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| | <StructureSection load='6nvp' size='340' side='right'caption='[[6nvp]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='6nvp' size='340' side='right'caption='[[6nvp]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6nvp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Psepk Psepk]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NVP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NVP FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6nvp]] 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=6NVP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NVP 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></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]] 2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6nv0|6nv0]]</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PP_1102 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=160488 PSEPK])</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=6nvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nvp OCA], [https://pdbe.org/6nvp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6nvp RCSB], [https://www.ebi.ac.uk/pdbsum/6nvp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6nvp 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=6nvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nvp OCA], [http://pdbe.org/6nvp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nvp RCSB], [http://www.ebi.ac.uk/pdbsum/6nvp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nvp ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/Q88NV2_PSEPK Q88NV2_PSEPK] |
| - | 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.
| + | |
| - | | + | |
| - | 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>
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| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 6nvp" style="background-color:#fffaf0;"></div>
| + | |
| - | == References ==
| + | |
| - | <references/>
| + | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Psepk]] | + | [[Category: Pseudomonas putida KT2440]] |
| - | [[Category: Ejaz, A]] | + | [[Category: Ejaz A]] |
| - | [[Category: Goldgur, Y]] | + | [[Category: Goldgur Y]] |
| - | [[Category: Shuman, S]] | + | [[Category: Shuman S]] |
| - | [[Category: Binuclear metallo-phosphodiesterase/nuclease]]
| + | |
| - | [[Category: Dna binding protein]]
| + | |
