4QCD

Neutron crystal structure of phycocyanobilin:ferredoxin oxidoreductase in complex with biliverdin IXalpha at room temperature.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.145 

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Insights into the Proton Transfer Mechanism of a Bilin Reductase PcyA Following Neutron Crystallography.

Unno, M.Ishikawa-Suto, K.Kusaka, K.Tamada, T.Hagiwara, Y.Sugishima, M.Wada, K.Yamada, T.Tomoyori, K.Hosoya, T.Tanaka, I.Niimura, N.Kuroki, R.Inaka, K.Ishihara, M.Fukuyama, K.

(2015) J Am Chem Soc 137: 5452-5460

  • DOI: 10.1021/jacs.5b00645
  • Primary Citation of Related Structures:  
    4QCD

  • PubMed Abstract: 
  • Phycocyanobilin, a light-harvesting and photoreceptor pigment in higher plants, algae, and cyanobacteria, is synthesized from biliverdin IXα (BV) by phycocyanobilin:ferredoxin oxidoreductase (PcyA) via two steps of two-proton-coupled two-electron reduction ...

    Phycocyanobilin, a light-harvesting and photoreceptor pigment in higher plants, algae, and cyanobacteria, is synthesized from biliverdin IXα (BV) by phycocyanobilin:ferredoxin oxidoreductase (PcyA) via two steps of two-proton-coupled two-electron reduction. We determined the neutron structure of PcyA from cyanobacteria complexed with BV, revealing the exact location of the hydrogen atoms involved in catalysis. Notably, approximately half of the BV bound to PcyA was BVH(+), a state in which all four pyrrole nitrogen atoms were protonated. The protonation states of BV complemented the protonation of adjacent Asp105. The "axial" water molecule that interacts with the neutral pyrrole nitrogen of the A-ring was identified. His88 Nδ was protonated to form a hydrogen bond with the lactam O atom of the BV A-ring. His88 and His74 were linked by hydrogen bonds via H3O(+). These results imply that Asp105, His88, and the axial water molecule contribute to proton transfer during PcyA catalysis.


    Organizational Affiliation

    ◆Graduate School of Engineering, Osaka University, Suita 565-0871, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phycocyanobilin:ferredoxin oxidoreductaseA248Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Gene Names: pcyAslr0116
EC: 1.3.7.5
UniProt
Find proteins for Q55891 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Explore Q55891 
Go to UniProtKB:  Q55891
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ55891
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BLA
Query on BLA

Download Ideal Coordinates CCD File 
B [auth A]BILIVERDINE IX ALPHA
C33 H34 N4 O6
GWZYPXHJIZCRAJ-SRVCBVSDSA-N
 Ligand Interaction
D3O
Query on D3O

Download Ideal Coordinates CCD File 
C [auth A]trideuteriooxidanium
D3 O
XLYOFNOQVPJJNP-ZRLBSURWSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.145 
  • Space Group: P 21 21 2
  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.107α = 90
b = 97.278β = 90
c = 43.174γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
CNSrefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-29
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Experimental preparation
  • Version 1.2: 2018-04-04
    Changes: Data collection, Database references
  • Version 2.0: 2021-06-09
    Changes: Derived calculations, Non-polymer description