5B4J

Crystal structure of I86D mutant of phycocyanobilin:ferredoxin oxidoreductase in complex with biliverdin (data 3)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.139 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Atomic-resolution structure of the phycocyanobilin:ferredoxin oxidoreductase I86D mutant in complex with fully protonated biliverdin

Hagiwara, Y.Wada, K.Irikawa, T.Sato, H.Unno, M.Yamamoto, K.Fukuyama, K.Sugishima, M.

(2016) FEBS Lett. 590: 3425-3434

  • DOI: 10.1002/1873-3468.12387
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Phycocyanobilin:ferredoxin oxidoreductase (PcyA) catalyzes the reduction of biliverdin (BV) to produce phycocyanobilin, a linear tetrapyrrole pigment used for light harvesting and light sensing. Spectroscopic and HPLC analyses inidicate that BV bound ...

    Phycocyanobilin:ferredoxin oxidoreductase (PcyA) catalyzes the reduction of biliverdin (BV) to produce phycocyanobilin, a linear tetrapyrrole pigment used for light harvesting and light sensing. Spectroscopic and HPLC analyses inidicate that BV bound to the I86D mutant of PcyA is fully protonated (BVH+ ) and can accept an electron, but I86D is unable to donate protons for the reduction; therefore, compared to the wild-type PcyA, the I86D mutant stabilizes BVH+ . To elucidate the structural basis of the I86D mutation, we determined the atomic-resolution structure of the I86D-BVH+ complex and the protonation states of the essential residues Asp105 and Glu76 in PcyA. Our study revealed that Asp105 adopted a fixed conformation in the I86D mutant, although it had dual conformations in wild-type PcyA which reflected the protonation states of BV. Taken together with biochemical/spectroscopic results, our analysis of the I86D-BVH+ structure supports the hypothesis that flexibility of Asp105 is essential for the catalytic activity of PcyA.


    Organizational Affiliation

    Department of Biochemistry and Applied Chemistry, National Institute of Technology, Kurume College, Kurume, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phycocyanobilin:ferredoxin oxidoreductase
A
248Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 1 
Gene Names: pcyA
EC: 1.3.7.5
Find proteins for Q55891 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  Q55891
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BLA
Query on BLA

Download SDF File 
Download CCD File 
A
BILIVERDINE IX ALPHA
C33 H34 N4 O6
GWZYPXHJIZCRAJ-SRVCBVSDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.139 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 70.823α = 90.00
b = 95.861β = 90.00
c = 42.378γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
HKL-2000data reduction
SHELXphasing
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPSJapan20370037
JSPSJapan22770096
JSPSJapan23370052
JSPSJapan24570122
JSPSJapan24870030
JSPSJapan25840026
Program to Dissiminate Tenura TrackingJapan--

Revision History 

  • Version 1.0: 2017-03-15
    Type: Initial release