4b20

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(Difference between revisions)

Revision as of 06:57, 31 August 2022

Structural basis of DNA loop recognition by Endonuclease V

Structural highlights

4b20 is a 6 chain structure with sequence from Atcc 43589. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	2w35, 2w36
Activity:	Deoxyribonuclease V, with EC number 3.1.21.7
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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]

Publication Abstract from PubMed

The DNA repair enzyme endonuclease V (EndoV) recognizes and cleaves DNA at deaminated adenine lesions (hypoxanthine). In addition, EndoV cleaves DNA containing various helical distortions such as loops, hairpins, and flaps. To understand the molecular basis of EndoV's ability to recognize and incise DNA structures with helical distortions, we solved the crystal structure of Thermotoga maritima EndoV in complex with DNA containing a one-nucleotide loop. The structure shows that a strand-separating wedge is crucial for DNA loop recognition, with DNA strands separated precisely at the helical distortion. The additional nucleotide forming the loop rests on the surface of the wedge, while the normal adenine opposite the loop is flipped into a base recognition pocket. Our data show a different principle for DNA loop recognition and cleavage by EndoV, in which a coordinated action of a DNA-intercalating wedge and a base pocket accommodating a flipped normal base facilitate strand incision.

Structural basis of DNA loop recognition by endonuclease V.,Rosnes I, Rowe AD, Vik ES, Forstrom RJ, Alseth I, Bjoras M, Dalhus B Structure. 2013 Feb 5;21(2):257-65. doi: 10.1016/j.str.2012.12.007. Epub 2013 Jan, 11. PMID:23313664^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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
↑ Rosnes I, Rowe AD, Vik ES, Forstrom RJ, Alseth I, Bjoras M, Dalhus B. Structural basis of DNA loop recognition by endonuclease V. Structure. 2013 Feb 5;21(2):257-65. doi: 10.1016/j.str.2012.12.007. Epub 2013 Jan, 11. PMID:23313664 doi:http://dx.doi.org/10.1016/j.str.2012.12.007

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4b20"

@@ Line 3: / Line 3: @@
 <StructureSection load='4b20' size='340' side='right'caption='[[4b20]], [[Resolution|resolution]] 2.75&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4b20]] 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=4B20 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4B20 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4b20]] is a 6 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=4B20 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4B20 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</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">[[2w35|2w35]], [[2w36|2w36]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2w35|2w35]], [[2w36|2w36]]</div></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='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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4b20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4b20 OCA], [http://pdbe.org/4b20 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4b20 RCSB], [http://www.ebi.ac.uk/pdbsum/4b20 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4b20 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=4b20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4b20 OCA], [https://pdbe.org/4b20 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4b20 RCSB], [https://www.ebi.ac.uk/pdbsum/4b20 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4b20 ProSAT]</span></td></tr>
 </table>
 == 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>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 22: @@
 ==See Also==
-*[[Endonuclease|Endonuclease]]
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
 == References ==
 <references/>

4b20

From Proteopedia

Revision as of 06:57, 31 August 2022

Structural basis of DNA loop recognition by Endonuclease V

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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