This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

3g91

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

1.2 Angstrom structure of the exonuclease III homologue Mth0212

Structural highlights

3g91 is a 1 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 1.23Å
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.

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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3g91"

Categories: Large Structures | Methanothermobacter thermautotrophicus str. Delta H | Dickmanns A | Ficner R | Lakomek K

@@ Line 1: / Line 1: @@
 ==1.2 Angstrom structure of the exonuclease III homologue Mth0212==
-<StructureSection load='3g91' size='340' side='right' caption='[[3g91]], [[Resolution|resolution]] 1.23&Aring;' scene=''>
+<StructureSection load='3g91' size='340' side='right'caption='[[3g91]], [[Resolution|resolution]] 1.23&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3g91]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Metth Metth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G91 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G91 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3g91]] 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=3G91 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G91 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=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.23&#8491;</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]], [[3g2c|3g2c]], [[3g2d|3g2d]], [[3g38|3g38]], [[3g3c|3g3c]], [[3g3y|3g3y]], [[3g4t|3g4t]], [[3g8v|3g8v]], [[3ga6|3ga6]]</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=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-<tr id='gene'><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=187420 METTH])</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=3g91 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g91 OCA], [https://pdbe.org/3g91 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g91 RCSB], [https://www.ebi.ac.uk/pdbsum/3g91 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g91 ProSAT]</span></td></tr>
-<tr id='activity'><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>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3g91 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g91 OCA], [http://pdbe.org/3g91 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g91 RCSB], [http://www.ebi.ac.uk/pdbsum/3g91 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3g91 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/g9/3g91_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g9/3g91_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 29: / Line 29: @@
 </div>
 <div class="pdbe-citations 3g91" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Exonuclease 3D structures|Exonuclease 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Exodeoxyribonuclease III]]
+[[Category: Large Structures]]
-[[Category: Metth]]
+[[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'-desoxyuridine endonuclease]]
-[[Category: Ap endonuclease]]
-[[Category: Double-strand specific 3'-5' exonuclease]]
-[[Category: Hydrolase]]

3g91

From Proteopedia

Current revision

1.2 Angstrom structure of the exonuclease III homologue Mth0212

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox