1yrq: Difference between revisions
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< | ==Structure of the ready oxidized form of [NiFe]-hydrogenase== | ||
<StructureSection load='1yrq' size='340' side='right'caption='[[1yrq]], [[Resolution|resolution]] 2.10Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1yrq]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Solidesulfovibrio_fructosivorans Solidesulfovibrio fructosivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YRQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YRQ 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]] 2.1Å, 2 models</td></tr> | |||
-- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FCO:CARBONMONOXIDE-(DICYANO)+IRON'>FCO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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=1yrq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yrq OCA], [https://pdbe.org/1yrq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yrq RCSB], [https://www.ebi.ac.uk/pdbsum/1yrq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yrq ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/PHNS_SOLFR PHNS_SOLFR] Involved in hydrogen uptake for the anaerobic reduction of sulfate to hydrogen sulfide in an electron transport chain. Cytochrome c3 is the physiological electron acceptor. | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yr/1yrq_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1yrq ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
[NiFe] hydrogenases catalyze the reversible heterolytic cleavage of molecular hydrogen. Several oxidized, inactive states of these enzymes are known that are distinguishable by their very different activation properties. So far, the structural basis for this difference has not been understood because of lack of relevant crystallographic data. Here, we present the crystal structure of the ready Ni-B state of Desulfovibrio fructosovorans [NiFe] hydrogenase and show it to have a putative mu-hydroxo Ni-Fe bridging ligand at the active site. On the other hand, a new, improved refinement procedure of the X-ray diffraction data obtained for putative unready Ni-A/Ni-SU states resulted in a more elongated electron density for the bridging ligand, suggesting that it is a diatomic species. The slow activation of the Ni-A state, compared with the rapid activation of the Ni-B state, is therefore proposed to result from the different chemical nature of the ligands in the two oxidized species. Our results along with very recent electrochemical studies suggest that the diatomic ligand could be hydro-peroxide. | |||
Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases.,Volbeda A, Martin L, Cavazza C, Matho M, Faber BW, Roseboom W, Albracht SP, Garcin E, Rousset M, Fontecilla-Camps JC J Biol Inorg Chem. 2005 May;10(3):239-49. Epub 2005 Apr 1. PMID:15803334<ref>PMID:15803334</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1yrq" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Large Structures]] | ||
[[Category: Solidesulfovibrio fructosivorans]] | |||
[[Category: Albracht SP]] | |||
== | [[Category: Cavazza C]] | ||
< | [[Category: Faber BW]] | ||
[[Category: | [[Category: Fontecilla-Camps JC]] | ||
[[Category: | [[Category: Garcin E]] | ||
[[Category: Albracht | [[Category: Martin L]] | ||
[[Category: Cavazza | [[Category: Matho M]] | ||
[[Category: Faber | [[Category: Roseboom W]] | ||
[[Category: Fontecilla-Camps | [[Category: Rousset M]] | ||
[[Category: Garcin | [[Category: Volbeda A]] | ||
[[Category: Martin | |||
[[Category: Matho | |||
[[Category: Roseboom | |||
[[Category: Rousset | |||
[[Category: Volbeda | |||
Latest revision as of 10:32, 9 October 2024
Structure of the ready oxidized form of [NiFe]-hydrogenaseStructure of the ready oxidized form of [NiFe]-hydrogenase
Structural highlights
FunctionPHNS_SOLFR Involved in hydrogen uptake for the anaerobic reduction of sulfate to hydrogen sulfide in an electron transport chain. Cytochrome c3 is the physiological electron acceptor. 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[NiFe] hydrogenases catalyze the reversible heterolytic cleavage of molecular hydrogen. Several oxidized, inactive states of these enzymes are known that are distinguishable by their very different activation properties. So far, the structural basis for this difference has not been understood because of lack of relevant crystallographic data. Here, we present the crystal structure of the ready Ni-B state of Desulfovibrio fructosovorans [NiFe] hydrogenase and show it to have a putative mu-hydroxo Ni-Fe bridging ligand at the active site. On the other hand, a new, improved refinement procedure of the X-ray diffraction data obtained for putative unready Ni-A/Ni-SU states resulted in a more elongated electron density for the bridging ligand, suggesting that it is a diatomic species. The slow activation of the Ni-A state, compared with the rapid activation of the Ni-B state, is therefore proposed to result from the different chemical nature of the ligands in the two oxidized species. Our results along with very recent electrochemical studies suggest that the diatomic ligand could be hydro-peroxide. Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases.,Volbeda A, Martin L, Cavazza C, Matho M, Faber BW, Roseboom W, Albracht SP, Garcin E, Rousset M, Fontecilla-Camps JC J Biol Inorg Chem. 2005 May;10(3):239-49. Epub 2005 Apr 1. PMID:15803334[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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