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| | ==1.9 Angstrom structure of the thermophilic exonuclease III homologue Mth0212== | | ==1.9 Angstrom structure of the thermophilic exonuclease III homologue Mth0212== |
| - | <StructureSection load='3fzi' size='340' side='right' caption='[[3fzi]], [[Resolution|resolution]] 1.90Å' scene=''> | + | <StructureSection load='3fzi' size='340' side='right'caption='[[3fzi]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3fzi]] is a 1 chain structure with sequence 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=3FZI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FZI FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3fzi]] is a 1 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=3FZI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FZI FirstGlance]. <br> |
| - | </td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3g00|3g00]], [[3g0a|3g0a]], [[3g0r|3g0r]], [[3g2c|3g2c]], [[3g2d|3g2d]], [[3g38|3g38]], [[3g3c|3g3c]], [[3g1k|3g1k]], [[3g3y|3g3y]], [[3g4t|3g4t]], [[3g8v|3g8v]], [[3g91|3g91]], [[3ga6|3ga6]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mth0212, MTH212, MTH_212 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 Methanothermobacter thermautotrophicus])</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=3fzi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fzi OCA], [https://pdbe.org/3fzi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fzi RCSB], [https://www.ebi.ac.uk/pdbsum/3fzi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fzi ProSAT]</span></td></tr> |
| - | <tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exodeoxyribonuclease_III Exodeoxyribonuclease III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.2 3.1.11.2] </span></td></tr>
| + | </table> |
| - | <tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3fzi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fzi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fzi RCSB], [http://www.ebi.ac.uk/pdbsum/3fzi PDBsum]</span></td></tr> | + | == Function == |
| - | <table> | + | [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> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fz/3fzi_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fz/3fzi_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> |
| | </jmolCheckbox> | | </jmolCheckbox> |
| - | </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/chain_selection.php?pdb_ID=2ata ConSurf]. | + | </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=3fzi ConSurf]. |
| | <div style="clear:both"></div> | | <div style="clear:both"></div> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 3fzi" style="background-color:#fffaf0;"></div> |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Exonuclease|Exonuclease]] | + | *[[Exonuclease 3D structures|Exonuclease 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Exodeoxyribonuclease III]] | + | [[Category: Large Structures]] |
| - | [[Category: Methanothermobacter thermautotrophicus]] | + | [[Category: Methanothermobacter thermautotrophicus str. Delta H]] |
| - | [[Category: Dickmanns, A.]] | + | [[Category: Dickmanns A]] |
| - | [[Category: Ficner, R.]] | + | [[Category: Ficner R]] |
| - | [[Category: Lakomek, K.]] | + | [[Category: Lakomek K]] |
| - | [[Category: 2'-deoxyuridine endonuclease]]
| + | |
| - | [[Category: Alpha/beta-sandwich]]
| + | |
| - | [[Category: Ap endonuclease]]
| + | |
| - | [[Category: Double-strand specific 3'-5' exonuclease]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
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).[1] [2] [3] [4]
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 PubMed
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'-->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[5]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Pfeifer S, Greiner-Stöffele T. A recombinant exonuclease III homologue of the thermophilic archaeon Methanothermobacter thermautotrophicus. DNA Repair (Amst). 2005 Apr 4;4(4):433-44. PMID:15725624 doi:10.1016/j.dnarep.2004.11.008
- ↑ Georg J, Schomacher L, Chong JP, Majernik AI, Raabe M, Urlaub H, Muller S, Ciirdaeva E, Kramer W, Fritz HJ. The Methanothermobacter thermautotrophicus ExoIII homologue Mth212 is a DNA uridine endonuclease. Nucleic Acids Res. 2006;34(18):5325-36. Epub 2006 Sep 29. PMID:17012282 doi:10.1093/nar/gkl604
- ↑ Schomacher L, Chong JP, McDermott P, Kramer W, Fritz HJ. DNA uracil repair initiated by the archaeal ExoIII homologue Mth212 via direct strand incision. Nucleic Acids Res. 2009 Apr;37(7):2283-93. PMID:19240141 doi:10.1093/nar/gkp102
- ↑ Schomacher L, Schürer KA, Ciirdaeva E, McDermott P, Chong JP, Kramer W, Fritz HJ. Archaeal DNA uracil repair via direct strand incision: A minimal system reconstituted from purified components. DNA Repair (Amst). 2010 Apr 4;9(4):438-47. PMID:20129830 doi:10.1016/j.dnarep.2010.01.004
- ↑ Lakomek K, Dickmanns A, Ciirdaeva E, Schomacher L, Ficner R. Crystal structure analysis of DNA uridine endonuclease Mth212 bound to DNA. J Mol Biol. 2010 Jun 18;399(4):604-17. Epub 2010 Apr 29. PMID:20434457 doi:10.1016/j.jmb.2010.04.044
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