5TOU

STRUCTURE OF C-PHYCOCYANIN FROM ARCTIC PSEUDANABAENA SP. LW0831

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

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Literature

Structural insights into the cold adaptation of the photosynthetic pigment-protein C-phycocyanin from an Arctic cyanobacterium

Su, H.N., Wang, Q.M., Li, C.Y., Li, K., Luo, W., Chen, B., Zhang, X.Y., Qin, Q.L., Zhou, B.C., Chen, X.L., Zhang, Y.Z., Xie, B.B.

(2017) Biochim Biophys Acta 1858: 325-335

  • DOI: https://doi.org/10.1016/j.bbabio.2017.02.004
  • Primary Citation of Related Structures:  
    5TOU

  • PubMed Abstract: 

    • The cold adaptation mechanism of phycobiliproteins, the major photosynthetic pigment-proteins in cyanobacteria and red algae, has rarely been studied. Here we reported the biochemical, structural, and molecular dynamics simulation study of the C-phycocyanin from Arctic cyanobacterial strain Pseudanabaena sp ...

    The cold adaptation mechanism of phycobiliproteins, the major photosynthetic pigment-proteins in cyanobacteria and red algae, has rarely been studied. Here we reported the biochemical, structural, and molecular dynamics simulation study of the C-phycocyanin from Arctic cyanobacterial strain Pseudanabaena sp. LW0831. We characterized the phycobilisome components of LW0831 and obtained their gene sequences. Compared to the mesophilic counterpart from Arthrospira platensis (Ar-C-PC), LW0831 C-phycocyanin (Ps-C-PC) has a decreased thermostability (∆T m of -16°C), one of the typical features of cold-adapted enzymes. To uncover its structural basis, we resolved the crystal structure of Ps-C-PC 1 at 2.04Å. Consistent with the decrease in thermostability, comparative structural analyses revealed decreased intra-trimer and inter-trimer interactions in Ps-C-PC 1, compared to Ar-C-PC. However, comparative molecular dynamics simulations indicated that Ps-C-PC 1 shows similar flexibilities to Ar-C-PC for both the (αβ) 3 trimer and (αβ) 6 hexamer. Therefore, the optimization mode is clearly different from cold-adapted enzymes, which usually have increased flexibilities. Detailed analyses demonstrated different optimization modes for the α and β subunits and it was revealed that hydrophobic interactions are key to this difference, though salt bridges, hydrogen bonds, and surface hydrophobicity are also involved. This study is the first report of the structure of cold-adapted phycobiliproteins and provides insights into the cold-adaptation strategies of non-enzyme proteins.

    Organizational Affiliation: 

    State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, China. Electronic address: xbb@sdu.edu.cn.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phycocyanin alpha-1 subunit162Pseudanabaena sp. lw0831Mutation(s): 0 
Gene Names: cpcA-1
UniProt
Find proteins for V5NXI0 (Pseudanabaena sp. lw0831)
Explore V5NXI0 
Go to UniProtKB:  V5NXI0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV5NXI0
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Phycocyanin beta-1 subunit172Pseudanabaena sp. lw0831Mutation(s): 0 
Gene Names: cpcB-1
UniProt
Find proteins for V5NZF0 (Pseudanabaena sp. lw0831)
Explore V5NZF0 
Go to UniProtKB:  V5NZF0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV5NZF0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CYC
Query on CYC
Download Ideal Coordinates CCD File 
AA [auth H],
BA [auth K],
CA [auth L],
DA [auth L],
M [auth C],
AA [auth H],
BA [auth K],
CA [auth L],
DA [auth L],
M [auth C],
N [auth D],
O [auth D],
P [auth A],
Q [auth B],
R [auth B],
S [auth E],
T [auth F],
U [auth F],
V [auth I],
W [auth J],
X [auth J],
Y [auth G],
Z [auth H]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MEN
Query on MEN
B [auth D],
D [auth B],
F,
H [auth J],
J [auth H],
B [auth D],
D [auth B],
F,
H [auth J],
J [auth H],
L
L-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.583α = 90
b = 175.718β = 90
c = 194.823γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
MLPHAREphasing
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-08
    Type: Initial release