3g2c: Difference between revisions
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==Mth0212 in complex with a short ssDNA (CGTA)== | ==Mth0212 in complex with a short ssDNA (CGTA)== | ||
<StructureSection load='3g2c' size='340' side='right' caption='[[3g2c]], [[Resolution|resolution]] 2.30Å' scene=''> | <StructureSection load='3g2c' size='340' side='right'caption='[[3g2c]], [[Resolution|resolution]] 2.30Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3g2c]] is a 3 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3g2c]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Metth Metth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G2C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G2C FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3fzi|3fzi]], [[3g00|3g00]], [[3g0a|3g0a]], [[3g0r|3g0r]], [[3g1k|3g1k]], [[3g2d|3g2d]], [[3g38|3g38]], [[3g3c|3g3c]], [[3g3y|3g3y]], [[3g4t|3g4t]], [[3g8v|3g8v]], [[3g91|3g91]], [[3ga6|3ga6]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3fzi|3fzi]], [[3g00|3g00]], [[3g0a|3g0a]], [[3g0r|3g0r]], [[3g1k|3g1k]], [[3g2d|3g2d]], [[3g38|3g38]], [[3g3c|3g3c]], [[3g3y|3g3y]], [[3g4t|3g4t]], [[3g8v|3g8v]], [[3g91|3g91]], [[3ga6|3ga6]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mth0212, MTH212, MTH_212 ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mth0212, MTH212, MTH_212 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=187420 METTH])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Exodeoxyribonuclease_III Exodeoxyribonuclease III], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.2 3.1.11.2] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3g2c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g2c OCA], [https://pdbe.org/3g2c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g2c RCSB], [https://www.ebi.ac.uk/pdbsum/3g2c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g2c ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
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Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g2/3g2c_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g2/3g2c_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
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</div> | </div> | ||
<div class="pdbe-citations 3g2c" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 3g2c" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Exonuclease 3D structures|Exonuclease 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Exodeoxyribonuclease III]] | [[Category: Exodeoxyribonuclease III]] | ||
[[Category: Large Structures]] | |||
[[Category: Metth]] | [[Category: Metth]] | ||
[[Category: Dickmanns, A]] | [[Category: Dickmanns, A]] | ||
Revision as of 10:54, 9 March 2022
Mth0212 in complex with a short ssDNA (CGTA)Mth0212 in complex with a short ssDNA (CGTA)
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe reliable repair of pre-mutagenic U/G mismatches that originated from hydrolytic cytosine deamination is crucial for the maintenance of the correct genomic information. In most organisms, any uracil base in DNA is attacked by uracil DNA glycosylases (UDGs), but at least in Methanothermobacter thermautotrophicus DeltaH, an alternative strategy has evolved. The exonuclease III homologue Mth212 from the thermophilic archaeon M. thermautotrophicus DeltaH exhibits a DNA uridine endonuclease activity in addition to the apyrimidinic/apurinic site endonuclease and 3'-->5'exonuclease functions. Mth212 alone compensates for the lack of a UDG in a single-step reaction thus substituting the two-step pathway that requires the consecutive action of UDG and apyrimidinic/apurinic site endonuclease. In order to gain deeper insight into the structural basis required for the specific uridine recognition by Mth212, we have characterized the enzyme by means of X-ray crystallography. Structures of Mth212 wild-type or mutant proteins either alone or in complex with DNA substrates and products have been determined to a resolution of up to 1.2 A, suggesting key residues for the uridine endonuclease activity. The insertion of the side chain of Arg209 into the DNA helical base stack resembles interactions observed in human UDG and seems to be crucial for the uridine recognition. In addition, Ser171, Asn153, and Lys125 in the substrate binding pocket appear to have important functions in the discrimination of aberrant uridine against naturally occurring thymidine and cytosine residues in double-stranded DNA. Crystal structure analysis of DNA uridine endonuclease Mth212 bound to DNA.,Lakomek K, Dickmanns A, Ciirdaeva E, Schomacher L, Ficner R J Mol Biol. 2010 Jun 18;399(4):604-17. Epub 2010 Apr 29. PMID:20434457[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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