Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29.84 kDa 
• Atom Count: 2500 
• Residue Count: 258 
• Unique protein chains: 1

2VVB

Human carbonic anhydrase II in complex with bicarbonate

• DOI: 10.2210/pdb2VVB/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-04 Released: 2009-07-14 
• Deposition Author(s): Sjoeblom, B., Polentarutti, M., Djinovic-Carugo, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 0.213 
• R-Value Work: 0.168 
• R-Value Observed: 0.171 

Literature

Structural Study of X-Ray Induced Activation of Carbonic Anhydrase.

Sjoblom, B., Polentarutti, M., Djinovic-Carugo, K.

(2009) Proc Natl Acad Sci U S A 106: 10609

• PubMed: 19520834 
• DOI: 10.1073/pnas.0904184106
• Primary Citation of Related Structures:  
  2VVB, 2VVA


• PubMed Abstract: 
  

Carbonic anhydrase, a zinc metalloenzyme, catalyzes the reversible hydration of carbon dioxide to bicarbonate. It is involved in processes connected with acid-base homeostasis, respiration, and photosynthesis. More than 100 distinct human carbonic anhydrase II (HCAII) 3D structures have been generated in last 3 decades [Liljas A, et al. (1972) Nat New Biol 235:131-137], but a structure of an HCAII in complex with CO(2) or HCO(3)(-) has remained elusive. Here, we report previously undescribed structures of HCAII:CO(2) and HCAII:HCO(3)(-) complexes, together with a 3D molecular film of the enzymatic reaction observed successively in the same crystal after extended exposure to X-ray. We demonstrate that the unexpected enzyme activation was caused in an X-ray dose-dependent manner. Although X-ray damage to macromolecular samples has long been recognized [Ravelli RB, Garman EF (2006) Curr Opin Struct Biol 16:624-629], the detailed structural analysis reports on X-ray-driven reactions have been very rare in literature to date. Here, we report on enzyme activation and the associated chemical reaction in a crystal at 100 K. We propose mechanisms based on water photoradiolysis and/or electron radiolysis as the main cause of enzyme activation.

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Organizational Affiliation: 

Department for Structural and Computational Biology, Max F Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CARBONIC ANHYDRASE 2	X	260	Homo sapiens	Mutation(s): 0  Gene Names: CA2 EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens) Explore P00918  Go to UniProtKB:  P00918
NIH Common Fund Data Resources
PHAROS  P00918 GTEx  ENSG00000104267

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	X	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	X	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	X	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
BCT	X	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
CO2	X	CARBON DIOXIDE C O2 CURLTUGMZLYLDI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 0.213 
• R-Value Work: 0.168 
• R-Value Observed: 0.171 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.667	α = 90
b = 41.653	β = 104.79
c = 72.91	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-06-04 
• Released Date: 2009-07-14 
Deposition Author(s): Sjoeblom, B., Polentarutti, M., Djinovic-Carugo, K.

Revision History 

• Version 1.0: 2009-07-14
  Type: Initial release
  
• Version 1.1: 2012-08-22
  Changes: Database references, Derived calculations, Non-polymer description, Other, Version format compliance