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| | <StructureSection load='3aal' size='340' side='right'caption='[[3aal]], [[Resolution|resolution]] 1.60Å' scene=''> | | <StructureSection load='3aal' size='340' side='right'caption='[[3aal]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3aal]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_kaustophilus"_prickett_1928 "bacillus kaustophilus" prickett 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AAL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AAL FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3aal]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AAL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AAL FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.6Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3aam|3aam]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GK2474 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1462 "Bacillus kaustophilus" Prickett 1928])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Deoxyribonuclease_IV_(phage-T(4)-induced) Deoxyribonuclease IV (phage-T(4)-induced)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.2 3.1.21.2] </span></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=3aal FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3aal OCA], [https://pdbe.org/3aal PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3aal RCSB], [https://www.ebi.ac.uk/pdbsum/3aal PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3aal ProSAT]</span></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=3aal FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3aal OCA], [https://pdbe.org/3aal PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3aal RCSB], [https://www.ebi.ac.uk/pdbsum/3aal PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3aal ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/END4_GEOKA END4_GEOKA]] Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic sites (AP sites) to produce new 5'-ends that are base-free deoxyribose 5-phosphate residues. It preferentially attacks modified AP sites created by bleomycin and neocarzinostatin.
| + | [https://www.uniprot.org/uniprot/END4_GEOKA END4_GEOKA] Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic sites (AP sites) to produce new 5'-ends that are base-free deoxyribose 5-phosphate residues. It preferentially attacks modified AP sites created by bleomycin and neocarzinostatin. |
| | <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: Bacillus kaustophilus prickett 1928]] | + | [[Category: Geobacillus kaustophilus]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Asano, R]] | + | [[Category: Asano R]] |
| - | [[Category: Ishikawa, H]] | + | [[Category: Ishikawa H]] |
| - | [[Category: Kuramitsu, S]] | + | [[Category: Kuramitsu S]] |
| - | [[Category: Masui, R]] | + | [[Category: Masui R]] |
| - | [[Category: Nakagawa, N]] | + | [[Category: Nakagawa N]] |
| - | [[Category: Nakane, S]] | + | [[Category: Nakane S]] |
| - | [[Category: Structural genomic]]
| + | |
| - | [[Category: Base excision repair]]
| + | |
| - | [[Category: Dna damage]]
| + | |
| - | [[Category: Dna repair]]
| + | |
| - | [[Category: Endoiv]]
| + | |
| - | [[Category: Endonuclease]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: National project on protein structural and functional analyse]]
| + | |
| - | [[Category: Nppsfa]]
| + | |
| - | [[Category: Nuclease]]
| + | |
| - | [[Category: Rsgi]]
| + | |
| - | [[Category: Tim barrel]]
| + | |
| Structural highlights
Function
END4_GEOKA Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic sites (AP sites) to produce new 5'-ends that are base-free deoxyribose 5-phosphate residues. It preferentially attacks modified AP sites created by bleomycin and neocarzinostatin.
Publication Abstract from PubMed
Endonuclease IV (EndoIV) is an endonuclease that acts at apurinic/apyrimidinic (AP) sites and is classified as either long-type or short-type. The crystal structures of representative types of EndoIV from Geobacillus kaustophilus and Thermus thermophilus HB8 were determined using X-ray crystallography. G. kaustophilus EndoIV (the long type) had a higher affinity for double-stranded DNA containing an AP-site analogue than T. thermophilus EndoIV (the short type). Structural analysis of the two different EndoIVs suggested that a C-terminal DNA-recognition loop that is only present in the long type contributes to its high affinity for AP sites. A mutation analysis showed that Lys267 in the C-terminal DNA-recognition loop plays an important role in DNA binding.
An additional C-terminal loop in endonuclease IV, an apurinic/apyrimidinic endonuclease, controls binding affinity to DNA.,Asano R, Ishikawa H, Nakane S, Nakagawa N, Kuramitsu S, Masui R Acta Crystallogr D Biol Crystallogr. 2011 Mar;67(Pt 3):149-55. Epub 2011, Feb 15. PMID:21358045[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Asano R, Ishikawa H, Nakane S, Nakagawa N, Kuramitsu S, Masui R. An additional C-terminal loop in endonuclease IV, an apurinic/apyrimidinic endonuclease, controls binding affinity to DNA. Acta Crystallogr D Biol Crystallogr. 2011 Mar;67(Pt 3):149-55. Epub 2011, Feb 15. PMID:21358045 doi:10.1107/S0907444910052479
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