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5b42

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==Crystal structure of the C-terminal endonuclease domain of Aquifex aeolicus MutL.==
==Crystal structure of the C-terminal endonuclease domain of Aquifex aeolicus MutL.==
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<StructureSection load='5b42' size='340' side='right' caption='[[5b42]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
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<StructureSection load='5b42' size='340' side='right'caption='[[5b42]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5b42]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B42 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B42 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5b42]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus_VF5 Aquifex aeolicus VF5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B42 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B42 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
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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]] 1.35&#8491;</td></tr>
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<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=5b42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b42 OCA], [http://pdbe.org/5b42 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b42 RCSB], [http://www.ebi.ac.uk/pdbsum/5b42 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b42 ProSAT]</span></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=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
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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=5b42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b42 OCA], [https://pdbe.org/5b42 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b42 RCSB], [https://www.ebi.ac.uk/pdbsum/5b42 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b42 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/MUTL_AQUAE MUTL_AQUAE]] This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. May act as a "molecular matchmaker", a protein that promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex (By similarity).
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[https://www.uniprot.org/uniprot/MUTL_AQUAE MUTL_AQUAE] This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. May act as a "molecular matchmaker", a protein that promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex (By similarity).
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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In early reactions of DNA mismatch repair, MutS recognizes mismatched bases and activates MutL endonuclease to incise the error-containing strand of the duplex. DNA sliding clamp is responsible for directing the MutL-dependent nicking to the newly synthesized/error-containing strand. In Bacillus subtilis MutL, the beta-clamp-interacting motif (beta motif) of the C-terminal domain (CTD) is essential for both in vitro direct interaction with beta-clamp and in vivo repair activity. A large cluster of negatively charged residues on the B. subtilis MutL CTD prevents nonspecific DNA binding until beta clamp interaction neutralizes the negative charge. We found that there are some bacterial phyla whose MutL endonucleases lack the beta motif. For example, the region corresponding to the beta motif is completely missing in Aquifex aeolicus MutL, and critical amino acid residues in the beta motif are not conserved in Thermus thermophilus MutL. We then revealed the 1.35 A-resolution crystal structure of A. aeolicus MutL CTD, which lacks the beta motif but retains the metal-binding site for the endonuclease activity. Importantly, there was no negatively charged cluster on its surface. It was confirmed that CTDs of beta motif-lacking MutLs, A. aeolicus MutL and T. thermophilus MutL, efficiently incise DNA even in the absence of beta-clamp and that beta-clamp shows no detectable enhancing effect on their activity. In contrast, CTD of Streptococcus mutans, a beta motif-containing MutL, required beta-clamp for the digestion of DNA. We propose that MutL endonucleases are divided into three subfamilies on the basis of their structural features and dependence on beta-clamp.
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Structural Features and Functional Dependency on beta-Clamp Define Distinct Subfamilies of Bacterial Mismatch Repair Endonuclease MutL.,Fukui K, Baba S, Kumasaka T, Yano T J Biol Chem. 2016 Aug 12;291(33):16990-7000. doi: 10.1074/jbc.M116.739664. Epub, 2016 Jul 1. PMID:27369079<ref>PMID:27369079</ref>
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==See Also==
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*[[DNA mismatch repair protein 3D structures|DNA mismatch repair protein 3D structures]]
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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 5b42" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Baba, S]]
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[[Category: Aquifex aeolicus VF5]]
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[[Category: Fukui, K]]
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[[Category: Large Structures]]
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[[Category: Kumasaka, T]]
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[[Category: Baba S]]
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[[Category: Yano, T]]
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[[Category: Fukui K]]
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[[Category: Cadmium]]
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[[Category: Kumasaka T]]
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[[Category: Dna binding protein]]
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[[Category: Yano T]]
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[[Category: Endonuclease]]
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[[Category: Mismatch repair]]
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Current revision

Crystal structure of the C-terminal endonuclease domain of Aquifex aeolicus MutL.

PDB ID 5b42

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