PDBsum entry 2d1e

Oxidoreductase

PDB id: 2d1e

Contents

Protein chain

243 a.a. *

Ligands

BLA

Metals

_NA

Waters ×363

* Residue conservation analysis

PDB id:

2d1e

Name:

Oxidoreductase

Title:

Crystal structure of pcya-biliverdin complex

Structure:

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

Source:

Synechocystis sp.. Organism_taxid: 1148. Strain: pcc 6803. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.51Å R-factor: 0.158 R-free: 0.183

Authors:

Y.Hagiwara,M.Sugishima,Y.Takahashi,K.Fukuyama

Key ref:

Y.Hagiwara et al. (2006). Crystal structure of phycocyanobilin:ferredoxin oxidoreductase in complex with biliverdin IXalpha, a key enzyme in the biosynthesis of phycocyanobilin. Proc Natl Acad Sci U S A, 103, 27-32. PubMed id: 16380422 DOI: 10.1073/pnas.0507266103

Date:

17-Aug-05 Release date: 24-Jan-06

Protein chain

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

Seq: 248 a.a.

Struc: 243 a.a.

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: 10.1073/pnas.0507266103

Proc Natl Acad Sci U S A 103:27-32 (2006)

PubMed id: 16380422

Crystal structure of phycocyanobilin:ferredoxin oxidoreductase in complex with biliverdin IXalpha, a key enzyme in the biosynthesis of phycocyanobilin.

Y.Hagiwara, M.Sugishima, Y.Takahashi, K.Fukuyama.

ABSTRACT

Phytobilins (light harvesting and photoreceptor pigments in higher plants, algae, and cyanobacteria) are synthesized from biliverdin IXalpha (BV) by ferredoxin-dependent bilin reductases (FDBRs). Phycocyanobilin:ferredoxin oxidoreductase (PcyA), one such FDBR, is a new class of radical enzymes that require neither cofactors nor metals and serially reduces the vinyl group of the D-ring and A-ring of BV using four electrons from ferredoxin to produce phycocyanobilin, one of the phytobilins. We have determined the crystal structure of PcyA from Synechocystis sp. PCC 6803 in complex with BV, revealing the first tertiary structure of an FDBR family member. PcyA is folded in a three-layer alpha/beta/alpha sandwich structure, in which BV in a cyclic conformation is positioned between the beta-sheet and C-terminal alpha-helices. The basic patch on the PcyA surface near the BV molecule may provide a binding site for acidic ferredoxin, allowing direct transfer of electrons to BV. The orientation of BV is definitely fixed in PcyA by several hydrophilic interactions and the shape of the BV binding pocket of PcyA. We propose the mechanism by which the sequential reduction of the D- and A-rings is controlled, where Asp-105, located between the two reduction sites, would play the central role by changing its conformation during the reaction. Homology modeling of other FDBRs based on the PcyA structure fits well with previous genetic and biochemical data, thereby providing a structural basis for the reaction mechanism of FDBRs.

Selected figure(s)

Figure 3.
Fig. 3. Environment of the BV binding site. A schematic diagram of interactions between PcyA and BV is shown. Dashed lines indicate hydrogen bonds and salt bridges. The residues involved in van der Waals interaction with BV are also shown. For clarity, only the major conformation of Asp-105 is shown. Carbon, nitrogen, and oxygen atoms are colored in black, blue, and red, respectively. BV is colored in purple. This figure was prepared with LIGPLOT (27).

Figure 4.
Fig. 4. Proposed reaction mechanism of PcyA. (a) Close-up view of BV. Omit electron density map for BV (contoured at 2.5 ) is superimposed on the stick model. The distances between the carboxyl group of Asp-105 in minor conformation and the lactam oxygen and nitrogen atoms of D-ring are 3.67 and 2.95 Å, respectively. (b) Proposed reaction mechanism catalyzed by PcyA. Reduction schemes at the D-ring (Upper) and at the A-ring (Lower) are shown.

Figures were selected by an automated process.