5mdk: Difference between revisions
New page: '''Unreleased structure''' The entry 5mdk is ON HOLD Authors: Schmidt, A., Kalms, J., Scheerer, P. Description: crystal structure of oxygen tolerant, membrane bound [NiFe] hydrogenase ... |
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The | ==Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its as-isolated form (oxidized state - state 3)== | ||
<StructureSection load='5mdk' size='340' side='right'caption='[[5mdk]], [[Resolution|resolution]] 1.50Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5mdk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Cupriavidus_necator_H16 Cupriavidus necator H16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MDK 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]] 1.5Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=F4S:FE4-S3+CLUSTER'>F4S</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NFV:NI-FE+OXIDIZED+ACTIVE+CENTER'>NFV</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=5mdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mdk OCA], [https://pdbe.org/5mdk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mdk RCSB], [https://www.ebi.ac.uk/pdbsum/5mdk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mdk ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/MBHL_CUPNH MBHL_CUPNH] This enzyme recycles the H(2) produced by nitrogenase to increase the production of ATP and to protect nitrogenase against inhibition or damage by O(2) under carbon- or phosphate-limited conditions. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
[NiFe] hydrogenases catalyze the reversible splitting of H2 into protons and electrons at a deeply buried active site. The catalytic center can be accessed by gas molecules through a hydrophobic tunnel network. While most [NiFe] hydrogenases are inactivated by O2, a small subgroup, including the membrane-bound [NiFe] hydrogenase (MBH) of Ralstonia eutropha, is able to overcome aerobic inactivation by catalytic reduction of O2 to water. This O2 tolerance relies on a special [4Fe3S] cluster that is capable of releasing two electrons upon O2 attack. Here, the O2 accessibility of the MBH gas tunnel network has been probed experimentally using a "soak-and-freeze" derivatization method, accompanied by protein X-ray crystallography and computational studies. This combined approach revealed several sites of O2 molecules within a hydrophobic tunnel network leading, via two tunnel entrances, to the catalytic center of MBH. The corresponding site occupancies were related to the O2 concentrations used for MBH crystal derivatization. The examination of the O2-derivatized data furthermore uncovered two unexpected structural alterations at the [4Fe3S] cluster, which might be related to the O2 tolerance of the enzyme. | |||
Tracking the route of molecular oxygen in O2-tolerant membrane-bound [NiFe] hydrogenase.,Kalms J, Schmidt A, Frielingsdorf S, Utesch T, Gotthard G, von Stetten D, van der Linden P, Royant A, Mroginski MA, Carpentier P, Lenz O, Scheerer P Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):E2229-E2237. doi:, 10.1073/pnas.1712267115. Epub 2018 Feb 20. PMID:29463722<ref>PMID:29463722</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5mdk" style="background-color:#fffaf0;"></div> | ||
[[Category: | == References == | ||
[[Category: Schmidt | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
[[Category: Cupriavidus necator H16]] | |||
[[Category: Large Structures]] | |||
[[Category: Kalms J]] | |||
[[Category: Scheerer P]] | |||
[[Category: Schmidt A]] | |||
Latest revision as of 21:39, 1 November 2023
Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its as-isolated form (oxidized state - state 3)Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its as-isolated form (oxidized state - state 3)
Structural highlights
FunctionMBHL_CUPNH This enzyme recycles the H(2) produced by nitrogenase to increase the production of ATP and to protect nitrogenase against inhibition or damage by O(2) under carbon- or phosphate-limited conditions. Publication Abstract from PubMed[NiFe] hydrogenases catalyze the reversible splitting of H2 into protons and electrons at a deeply buried active site. The catalytic center can be accessed by gas molecules through a hydrophobic tunnel network. While most [NiFe] hydrogenases are inactivated by O2, a small subgroup, including the membrane-bound [NiFe] hydrogenase (MBH) of Ralstonia eutropha, is able to overcome aerobic inactivation by catalytic reduction of O2 to water. This O2 tolerance relies on a special [4Fe3S] cluster that is capable of releasing two electrons upon O2 attack. Here, the O2 accessibility of the MBH gas tunnel network has been probed experimentally using a "soak-and-freeze" derivatization method, accompanied by protein X-ray crystallography and computational studies. This combined approach revealed several sites of O2 molecules within a hydrophobic tunnel network leading, via two tunnel entrances, to the catalytic center of MBH. The corresponding site occupancies were related to the O2 concentrations used for MBH crystal derivatization. The examination of the O2-derivatized data furthermore uncovered two unexpected structural alterations at the [4Fe3S] cluster, which might be related to the O2 tolerance of the enzyme. Tracking the route of molecular oxygen in O2-tolerant membrane-bound [NiFe] hydrogenase.,Kalms J, Schmidt A, Frielingsdorf S, Utesch T, Gotthard G, von Stetten D, van der Linden P, Royant A, Mroginski MA, Carpentier P, Lenz O, Scheerer P Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):E2229-E2237. doi:, 10.1073/pnas.1712267115. Epub 2018 Feb 20. PMID:29463722[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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