5o4m: Difference between revisions
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<StructureSection load='5o4m' size='340' side='right'caption='[[5o4m]], [[Resolution|resolution]] 2.10Å' scene=''> | <StructureSection load='5o4m' size='340' side='right'caption='[[5o4m]], [[Resolution|resolution]] 2.10Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5o4m]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O4M OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[5o4m]] 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=5O4M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5O4M FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9KH:6-carboxy+methyl-4-hydroxy-2-pyridinol'>9KH</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</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]] 2.1Å</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=9KH:6-carboxy+methyl-4-hydroxy-2-pyridinol'>9KH</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</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=5o4m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o4m OCA], [https://pdbe.org/5o4m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5o4m RCSB], [https://www.ebi.ac.uk/pdbsum/5o4m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5o4m 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 22:08, 29 November 2023
Fresh crystals of HcgC from Methanococcus maripaludis cocrystallized with SAH and pyridinolFresh crystals of HcgC from Methanococcus maripaludis cocrystallized with SAH 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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