6nvo: Difference between revisions

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'''Unreleased structure'''


The entry 6nvo is ON HOLD  until Paper Publication
==Crystal structure of Pseudomonas putida nuclease MPE==
<StructureSection load='6nvo' size='340' side='right'caption='[[6nvo]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6nvo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida_KT2440 Pseudomonas putida KT2440]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NVO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NVO FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.196&#8491;</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></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=6nvo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nvo OCA], [https://pdbe.org/6nvo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6nvo RCSB], [https://www.ebi.ac.uk/pdbsum/6nvo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6nvo ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q88NV2_PSEPK Q88NV2_PSEPK]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A recently identified and widely prevalent prokaryal gene cluster encodes a suite of enzymes with imputed roles in nucleic acid repair. The enzymes are: MPE, a DNA endonuclease; Lhr-Core, a 3'-5' DNA helicase; LIG, an ATP-dependent DNA ligase; and Exo, a metallo-beta-lactamase-family nuclease. Bacterial and archaeal MPE proteins belong to the binuclear metallophosphoesterase superfamily that includes the well-studied DNA repair nucleases Mre11 and SbcD. Here we report that the Pseudomonas putida MPE protein is a manganese-dependent DNA endonuclease that incises either linear single strands or the single-strand loops of stem-loop DNA structures. MPE has feeble activity on duplex DNA. A crystal structure of MPE at 2.2 A resolution revealed that the active site includes two octahedrally coordinated manganese ions. Seven signature amino acids of the binuclear metallophosphoesterase superfamily serve as the enzymic metal ligands in MPE: Asp33, His35, Asp78, Asn112, His124, His146, and His158. A swath of positive surface potential on either side of the active site pocket suggests a binding site for the single-strand DNA substrate. The structure of MPE differs significantly from Mre11 and SbcD in several key respects: (i) MPE is a monomer, whereas Mre11 and SbcD are homodimers; (ii) MPE lacks the capping domain present in Mre11 and SbcD; and (iii) the topology of the bsandwich that comprises the core of the metallophosphoesterase fold differs in MPE vis-a-vis Mre11 and SbcD. We surmise that MPE exemplifies a novel clade of DNA endonuclease within the binuclear metallophosphoesterase superfamily.


Authors: Goldgur, Y., Shuman, S., Ejaz, A.
Activity and structure of Pseudomonas putida MPE, a manganese-dependent single-strand DNA endonuclease encoded in a nucleic acid repair gene cluster.,Ejaz A, Goldgur Y, Shuman S J Biol Chem. 2019 Mar 20. pii: RA119.008049. doi: 10.1074/jbc.RA119.008049. PMID:30894417<ref>PMID:30894417</ref>


Description: Crystal structure of Pseudomonas putida nuclease MPE
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Goldgur, Y]]
<div class="pdbe-citations 6nvo" style="background-color:#fffaf0;"></div>
[[Category: Ejaz, A]]
== References ==
[[Category: Shuman, S]]
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pseudomonas putida KT2440]]
[[Category: Ejaz A]]
[[Category: Goldgur Y]]
[[Category: Shuman S]]
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