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| | ==Crystal structure of oxidized H88Q Synechocystis sp. PCYA== | | ==Crystal structure of oxidized H88Q Synechocystis sp. PCYA== |
| - | <StructureSection load='3nb8' size='340' side='right' caption='[[3nb8]], [[Resolution|resolution]] 1.30Å' scene=''> | + | <StructureSection load='3nb8' size='340' side='right'caption='[[3nb8]], [[Resolution|resolution]] 1.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3nb8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aphanocapsa_sp._(strain_n-1) Aphanocapsa sp. (strain n-1)]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3f0j 3f0j]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NB8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NB8 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3nb8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechocystis_sp._PCC_6803 Synechocystis sp. PCC 6803]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3f0j 3f0j]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NB8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NB8 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3f0j|3f0j]], [[3nb9|3nb9]]</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=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pcyA, slr0116 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1148 Aphanocapsa sp. (strain N-1)])</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=3nb8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nb8 OCA], [https://pdbe.org/3nb8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nb8 RCSB], [https://www.ebi.ac.uk/pdbsum/3nb8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nb8 ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phycocyanobilin:ferredoxin_oxidoreductase Phycocyanobilin:ferredoxin oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.7.5 1.3.7.5] </span></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=3nb8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nb8 OCA], [http://pdbe.org/3nb8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3nb8 RCSB], [http://www.ebi.ac.uk/pdbsum/3nb8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3nb8 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PCYA_SYNY3 PCYA_SYNY3]] Catalyzes the four-electron reduction of biliverdin IX-alpha (2-electron reduction at both the A and D rings); the reaction proceeds via an isolatable 2-electron intermediate, 181,182-dihydrobiliverdin (By similarity). | + | [https://www.uniprot.org/uniprot/PCYA_SYNY3 PCYA_SYNY3] Catalyzes the four-electron reduction of biliverdin IX-alpha (2-electron reduction at both the A and D rings); the reaction proceeds via an isolatable 2-electron intermediate, 181,182-dihydrobiliverdin (By similarity). |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nb/3nb8_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nb/3nb8_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
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| | </div> | | </div> |
| | <div class="pdbe-citations 3nb8" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 3nb8" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Phycocyanobilin:ferredoxin oxidoreductase|Phycocyanobilin:ferredoxin oxidoreductase]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Phycocyanobilin:ferredoxin oxidoreductase]] | + | [[Category: Large Structures]] |
| - | [[Category: Gae, D D]] | + | [[Category: Synechocystis sp. PCC 6803]] |
| - | [[Category: Alpha-beta-alpha sandwich]] | + | [[Category: Gae DD]] |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Radical chemistry]]
| + | |
| Structural highlights
Function
PCYA_SYNY3 Catalyzes the four-electron reduction of biliverdin IX-alpha (2-electron reduction at both the A and D rings); the reaction proceeds via an isolatable 2-electron intermediate, 181,182-dihydrobiliverdin (By similarity).
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Heme-derived linear tetrapyrroles (phytobilins) in phycobiliproteins and phytochromes perform critical light-harvesting and light-sensing roles in oxygenic photosynthetic organisms. A key enzyme in their biogenesis, phycocyanobilin:ferredoxin oxidoreductase (PcyA), catalyzes the overall four-electron reduction of biliverdin IXalpha to phycocyanobilin--the common chromophore precursor for both classes of biliproteins. This interconversion occurs via semireduced bilin radical intermediates that are profoundly stabilized by selected mutations of two critical catalytic residues, Asp105 and His88. To understand the structural basis for this stabilization and to gain insight into the overall catalytic mechanism, we report the high-resolution crystal structures of substrate-loaded Asp105Asn and His88Gln mutants of Synechocystis sp. PCC 6803 PcyA in the initial oxidized and one-electron reduced radical states. Unlike wild-type PcyA, both mutants possess a bilin-interacting axial water molecule that is ejected from the active site upon formation of the enzyme-bound neutral radical complex. Structural studies of both mutants also show that the side chain of Glu76 is unfavorably located for D-ring vinyl reduction. On the basis of these structures and companion (15)N-(1)H long-range HMQC NMR analyses to assess the protonation state of histidine residues, we propose a new mechanistic scheme for PcyA-mediated reduction of both vinyl groups of biliverdin wherein an axial water molecule, which prematurely binds and ejects from both mutants upon one electron reduction, is required for catalytic turnover of the semireduced state.
Structural basis for hydration dynamics in radical stabilization of bilin reductase mutants.,Kohler AC, Gae DD, Richley MA, Stoll S, Gunn A, Lim S, Martin SS, Doukov TI, Britt RD, Ames JB, Lagarias JC, Fisher AJ Biochemistry. 2010 Jul 27;49(29):6206-18. PMID:20557110[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Kohler AC, Gae DD, Richley MA, Stoll S, Gunn A, Lim S, Martin SS, Doukov TI, Britt RD, Ames JB, Lagarias JC, Fisher AJ. Structural basis for hydration dynamics in radical stabilization of bilin reductase mutants. Biochemistry. 2010 Jul 27;49(29):6206-18. PMID:20557110 doi:10.1021/bi100728q
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