5o4h: Difference between revisions
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<StructureSection load='5o4h' size='340' side='right'caption='[[5o4h]], [[Resolution|resolution]] 1.75Å' scene=''> | <StructureSection load='5o4h' size='340' side='right'caption='[[5o4h]], [[Resolution|resolution]] 1.75Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5o4h]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O4H OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[5o4h]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanococcus_maripaludis_S2 Methanococcus maripaludis S2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O4H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5O4H FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PE4:2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL'>PE4</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</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]] 1.75Å</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PE4:2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL'>PE4</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5o4h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o4h OCA], [https://pdbe.org/5o4h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5o4h RCSB], [https://www.ebi.ac.uk/pdbsum/5o4h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5o4h ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/Q6LX54_METMP Q6LX54_METMP] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Bai | [[Category: Methanococcus maripaludis S2]] | ||
[[Category: Ermler | [[Category: Bai L]] | ||
[[Category: Hu | [[Category: Ermler U]] | ||
[[Category: Shima | [[Category: Hu X]] | ||
[[Category: Wagner | [[Category: Shima S]] | ||
[[Category: Xu | [[Category: Wagner T]] | ||
[[Category: Xu T]] | |||
Latest revision as of 22:07, 29 November 2023
HcgC from Methanococcus maripaludis cocrystallized with SAM and pyridinolHcgC from Methanococcus maripaludis cocrystallized with SAM and pyridinol
Structural highlights
FunctionPublication Abstract from PubMed[Fe]-hydrogenase hosts an iron-guanylylpyridinol (FeGP) cofactor. The FeGP cofactor contains a pyridinol ring substituted with GMP, two methyl groups, and an acylmethyl group. HcgC, an enzyme involved in FeGP biosynthesis, catalyzes methyl transfer from S-adenosylmethionine (SAM) to C3 of 6-carboxymethyl-5-methyl-4-hydroxy-2-pyridinol (2). We report on the ternary structure of HcgC/S-adenosylhomocysteine (SAH, the demethylated product of SAM) and 2 at 1.7 A resolution. The proximity of C3 of substrate 2 and the S atom of SAH indicates a catalytically productive geometry. The hydroxy and carboxy groups of substrate 2 are hydrogen-bonded with I115 and T179, as well as through a series of water molecules linked with polar and a few protonatable groups. These interactions stabilize the deprotonated state of the hydroxy groups and a keto form of substrate 2, through which the nucleophilicity of C3 is increased by resonance effects. Complemented by mutational analysis, a structure-based catalytic mechanism was proposed. A Water-Bridged H-Bonding Network Contributes to the Catalysis of the SAM-Dependent C-Methyltransferase HcgC.,Bai L, Wagner T, Xu T, Hu X, Ermler U, Shima S Angew Chem Int Ed Engl. 2017 Jul 6. doi: 10.1002/anie.201705605. PMID:28682478[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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