3DBJ

Allophycocyanin from Thermosynechococcus vulcanus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Allophycocyanin Trimer Stability and Functionality Are Primarily Due to Polar Enhanced Hydrophobicity of the Phycocyanobilin Binding Pocket

McGregor, A.Klartag, M.David, L.Adir, N.

(2008) J.Mol.Biol. 384: 406-421

  • DOI: 10.1016/j.jmb.2008.09.018

  • PubMed Abstract: 
  • Allophycocyanin (APC) is the primary pigment-protein component of the cores of the phycobilisome antenna complex. In addition to an extremely high degree of amino acid sequence conservation, the overall structures of APC from both mesophilic and ther ...

    Allophycocyanin (APC) is the primary pigment-protein component of the cores of the phycobilisome antenna complex. In addition to an extremely high degree of amino acid sequence conservation, the overall structures of APC from both mesophilic and thermophilic species are almost identical at all levels of assembly, yet APC from thermophilic organisms should have structural attributes that prevent thermally induced denaturation. We determined the structure of APC from the thermophilic cyanobacterium Thermosynechococcus vulcanus to 2.9 A, reaffirming the conservation of structural similarity with APC from mesophiles. We provide spectroscopic evidence that T. vulcanus APC is indeed more stable at elevated temperatures in vitro, when compared with the APC from mesophilic species. APC thermal and chemical stability levels are further enhanced when monitored in the presence of high concentrations of buffered phosphate, which increases the strength of hydrophobic interactions, and may mimic the effect of cytosolic crowding. Absorption spectroscopy, size-exclusion HPLC, and native gel electrophoresis also show that the thermally or chemically induced changes in the APC absorption spectra that result in the loss of the prominent 652-nm band in trimeric APC are not a result of physical monomerization. We propose that the bathochromic shift that occurs in APC upon trimerization is due to the coupling of the hydrophobicity of the alpha84 phycocyanobilin cofactor environment created by a deep cleft formed by the beta subunit with highly charged flanking regions. This arrangement also provides the additional stability required by thermophiles at elevated temperatures. The chemical environment that induces the bathochromic shift in APC trimers is different from the source of shifts in the absorption of monomers of the terminal energy acceptors APC(B) and L(CM), as visualized by the building of molecular models.


    Organizational Affiliation

    Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Allophycocyanin
A, C, E, G
161Thermosynechococcus vulcanus str. CopelandGene Names: apcA
Find proteins for B3VNK2 (Thermosynechococcus vulcanus str. Copeland)
Go to UniProtKB:  B3VNK2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Allophycocyanin
B, D, F, H
161Thermosynechococcus vulcanus str. CopelandGene Names: apcB
Find proteins for B3VNK3 (Thermosynechococcus vulcanus str. Copeland)
Go to UniProtKB:  B3VNK3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CYC
Query on CYC

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MEN
Query on MEN
B, D, F, H
L-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.212 
  • Space Group: P 3
Unit Cell:
Length (Å)Angle (°)
a = 102.597α = 90.00
b = 102.597β = 90.00
c = 128.860γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
DNAdata collection
MOSFLMdata reduction
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance