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| | <StructureSection load='2w35' size='340' side='right'caption='[[2w35]], [[Resolution|resolution]] 2.15Å' scene=''> | | <StructureSection load='2w35' size='340' side='right'caption='[[2w35]], [[Resolution|resolution]] 2.15Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2w35]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W35 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2W35 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2w35]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W35 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2W35 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.15Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DI:2-DEOXYINOSINE-5-MONOPHOSPHATE'>DI</scene></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2w36|2w36]]</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=2w35 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w35 OCA], [https://pdbe.org/2w35 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2w35 RCSB], [https://www.ebi.ac.uk/pdbsum/2w35 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2w35 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/Deoxyribonuclease_V Deoxyribonuclease V], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.7 3.1.21.7] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2w35 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w35 OCA], [http://pdbe.org/2w35 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2w35 RCSB], [http://www.ebi.ac.uk/pdbsum/2w35 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2w35 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/NFI_THEMA NFI_THEMA]] Selectively cleaves double-stranded DNA at the second phosphodiester bond 3' to a deoxyinosine leaving behind the intact lesion on the nicked DNA. Acts in DNA repair. In vitro, can also cleave single-stranded substrates with inosine, double-stranded DNA with apurinic sites, or DNA sites with uracil or a mismatched base. When present in molar excess, two protein molecules can bind to the same DNA substrate and effect cleavage of both strands (in vitro).<ref>PMID:12081482</ref> | + | [https://www.uniprot.org/uniprot/NFI_THEMA NFI_THEMA] Selectively cleaves double-stranded DNA at the second phosphodiester bond 3' to a deoxyinosine leaving behind the intact lesion on the nicked DNA. Acts in DNA repair. In vitro, can also cleave single-stranded substrates with inosine, double-stranded DNA with apurinic sites, or DNA sites with uracil or a mismatched base. When present in molar excess, two protein molecules can bind to the same DNA substrate and effect cleavage of both strands (in vitro).<ref>PMID:12081482</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 43589]] | |
| - | [[Category: Deoxyribonuclease V]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Alseth, I]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Arvai, A S]] | + | [[Category: Thermotoga maritima]] |
| - | [[Category: Backe, P H]] | + | [[Category: Alseth I]] |
| - | [[Category: Bjoras, M]] | + | [[Category: Arvai AS]] |
| - | [[Category: Cao, W]] | + | [[Category: Backe PH]] |
| - | [[Category: Dalhus, B]] | + | [[Category: Bjoras M]] |
| - | [[Category: Gao, H]] | + | [[Category: Cao W]] |
| - | [[Category: Olsen, O E]] | + | [[Category: Dalhus B]] |
| - | [[Category: Rosnes, I]] | + | [[Category: Gao H]] |
| - | [[Category: Tainer, J A]] | + | [[Category: Olsen OE]] |
| - | [[Category: Dna damage]]
| + | [[Category: Rosnes I]] |
| - | [[Category: Dna repair]]
| + | [[Category: Tainer JA]] |
| - | [[Category: Endonuclease]]
| + | |
| - | [[Category: Endonucleasev]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Hypoxanthine]]
| + | |
| - | [[Category: Inosine]]
| + | |
| Structural highlights
Function
NFI_THEMA Selectively cleaves double-stranded DNA at the second phosphodiester bond 3' to a deoxyinosine leaving behind the intact lesion on the nicked DNA. Acts in DNA repair. In vitro, can also cleave single-stranded substrates with inosine, double-stranded DNA with apurinic sites, or DNA sites with uracil or a mismatched base. When present in molar excess, two protein molecules can bind to the same DNA substrate and effect cleavage of both strands (in vitro).[1]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Endonuclease V (EndoV) initiates a major base-repair pathway for nitrosative deamination resulting from endogenous processes and increased by oxidative stress from mitochondrial dysfunction or inflammatory responses. We solved the crystal structures of Thermotoga maritima EndoV in complex with a hypoxanthine lesion substrate and with product DNA. The PYIP wedge motif acts as a minor groove-damage sensor for helical distortions and base mismatches and separates DNA strands at the lesion. EndoV incises DNA with an unusual offset nick 1 nucleotide 3' of the lesion, as the deaminated adenine is rotated approximately 90 degrees into a recognition pocket approximately 8 A from the catalytic site. Tight binding by the lesion-recognition pocket in addition to Mg(2+) and hydrogen-bonding interactions to the DNA ends stabilize the product complex, suggesting an orderly recruitment of downstream proteins in this base-repair pathway.
Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair.,Dalhus B, Arvai AS, Rosnes I, Olsen OE, Backe PH, Alseth I, Gao H, Cao W, Tainer JA, Bjoras M Nat Struct Mol Biol. 2009 Feb;16(2):138-43. Epub 2009 Jan 11. PMID:19136958[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Huang J, Lu J, Barany F, Cao W. Mutational analysis of endonuclease V from Thermotoga maritima. Biochemistry. 2002 Jul 2;41(26):8342-50. PMID:12081482
- ↑ Dalhus B, Arvai AS, Rosnes I, Olsen OE, Backe PH, Alseth I, Gao H, Cao W, Tainer JA, Bjoras M. Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair. Nat Struct Mol Biol. 2009 Feb;16(2):138-43. Epub 2009 Jan 11. PMID:19136958 doi:10.1038/nsmb.1538
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