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6c33

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Current revision (14:26, 13 March 2024) (edit) (undo)
 
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<StructureSection load='6c33' size='340' side='right'caption='[[6c33]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='6c33' size='340' side='right'caption='[[6c33]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6c33]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycs2 Mycs2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C33 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C33 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6c33]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis_MC2_155 Mycolicibacterium smegmatis MC2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C33 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6C33 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=MN:MANGANESE+(II)+ION'>MN</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]] 1.8&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MSMEI_3793 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2])</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=MN:MANGANESE+(II)+ION'>MN</scene></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=6c33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c33 OCA], [http://pdbe.org/6c33 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c33 RCSB], [http://www.ebi.ac.uk/pdbsum/6c33 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c33 ProSAT]</span></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=6c33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c33 OCA], [https://pdbe.org/6c33 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6c33 RCSB], [https://www.ebi.ac.uk/pdbsum/6c33 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6c33 ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/I7GAS0_MYCS2 I7GAS0_MYCS2]
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Mycobacterium smegmatis FenA is a nucleic acid phosphodiesterase with flap endonuclease and 5' exonuclease activities. The 1.8 A crystal structure of FenA reported here highlights as its closest homologs bacterial FEN-family enzymes ExoIX, the Pol1 exonuclease domain and phage T5 Fen. Mycobacterial FenA assimilates three active site manganese ions (M1, M2, M3) that are coordinated, directly and via waters, to a constellation of eight carboxylate side chains. We find via mutagenesis that the carboxylate contacts to all three manganese ions are essential for FenA's activities. Structures of nuclease-dead FenA mutants D125N, D148N and D208N reveal how they fail to bind one of the three active site Mn2+ ions, in a distinctive fashion for each Asn change. The structure of FenA D208N with a phosphate anion engaged by M1 and M2 in a state mimetic of a product complex suggests a mechanism for metal-catalyzed phosphodiester hydrolysis similar to that proposed for human Exo1. A distinctive feature of FenA is that it does not have the helical arch module found in many other FEN/FEN-like enzymes. Instead, this segment of FenA adopts a unique structure comprising a short 310 helix and surface beta-loop that coordinates a fourth manganese ion (M4).
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Crystal structure and mutational analysis of Mycobacterium smegmatis FenA highlight active site amino acids and three metal ions essential for flap endonuclease and 5' exonuclease activities.,Uson ML, Carl A, Goldgur Y, Shuman S Nucleic Acids Res. 2018 Apr 9. pii: 4964820. doi: 10.1093/nar/gky238. PMID:29635474<ref>PMID:29635474</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 6c33" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
*[[Exonuclease 3D structures|Exonuclease 3D structures]]
*[[Exonuclease 3D structures|Exonuclease 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Mycs2]]
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[[Category: Mycolicibacterium smegmatis MC2 155]]
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[[Category: Carl, A]]
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[[Category: Carl A]]
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[[Category: Goldgur, Y]]
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[[Category: Goldgur Y]]
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[[Category: Shuman, S]]
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[[Category: Shuman S]]
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[[Category: Uson, M L]]
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[[Category: Uson ML]]
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[[Category: Dna binding protein]]
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[[Category: Mycobacterium dna flab endonuclease fena]]
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Current revision

Mycobacterium smegmatis DNA flap endonuclease

PDB ID 6c33

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OCA

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