3UCO

Coccomyxa beta-carbonic anhydrase in complex with iodide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural studies of [beta]-carbonic anhydrase from the green alga Coccomyxa: inhibitor complexes with anions and acetazolamide.

Huang, S.Hainzl, T.Grundstrom, C.Forsman, C.Samuelsson, G.Sauer-Eriksson, A.E.

(2011) Plos One 6: e28458-e28458

  • DOI: 10.1371/journal.pone.0028458
  • Primary Citation of Related Structures:  3UCJ, 3UCK, 3UCM, 3UCN

  • PubMed Abstract: 
  • The β-class carbonic anhydrases (β-CAs) are widely distributed among lower eukaryotes, prokaryotes, archaea, and plants. Like all CAs, the β-enzymes catalyze an important physiological reaction, namely the interconversion between carbon dioxide and b ...

    The β-class carbonic anhydrases (β-CAs) are widely distributed among lower eukaryotes, prokaryotes, archaea, and plants. Like all CAs, the β-enzymes catalyze an important physiological reaction, namely the interconversion between carbon dioxide and bicarbonate. In plants the enzyme plays an important role in carbon fixation and metabolism. To further explore the structure-function relationship of β-CA, we have determined the crystal structures of the photoautotroph unicellular green alga Coccomyxa β-CA in complex with five different inhibitors: acetazolamide, thiocyanate, azide, iodide, and phosphate ions. The tetrameric Coccomyxa β-CA structure is similar to other β-CAs but it has a 15 amino acid extension in the C-terminal end, which stabilizes the tetramer by strengthening the interface. Four of the five inhibitors bind in a manner similar to what is found in complexes with α-type CAs. Iodide ions, however, make contact to the zinc ion via a zinc-bound water molecule or hydroxide ion--a type of binding mode not previously observed in any CA. Binding of inhibitors to Coccomyxa β-CA is mediated by side-chain movements of the conserved residue Tyr-88, extending the width of the active site cavity with 1.5-1.8 Å. Structural analysis and comparisons with other α- and β-class members suggest a catalytic mechanism in which the movements of Tyr-88 are important for the CO(2)-HCO(3)(-) interconversion, whereas a structurally conserved water molecule that bridges residues Tyr-88 and Gln-38, seems important for proton transfer, linking water molecules from the zinc-bound water to His-92 and buffer molecules.


    Organizational Affiliation

    Department of Chemistry, Umeå University, Umeå, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase
A, B
227Coccomyxa sp. PAEC: 4.2.1.1
Find proteins for Q96554 (Coccomyxa sp. PA)
Go to UniProtKB:  Q96554
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A, B
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.153 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 75.478α = 90.00
b = 75.478β = 90.00
c = 222.405γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSphasing
REFMACrefinement
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-23
    Type: Initial release
  • Version 1.1: 2012-03-28
    Type: Database references