3g2c: Difference between revisions

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{{Seed}}
[[Image:3g2c.png|left|200px]]


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==Mth0212 in complex with a short ssDNA (CGTA)==
The line below this paragraph, containing "STRUCTURE_3g2c", creates the "Structure Box" on the page.
<StructureSection load='3g2c' size='340' side='right'caption='[[3g2c]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[3g2c]] is a 3 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=3G2C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G2C FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
{{STRUCTURE_3g2c|  PDB=3g2c  |  SCENE=  }}
<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>
== Function ==
[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 ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <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>
    <text>to colour the structure by Evolutionary Conservation</text>
  </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/main_output.php?pdb_ID=3g2c ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== 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'--&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.


===Mth0212 in complex with a short ssDNA (CGTA)===
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>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3g2c" style="background-color:#fffaf0;"></div>


<!--
==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_20434457}}, adds the Publication Abstract to the page
*[[Exonuclease 3D structures|Exonuclease 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 20434457 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_20434457}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
3G2C is a 3 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=3G2C OCA].
[[Category: Methanothermobacter thermautotrophicus str. Delta H]]
 
[[Category: Dickmanns A]]
==Reference==
[[Category: Ficner R]]
<ref group="xtra">PMID:20434457</ref><ref group="xtra">PMID:17012282</ref><references group="xtra"/>
[[Category: Lakomek K]]
[[Category: Exodeoxyribonuclease III]]
[[Category: Methanothermobacter thermautotrophicus]]
[[Category: Dickmanns, A.]]
[[Category: Ficner, R.]]
[[Category: Lakomek, K.]]
[[Category: Flipped nucleotide]]
[[Category: Hydrolase-dna complex]]
[[Category: Mg2+]]
[[Category: Po4]]
[[Category: Protein-dna complex]]
[[Category: Single-stranded dna]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu May 20 09:05:42 2010''

Latest revision as of 18:35, 1 November 2023

Mth0212 in complex with a short ssDNA (CGTA)Mth0212 in complex with a short ssDNA (CGTA)

Structural highlights

3g2c is a 3 chain structure with sequence from Methanothermobacter thermautotrophicus str. Delta H. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.3Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

  1. ↑ 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
  2. ↑ 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
  3. ↑ 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
  4. ↑ 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
  5. ↑ 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

3g2c, resolution 2.30Å

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