View source for 5mdl


==Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its O2-derivatized form by a "soak-and-freeze" derivatization method==
<StructureSection load='5mdl' size='340' side='right' caption='[[5mdl]], [[Resolution|resolution]] 1.41&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5mdl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_eutropha_h16 Alcaligenes eutropha h16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MDL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MDL FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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=O:OXYGEN+ATOM'>O</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Hydrogenase_(acceptor) Hydrogenase (acceptor)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.99.6 1.12.99.6] </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=5mdl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mdl OCA], [http://pdbe.org/5mdl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mdl RCSB], [http://www.ebi.ac.uk/pdbsum/5mdl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mdl ProSAT]</span></td></tr>
</table>
== Function ==
[[http://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. [[http://www.uniprot.org/uniprot/MBHS_CUPNH MBHS_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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5mdl" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Alcaligenes eutropha h16]]
[[Category: Kalms, J]]
[[Category: Scheerer, P]]
[[Category: Schmidt, A]]
[[Category: Aerobic hydrogen bacteria]]
[[Category: Bimetallic]]
[[Category: Dehydrogenase]]
[[Category: Dihydrogen]]
[[Category: Fe-s cluster]]
[[Category: Gas transport]]
[[Category: Hydrogen catalysis]]
[[Category: Hydrophobic tunnel]]
[[Category: Knallgasbacteria]]
[[Category: Membrane]]
[[Category: Membrane bound]]
[[Category: Metalloenzyme]]
[[Category: Metalloprotein catalytic center]]
[[Category: Ni-fe active site]]
[[Category: Oxidized state]]
[[Category: Oxidoreductase]]
[[Category: Oxygen derivatisation]]
[[Category: Oxygen derivatised state]]
[[Category: Oxygen tolerant hydrogenase]]
[[Category: Proteobacteria]]
[[Category: T-cluster]]