View source for 6kmd


==Crystal structure of SeMet-phytochromobilin synthase from tomato in complex with biliverdin==
<StructureSection load='6kmd' size='340' side='right'caption='[[6kmd]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6kmd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Solanum_lycopersicum Solanum lycopersicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KMD FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6kmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kmd OCA], [https://pdbe.org/6kmd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kmd RCSB], [https://www.ebi.ac.uk/pdbsum/6kmd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kmd ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q588D6_SOLLC Q588D6_SOLLC] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Phytochromobilin (PPhiB) is a red/far-red light sensory pigment in plant phytochrome. PPhiB synthase is a ferredoxin-dependent bilin reductase (FDBR) that catalyzes the site-specific reduction of bilins, which are sensory and photosynthesis pigments, and produces PPhiB from biliverdin, a heme-derived linear tetrapyrrole pigment. Here, we determined the crystal structure of tomato PPhiB synthase in complex with biliverdin at 1.95 A resolution. The overall structure of tomato PPhiB synthase was similar to those of other FDBRs, except for the addition of a long C-terminal loop and short helices. The structure further revealed that the C-terminal loop is part of the biliverdin-binding pocket and that two basic residues in the C-terminal loop form salt bridges with the propionate groups of biliverdin. This suggested that the C-terminal loop is involved in the interaction with ferredoxin and biliverdin. The configuration of biliverdin bound to tomato PPhiB synthase differed from that of biliverdin bound to other FDBRs, and its orientation in PPhiB synthase was inverted relative to its orientation in the other FDBRs. Structural and enzymatic analyses disclosed that two aspartic acid residues, Asp-123 and Asp-263, form hydrogen bonds with water molecules and are essential for the site-specific A-ring reduction of biliverdin. On the basis of these observations and enzymatic assays with a V121A PPhiB synthase variant, we propose the following mechanistic product release mechanism: PPhiB synthase-catalyzed stereospecific reduction produces 2(R)-PPhiB, which when bound to PPhiB synthase, collides with the side chain of Val-121, releasing 2(R)-PPhiB from the synthase.

Crystal structure of phytochromobilin synthase in complex with biliverdin IXalpha, a key enzyme in the biosynthesis of phytochrome.,Sugishima M, Wada K, Fukuyama K, Yamamoto K J Biol Chem. 2019 Dec 10. pii: RA119.011431. doi: 10.1074/jbc.RA119.011431. PMID:31822504<ref>PMID:31822504</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6kmd" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Solanum lycopersicum]]
[[Category: Fukuyama K]]
[[Category: Sugishima M]]
[[Category: Wada K]]