catalytic activity despite a mutation that would otherwise severely hinder function. Our results provide new insights into active-site dynamics in CAII and offer a foundation for designing isoform-specific inhibitors or engineered carbonic anhydrase variants with tunable catalytic properties.


  • 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 2266Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (PDB Primary Data)
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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free:  0.170 (Depositor), 0.170 (DCC) 
  • R-Value Work:  0.138 (Depositor), 0.138 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.133α = 90
b = 41.234β = 104.411
c = 72.384γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2022R1A2C2091815

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release