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| | <StructureSection load='4b5h' size='340' side='right'caption='[[4b5h]], [[Resolution|resolution]] 3.05Å' scene=''> | | <StructureSection load='4b5h' size='340' side='right'caption='[[4b5h]], [[Resolution|resolution]] 3.05Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4b5h]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"diplokokkus_intracellularis_meningitidis"_(sic)_weichselbaum_1887 "diplokokkus intracellularis meningitidis" (sic) weichselbaum 1887]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4B5H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4B5H FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4b5h]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Neisseria_meningitidis Neisseria meningitidis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4B5H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4B5H 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]] 3.05Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4b5f|4b5f]], [[4b5g|4b5g]], [[4b5i|4b5i]], [[4b5j|4b5j]], [[4b5m|4b5m]]</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=4b5h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4b5h OCA], [https://pdbe.org/4b5h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4b5h RCSB], [https://www.ebi.ac.uk/pdbsum/4b5h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4b5h ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exodeoxyribonuclease_III Exodeoxyribonuclease III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.2 3.1.11.2] </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=4b5h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4b5h OCA], [http://pdbe.org/4b5h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4b5h RCSB], [http://www.ebi.ac.uk/pdbsum/4b5h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4b5h ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q7DD47_NEIMB Q7DD47_NEIMB] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Exodeoxyribonuclease III]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Baldwin, G S]] | + | [[Category: Neisseria meningitidis]] |
| - | [[Category: Carpenter, E P]] | + | [[Category: Baldwin GS]] |
| - | [[Category: Freemont, P S]] | + | [[Category: Carpenter EP]] |
| - | [[Category: Jensen, K]] | + | [[Category: Freemont PS]] |
| - | [[Category: Lu, D]] | + | [[Category: Jensen K]] |
| - | [[Category: MacDonald, J T]] | + | [[Category: Lu D]] |
| - | [[Category: Silhan, J]] | + | [[Category: MacDonald JT]] |
| - | [[Category: Tang, C M]] | + | [[Category: Silhan J]] |
| - | [[Category: Hydrolase-dna complex]]
| + | [[Category: Tang CM]] |
| Structural highlights
Function
Q7DD47_NEIMB
Publication Abstract from PubMed
Base excision repair (BER) is a highly conserved DNA repair pathway throughout all kingdoms from bacteria to humans. Whereas several enzymes are required to complete the multistep repair process of damaged bases, apurinic-apyrimidic (AP) endonucleases play an essential role in enabling the repair process by recognizing intermediary abasic sites cleaving the phosphodiester backbone 5' to the abasic site. Despite extensive study, there is no structure of a bacterial AP endonuclease bound to substrate DNA. Furthermore, the structural mechanism for AP-site cleavage is incomplete. Here we report a detailed structural and biochemical study of the AP endonuclease from Neisseria meningitidis that has allowed us to capture structural intermediates providing more complete snapshots of the catalytic mechanism. Our data reveal subtle differences in AP-site recognition and kinetics between the human and bacterial enzymes that may reflect different evolutionary pressures.
Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis.,Lu D, Silhan J, Macdonald JT, Carpenter EP, Jensen K, Tang CM, Baldwin GS, Freemont PS Proc Natl Acad Sci U S A. 2012 Oct 3. PMID:23035246[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Lu D, Silhan J, Macdonald JT, Carpenter EP, Jensen K, Tang CM, Baldwin GS, Freemont PS. Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis. Proc Natl Acad Sci U S A. 2012 Oct 3. PMID:23035246 doi:http://dx.doi.org/10.1073/pnas.1206563109
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