PDBsum entry 5b4j

Oxidoreductase

PDB id: 5b4j

Contents

Protein chain

240 a.a.

Ligands

BLA

Waters ×368

PDB id:

5b4j

Name:

Oxidoreductase

Title:

Crystal structure of i86d mutant of phycocyanobilin:ferredoxin oxidoreductase in complex with biliverdin (data 3)

Structure:

Phycocyanobilin:ferredoxin oxidoreductase. Chain: a. Engineered: yes. Mutation: yes

Source:

Synechocystis sp. Pcc 6803. Organism_taxid: 1148. Strain: pcc 6803. Gene: pcya. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.05Å R-factor: 0.139 R-free: 0.168

Authors:

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

Key ref:

Y.Hagiwara et al. (2016). Atomic-resolution structure of the phycocyanobilin:ferredoxin oxidoreductase I86D mutant in complex with fully protonated biliverdin. Febs Lett, 590, 3425-3434. PubMed id: 27596987 DOI: 10.1002/1873-3468.12387

Date:

04-Apr-16 Release date: 15-Mar-17

Protein chain

Q55891  (PCYA_SYNY3) -  Phycocyanobilin:ferredoxin oxidoreductase from Synechocystis sp. (strain PCC 6803 / Kazusa)

Seq: 248 a.a.

Struc: 240 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.3.7.5 - phycocyanobilin:ferredoxin oxidoreductase.
• Pathway: Biliverdin metabolism
• Reaction: (2R,3Z)-phycocyanobilin + 4 oxidized [2Fe-2S]-[ferredoxin] = biliverdin IXalpha + 4 reduced [2Fe-2S]-[ferredoxin] + 4 H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1002/1873-3468.12387

Febs Lett 590:3425-3434 (2016)

PubMed id: 27596987

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

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

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.