5d51: Difference between revisions

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New page: '''Unreleased structure''' The entry 5d51 is ON HOLD Authors: Kalms, J., Schmidt, A., Frielingsdorf, S., van der Linden, P., von Stetten, D., Lenz, O., Carpentier, P., Scheerer, P. Des...
 
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'''Unreleased structure'''


The entry 5d51 is ON HOLD
==Krypton derivatization of an O2-tolerant membrane-bound [NiFe] hydrogenase reveals a hydrophobic gas tunnel network==
<StructureSection load='5d51' size='340' side='right'caption='[[5d51]], [[Resolution|resolution]] 1.47&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5d51]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Cupriavidus_necator Cupriavidus necator]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D51 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D51 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]] 1.47&#8491;</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=KR:KRYPTON'>KR</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=5d51 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d51 OCA], [https://pdbe.org/5d51 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d51 RCSB], [https://www.ebi.ac.uk/pdbsum/5d51 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d51 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 are metalloenzymes catalyzing the reversible heterolytic cleavage of hydrogen into protons and electrons. Gas tunnels make the deeply buried active site accessible to substrates and inhibitors. Understanding the architecture and function of the tunnels is pivotal to modulating the feature of O2 tolerance in a subgroup of these [NiFe] hydrogenases, as they are interesting for developments in renewable energy technologies. Here we describe the crystal structure of the O2 -tolerant membrane-bound [NiFe] hydrogenase of Ralstonia eutropha (ReMBH), using krypton-pressurized crystals. The positions of the krypton atoms allow a comprehensive description of the tunnel network within the enzyme. A detailed overview of tunnel sizes, lengths, and routes is presented from tunnel calculations. A comparison of the ReMBH tunnel characteristics with crystal structures of other O2 -tolerant and O2 -sensitive [NiFe] hydrogenases revealed considerable differences in tunnel size and quantity between the two groups, which might be related to the striking feature of O2 tolerance.


Authors: Kalms, J., Schmidt, A., Frielingsdorf, S., van der Linden, P., von Stetten, D., Lenz, O., Carpentier, P., Scheerer, P.
Krypton Derivatization of an O2 -Tolerant Membrane-Bound [NiFe] Hydrogenase Reveals a Hydrophobic Tunnel Network for Gas Transport.,Kalms J, Schmidt A, Frielingsdorf S, van der Linden P, von Stetten D, Lenz O, Carpentier P, Scheerer P Angew Chem Int Ed Engl. 2016 Apr 25;55(18):5586-90. doi: 10.1002/anie.201508976. , Epub 2016 Feb 23. PMID:26913499<ref>PMID:26913499</ref>


Description:  
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Von Stetten, D]]
<div class="pdbe-citations 5d51" style="background-color:#fffaf0;"></div>
[[Category: Lenz, O]]
== References ==
[[Category: Frielingsdorf, S]]
<references/>
[[Category: Scheerer, P]]
__TOC__
[[Category: Van Der Linden, P]]
</StructureSection>
[[Category: Kalms, J]]
[[Category: Cupriavidus necator]]
[[Category: Schmidt, A]]
[[Category: Large Structures]]
[[Category: Carpentier, P]]
[[Category: Carpentier P]]
[[Category: Frielingsdorf S]]
[[Category: Kalms J]]
[[Category: Lenz O]]
[[Category: Scheerer P]]
[[Category: Schmidt A]]
[[Category: Van der Linden P]]
[[Category: Von Stetten D]]

Latest revision as of 14:24, 10 January 2024

Krypton derivatization of an O2-tolerant membrane-bound [NiFe] hydrogenase reveals a hydrophobic gas tunnel networkKrypton derivatization of an O2-tolerant membrane-bound [NiFe] hydrogenase reveals a hydrophobic gas tunnel network

Structural highlights

5d51 is a 2 chain structure with sequence from Cupriavidus necator. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.47Å
Ligands:, , , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.

Publication Abstract from PubMed

[NiFe] hydrogenases are metalloenzymes catalyzing the reversible heterolytic cleavage of hydrogen into protons and electrons. Gas tunnels make the deeply buried active site accessible to substrates and inhibitors. Understanding the architecture and function of the tunnels is pivotal to modulating the feature of O2 tolerance in a subgroup of these [NiFe] hydrogenases, as they are interesting for developments in renewable energy technologies. Here we describe the crystal structure of the O2 -tolerant membrane-bound [NiFe] hydrogenase of Ralstonia eutropha (ReMBH), using krypton-pressurized crystals. The positions of the krypton atoms allow a comprehensive description of the tunnel network within the enzyme. A detailed overview of tunnel sizes, lengths, and routes is presented from tunnel calculations. A comparison of the ReMBH tunnel characteristics with crystal structures of other O2 -tolerant and O2 -sensitive [NiFe] hydrogenases revealed considerable differences in tunnel size and quantity between the two groups, which might be related to the striking feature of O2 tolerance.

Krypton Derivatization of an O2 -Tolerant Membrane-Bound [NiFe] Hydrogenase Reveals a Hydrophobic Tunnel Network for Gas Transport.,Kalms J, Schmidt A, Frielingsdorf S, van der Linden P, von Stetten D, Lenz O, Carpentier P, Scheerer P Angew Chem Int Ed Engl. 2016 Apr 25;55(18):5586-90. doi: 10.1002/anie.201508976. , Epub 2016 Feb 23. PMID:26913499[1]

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

References

  1. ↑ Kalms J, Schmidt A, Frielingsdorf S, van der Linden P, von Stetten D, Lenz O, Carpentier P, Scheerer P. Krypton Derivatization of an O2 -Tolerant Membrane-Bound [NiFe] Hydrogenase Reveals a Hydrophobic Tunnel Network for Gas Transport. Angew Chem Int Ed Engl. 2016 Apr 25;55(18):5586-90. doi: 10.1002/anie.201508976. , Epub 2016 Feb 23. PMID:26913499 doi:http://dx.doi.org/10.1002/anie.201508976

5d51, resolution 1.47Å

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