5B4I | pdb_00005b4i

Crystal structure of I86D mutant of phycocyanobilin:ferredoxin oxidoreductase in complex with biliverdin (data 2)

• PDB DOI: https://doi.org/10.2210/pdb5B4I/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Synechocystis sp. PCC 6803
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-04-04 Released: 2017-03-15 
• Deposition Author(s): Hagiwara, Y., Wada, K., Irikawa, T., Unno, M., Fukuyama, K., Sugishima, M.
• Funding Organization(s): JSPS, MEXT, Program to Disseminate Tenura Tracking

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.11 Å
• R-Value Free: 
  0.152 (Depositor), 0.139 (DCC) 
• R-Value Work: 
  0.127 (Depositor), 0.135 (DCC) 

Starting Model: experimental

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

• PubMed: 27596987 
• DOI: https://doi.org/10.1002/1873-3468.12387
• Primary Citation Related Structures: 
  5B4H, 5B4I, 5B4J


• 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 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.

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Organizational Affiliation: 
• Department of Biochemistry and Applied Chemistry, National Institute of Technology, Kurume College, Kurume, Japan.
Organization for Promotion of Tenure Track, University of Miyazaki, Kiyotake, Japan.
Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan.
Department of Medical Biochemistry, Kurume University School of Medicine, Kurume, Japan.
Graduate School of Science and Engineering, Ibaraki University, Hitachi, Japan.
Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka, Japan.
Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan. [e-mail].
Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Japan. [e-mail].
Department of Medical Biochemistry, Kurume University School of Medicine, Kurume, Japan. [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 28.74 kDa 
• Atom Count: 2,457 
• Modeled Residue Count: 240 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phycocyanobilin:ferredoxin oxidoreductase	A	248	Synechocystis sp. PCC 6803	Mutation(s): 1  Gene Names: pcyA EC: 1.3.7.5
UniProt
Find proteins for Q55891 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore Q55891  Go to UniProtKB:  Q55891

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BLA	B [auth A]	BILIVERDINE IX ALPHA C33 H34 N4 O6 GWZYPXHJIZCRAJ-SRVCBVSDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.11 Å
• R-Value Free:  0.152 (Depositor), 0.139 (DCC) 
• R-Value Work:  0.127 (Depositor), 0.135 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.833	α = 90
b = 95.691	β = 90
c = 42.398	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
PHENIX	phasing
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-03-15 
Deposition Author(s): Hagiwara, Y., Wada, K., Irikawa, T., Unno, M., Fukuyama, K., Sugishima, M.

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Funding Organization	Location	Grant Number
JSPS	Japan	20370037
JSPS	Japan	22770096
JSPS	Japan	23370052
JSPS	Japan	24570122
JSPS	Japan	24870030
JSPS	Japan	25840026
MEXT, Program to Disseminate Tenura Tracking	Japan	--

Revision History  

• Version 1.0: 2017-03-15
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Data collection
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description