3g0r

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{{Seed}}
 
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[[Image:3g0r.jpg|left|200px]]
 
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==Complex of Mth0212 and an 8bp dsDNA with distorted ends==
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The line below this paragraph, containing "STRUCTURE_3g0r", creates the "Structure Box" on the page.
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<StructureSection load='3g0r' size='340' side='right'caption='[[3g0r]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3g0r]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus_str._Delta_H Methanothermobacter thermautotrophicus str. Delta H]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G0R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G0R FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
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<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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
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{{STRUCTURE_3g0r| PDB=3g0r | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3g0r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g0r OCA], [https://pdbe.org/3g0r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g0r RCSB], [https://www.ebi.ac.uk/pdbsum/3g0r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g0r ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/UREND_METTH UREND_METTH] Involved in DNA uracil repair (PubMed:17012282, PubMed:19240141, PubMed:20129830). Recognizes DNA uracil residues within double-stranded DNA and initiates DNA-U repair by endonucleotic incision on the 5'-side of the 2'-d-uridine residue, irrespective of the nature of the opposing nucleotide (PubMed:17012282, PubMed:19240141, PubMed:20129830). In addition, acts as an apurinic/apyrimidinic (AP) endonuclease hydrolyzing the DNA phosphodiester backbone immediately at the 5'-side of AP sites, and as a 3'-5' exonuclease (PubMed:15725624, PubMed:17012282). Strongly binds to double-stranded DNA (PubMed:15725624).<ref>PMID:15725624</ref> <ref>PMID:17012282</ref> <ref>PMID:19240141</ref> <ref>PMID:20129830</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g0/3g0r_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3g0r ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The 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'--&gt;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.
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===Complex of Mth0212 and an 8bp dsDNA with distorted ends===
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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<ref>PMID:20434457</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3g0r" style="background-color:#fffaf0;"></div>
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==About this Structure==
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==See Also==
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3G0R is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G0R OCA].
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*[[Exonuclease 3D structures|Exonuclease 3D structures]]
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== References ==
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==Reference==
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<references/>
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<ref group="xtra">PMID:17012282</ref><references group="xtra"/>
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__TOC__
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[[Category: Exodeoxyribonuclease III]]
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</StructureSection>
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[[Category: Methanothermobacter thermautotrophicus]]
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[[Category: Large Structures]]
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[[Category: Dickmanns, A.]]
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[[Category: Methanothermobacter thermautotrophicus str. Delta H]]
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[[Category: Ficner, R.]]
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[[Category: Dickmanns A]]
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[[Category: Lakomek, K.]]
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[[Category: Ficner R]]
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[[Category: 2'-deoxyuridine endonuclease]]
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[[Category: Lakomek K]]
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[[Category: Ap endonuclease]]
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[[Category: Double-strand specific 3'-5' exonuclease]]
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[[Category: Hydrolase-dna complex]]
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[[Category: Protein-dna complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 10 14:26:07 2010''
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Current revision

Complex of Mth0212 and an 8bp dsDNA with distorted ends

PDB ID 3g0r

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