6c36: Difference between revisions

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<StructureSection load='6c36' size='340' side='right'caption='[[6c36]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='6c36' size='340' side='right'caption='[[6c36]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6c36]] 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=6C36 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C36 FirstGlance]. <br>
<table><tr><td colspan='2'>[[6c36]] 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=6C36 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6C36 FirstGlance]. <br>
</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>, <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]] 1.9&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6c33|6c33]]</td></tr>
<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>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
<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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6c36 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c36 OCA], [https://pdbe.org/6c36 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6c36 RCSB], [https://www.ebi.ac.uk/pdbsum/6c36 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6c36 ProSAT]</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=6c36 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c36 OCA], [http://pdbe.org/6c36 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c36 RCSB], [http://www.ebi.ac.uk/pdbsum/6c36 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c36 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/I7GAS0_MYCS2 I7GAS0_MYCS2]
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).
 
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>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6c36" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
*[[Exonuclease 3D structures|Exonuclease 3D structures]]
*[[Exonuclease 3D structures|Exonuclease 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Mycs2]]
[[Category: Mycolicibacterium smegmatis MC2 155]]
[[Category: Carl, A]]
[[Category: Carl A]]
[[Category: Goldgur, Y]]
[[Category: Goldgur Y]]
[[Category: Shuman, S]]
[[Category: Shuman S]]
[[Category: Uson, M L]]
[[Category: Uson ML]]
[[Category: Dna binding protein]]
[[Category: Mycobacterium dna flab endonuclease fena]]

Latest revision as of 17:26, 13 March 2024

Mycobacterium smegmatis flap endonuclease mutant D208NMycobacterium smegmatis flap endonuclease mutant D208N

Structural highlights

6c36 is a 1 chain structure with sequence from Mycolicibacterium smegmatis MC2 155. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.9Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

I7GAS0_MYCS2

See Also

6c36, resolution 1.90Å

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