3hd0
From Proteopedia
(Difference between revisions)
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==Crystal structure of Tm1865, an Endonuclease V from Thermotoga Maritima== | ==Crystal structure of Tm1865, an Endonuclease V from Thermotoga Maritima== | ||
| - | <StructureSection load='3hd0' size='340' side='right' caption='[[3hd0]], [[Resolution|resolution]] 2.70Å' scene=''> | + | <StructureSection load='3hd0' size='340' side='right'caption='[[3hd0]], [[Resolution|resolution]] 2.70Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[3hd0]] is a 3 chain structure with sequence from [ | + | <table><tr><td colspan='2'>[[3hd0]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HD0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HD0 FirstGlance]. <br> |
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | ||
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nfi, TM_1865 ([ | + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nfi, TM_1865 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Deoxyribonuclease_V Deoxyribonuclease V], with EC number [https://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'>[ | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3hd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hd0 OCA], [https://pdbe.org/3hd0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hd0 RCSB], [https://www.ebi.ac.uk/pdbsum/3hd0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hd0 ProSAT]</span></td></tr> |
</table> | </table> | ||
== Function == | == Function == | ||
| - | [[ | + | [[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]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hd/3hd0_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hd/3hd0_consurf.spt"</scriptWhenChecked> |
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
| Line 21: | Line 21: | ||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3hd0 ConSurf]. | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3hd0 ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| + | |||
| + | ==See Also== | ||
| + | *[[Endonuclease 3D structures|Endonuclease 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
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[[Category: Atcc 43589]] | [[Category: Atcc 43589]] | ||
[[Category: Deoxyribonuclease V]] | [[Category: Deoxyribonuclease V]] | ||
| + | [[Category: Large Structures]] | ||
[[Category: Cooper, D R]] | [[Category: Cooper, D R]] | ||
[[Category: Derewenda, U]] | [[Category: Derewenda, U]] | ||
Revision as of 12:44, 23 March 2022
Crystal structure of Tm1865, an Endonuclease V from Thermotoga Maritima
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Categories: Atcc 43589 | Deoxyribonuclease V | Large Structures | Cooper, D R | Derewenda, U | Derewenda, Z S | ISFI, Integrated Center for Structure and Function Innovation | Utepbergenov, D | Cytoplasm | Dna damage | Dna repair | Endonuclease | Endonuclease v | Hydrolase | Integrated center for structure and function innovation | Isfi | Magnesium | Nuclease | PSI, Protein structure initiative | Rnaseh superfamily | Structural genomic
