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| | ==The mechanism of Hydrogen Activation by NiFe-hydrogenases.== | | ==The mechanism of Hydrogen Activation by NiFe-hydrogenases.== |
| - | <StructureSection load='5a4f' size='340' side='right' caption='[[5a4f]], [[Resolution|resolution]] 1.25Å' scene=''> | + | <StructureSection load='5a4f' size='340' side='right'caption='[[5a4f]], [[Resolution|resolution]] 1.25Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5a4f]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_str._k-12_substr._mc4100 Escherichia coli str. k-12 substr. mc4100]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5A4F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5A4F FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5a4f]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_str._K-12_substr._MC4100 Escherichia coli str. K-12 substr. MC4100]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5A4F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5A4F 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=FCO:CARBONMONOXIDE-(DICYANO)+IRON'>FCO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SF3:FE4-S3+CLUSTER'>SF3</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.25Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></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=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <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>, <scene name='pdbligand=SF3:FE4-S3+CLUSTER'>SF3</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5a4i|5a4i]], [[5a4m|5a4m]]</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=5a4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a4f OCA], [https://pdbe.org/5a4f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5a4f RCSB], [https://www.ebi.ac.uk/pdbsum/5a4f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5a4f 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/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=5a4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a4f OCA], [http://pdbe.org/5a4f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5a4f RCSB], [http://www.ebi.ac.uk/pdbsum/5a4f PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/MBHL_ECOLI MBHL_ECOLI]] This is one of three E.coli hydrogenases synthesized in response to different physiological conditions. HYD1 is believed to have a role in hydrogen cycling during fermentative growth. [[http://www.uniprot.org/uniprot/MBHS_ECOLI MBHS_ECOLI]] This is one of three E.coli hydrogenases synthesized in response to different physiological conditions. HYD1 is believed to have a role in hydrogen cycling during fermentative growth. | + | [https://www.uniprot.org/uniprot/MBHL_ECOLI MBHL_ECOLI] This is one of three E.coli hydrogenases synthesized in response to different physiological conditions. HYD1 is believed to have a role in hydrogen cycling during fermentative growth. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Escherichia coli str. k-12 substr. mc4100]] | + | [[Category: Escherichia coli str. K-12 substr. MC4100]] |
| - | [[Category: Armstrong, F A]] | + | [[Category: Large Structures]] |
| - | [[Category: Brooke, E J]] | + | [[Category: Armstrong FA]] |
| - | [[Category: Carr, S B]] | + | [[Category: Brooke EJ]] |
| - | [[Category: Evans, R M]] | + | [[Category: Carr SB]] |
| - | [[Category: Nomerotskaia, E]] | + | [[Category: Evans RM]] |
| - | [[Category: Phillips, S E.V]] | + | [[Category: Nomerotskaia E]] |
| - | [[Category: Sargent, F]] | + | [[Category: Phillips SEV]] |
| - | [[Category: Wehlin, S A.M]] | + | [[Category: Sargent F]] |
| - | [[Category: Catalysis]]
| + | [[Category: Wehlin SAM]] |
| - | [[Category: Fes cluster]]
| + | |
| - | [[Category: Hydrogen lysis]]
| + | |
| - | [[Category: Nife-hydrogenase]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Redox]]
| + | |
| Structural highlights
5a4f is a 4 chain structure with sequence from Escherichia coli str. K-12 substr. MC4100. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.25Å |
| Ligands: | , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
MBHL_ECOLI This is one of three E.coli hydrogenases synthesized in response to different physiological conditions. HYD1 is believed to have a role in hydrogen cycling during fermentative growth.
Publication Abstract from PubMed
The active site of [NiFe] hydrogenases contains a strictly conserved arginine that suspends a guanidine nitrogen atom <4.5 A above the nickel and iron atoms. The guanidine headgroup interacts with the side chains of two conserved aspartic acid residues to complete an outer-shell canopy that has thus far proved intractable to investigation by site-directed mutagenesis. Using hydrogenase-1 from Escherichia coli, the strictly conserved residues R509 and D574 have been replaced by lysine (R509K) and asparagine (D574N) and the highly conserved D118 has been replaced by alanine (D118A) or asparagine (D118N/D574N). Each enzyme variant is stable, and their [(RS)2Nimu(SR)2Fe(CO)(CN)2] inner coordination shells are virtually unchanged. The R509K variant had >100-fold lower activity than native enzyme. Conversely, the variants D574N, D118A and D118N/D574N, in which the position of the guanidine headgroup is retained, showed 83%, 26% and 20% activity, respectively. The special kinetic requirement for R509 implicates the suspended guanidine group as the general base in H2 activation by [NiFe] hydrogenases.
Mechanism of hydrogen activation by [NiFe] hydrogenases.,Evans RM, Brooke EJ, Wehlin SA, Nomerotskaia E, Sargent F, Carr SB, Phillips SE, Armstrong FA Nat Chem Biol. 2015 Nov 30. doi: 10.1038/nchembio.1976. PMID:26619250[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Evans RM, Brooke EJ, Wehlin SA, Nomerotskaia E, Sargent F, Carr SB, Phillips SE, Armstrong FA. Mechanism of hydrogen activation by [NiFe] hydrogenases. Nat Chem Biol. 2015 Nov 30. doi: 10.1038/nchembio.1976. PMID:26619250 doi:http://dx.doi.org/10.1038/nchembio.1976
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