Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.38 kDa 
• Atom Count: 2188 
• Modelled Residue Count: 258 
• Deposited Residue Count: 260 
• Unique protein chains: 1

1THK

Effect of Shuttle Location and pH Environment on H+ Transfer in Human Carbonic Anhydrase II

• PDB DOI: 10.2210/pdb1THK/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-06-01 Released: 2005-01-25 
• Deposition Author(s): Fisher, Z., Hernandez Prada, J.A., Tu, C.K., Duda, D., Yoshioka, C., An, H., Govindasamy, L., Silverman, D.N., McKenna, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.209 
• R-Value Work: 0.166 

Literature

Structural and Kinetic Characterization of Active-Site Histidine as a Proton Shuttle in Catalysis by Human Carbonic Anhydrase II

Fisher, Z., Hernandez Prada, J.A., Tu, C.K., Duda, D., Yoshioka, C., An, H., Govindasamy, L., Silverman, D.N., McKenna, R.

(2005) Biochemistry 44: 1097-1105

• PubMed: 15667203 
• DOI: 10.1021/bi0480279
• Primary Citation of Related Structures:  
  1T9N, 1TB0, 1TBT, 1TE3, 1TEQ, 1TEU, 1TG3, 1TG9, 1TH9, 1THK


• PubMed Abstract: 
  

In the catalysis of the hydration of carbon dioxide and dehydration of bicarbonate by human carbonic anhydrase II (HCA II), a histidine residue (His64) shuttles protons between the zinc-bound solvent molecule and the bulk solution. To evaluate the effect of the position of the shuttle histidine and pH on proton shuttling, we have examined the catalysis and crystal structures of wild-type HCA II and two double mutants: H64A/N62H and H64A/N67H HCA II. His62 and His67 both have their side chains extending into the active-site cavity with distances from the zinc approximately equivalent to that of His64. Crystal structures were determined at pH 5.1-10.0, and the catalysis of the exchange of (18)O between CO(2) and water was assessed by mass spectrometry. Efficient proton shuttle exceeding a rate of 10(5) s(-)(1) was observed for histidine at positions 64 and 67; in contrast, relatively inefficient proton transfer at a rate near 10(3) s(-)(1) was observed for His62. The observation, in the crystal structures, of a completed hydrogen-bonded water chain between the histidine shuttle residue and the zinc-bound solvent does not appear to be required for efficient proton transfer. The data suggest that the number of intervening water molecules between the donor and acceptor supporting efficient proton transfer in HCA II is important, and furthermore suggest that a water bridge consisting of two intervening water molecules is consistent with efficient proton transfer.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase II	A	260	Homo sapiens	Mutation(s): 1  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.209 
• R-Value Work: 0.166 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.529	α = 90
b = 41.607	β = 104.47
c = 72.852	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-06-01 
• Released Date: 2005-01-25 
Deposition Author(s): Fisher, Z., Hernandez Prada, J.A., Tu, C.K., Duda, D., Yoshioka, C., An, H., Govindasamy, L., Silverman, D.N., McKenna, R.

Revision History  

• Version 1.0: 2005-01-25
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2021-10-27
  Changes: Database references, Derived calculations