5b3t: Difference between revisions

Revision as of 10:03, 26 February 2020

Crystal structure of apo-form biliverdin reductase from Synechocystis sp. PCC 6803

Structural highlights

5b3t is a 2 chain structure with sequence from Syny3. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	PO4
Related:	5b3u, 5b3v
Gene:	bvdR (SYNY3)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

Biliverdin reductase catalyses the last step in haem degradation and produces the major lipophilic antioxidant bilirubin via reduction of biliverdin, using NAD(P)H as a cofactor. Despite the importance of biliverdin reductase in maintaining the redox balance, the molecular details of the reaction it catalyses remain unknown. Here we present the crystal structure of biliverdin reductase in complex with biliverdin and NADP+. Unexpectedly, two biliverdin molecules, which we designated the proximal and distal biliverdins, bind with stacked geometry in the active site. The nicotinamide ring of the NADP+ is located close to the reaction site on the proximal biliverdin, supporting that the hydride directly attacks this position of the proximal biliverdin. The results of mutagenesis studies suggest that a conserved Arg185 is essential for the catalysis. The distal biliverdin probably acts as a conduit to deliver the proton from Arg185 to the proximal biliverdin, thus yielding bilirubin.

A substrate-bound structure of cyanobacterial biliverdin reductase identifies stacked substrates as critical for activity.,Takao H, Hirabayashi K, Nishigaya Y, Kouriki H, Nakaniwa T, Hagiwara Y, Harada J, Sato H, Yamazaki T, Sakakibara Y, Suiko M, Asada Y, Takahashi Y, Yamamoto K, Fukuyama K, Sugishima M, Wada K Nat Commun. 2017 Feb 7;8:14397. doi: 10.1038/ncomms14397. PMID:28169272^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Takao H, Hirabayashi K, Nishigaya Y, Kouriki H, Nakaniwa T, Hagiwara Y, Harada J, Sato H, Yamazaki T, Sakakibara Y, Suiko M, Asada Y, Takahashi Y, Yamamoto K, Fukuyama K, Sugishima M, Wada K. A substrate-bound structure of cyanobacterial biliverdin reductase identifies stacked substrates as critical for activity. Nat Commun. 2017 Feb 7;8:14397. doi: 10.1038/ncomms14397. PMID:28169272 doi:https://dx.doi.org/10.1038/ncomms14397

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OCA

[1] Takao H, Hirabayashi K, Nishigaya Y, Kouriki H, Nakaniwa T, Hagiwara Y, Harada J, Sato H, Yamazaki T, Sakakibara Y, Suiko M, Asada Y, Takahashi Y, Yamamoto K, Fukuyama K, Sugishima M, Wada K. A substrate-bound structure of cyanobacterial biliverdin reductase identifies stacked substrates as critical for activity. Nat Commun. 2017 Feb 7;8:14397. doi: 10.1038/ncomms14397. PMID:28169272 doi:https://dx.doi.org/10.1038/ncomms14397

[1]

@@ Line 1: / Line 1: @@
 ==Crystal structure of apo-form biliverdin reductase from Synechocystis sp. PCC 6803==
-<StructureSection load='5b3t' size='340' side='right' caption='[[5b3t]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='5b3t' size='340' side='right'caption='[[5b3t]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5b3t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B3T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B3T FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5b3t]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Syny3 Syny3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B3T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B3T FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5b3u|5b3u]], [[5b3v|5b3v]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bvdR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1111708 SYNY3])</td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5b3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b3t OCA], [http://pdbe.org/5b3t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b3t RCSB], [http://www.ebi.ac.uk/pdbsum/5b3t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b3t ProSAT]</span></td></tr>
 </table>
@@ Line 21: / Line 22: @@
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
+[[Category: Syny3]]
 [[Category: Takao, H]]
 [[Category: Wada, K]]

5b3t: Difference between revisions

Revision as of 10:03, 26 February 2020

Crystal structure of apo-form biliverdin reductase from Synechocystis sp. PCC 6803

Structural highlights

Publication Abstract from PubMed

References

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