This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2w36

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 20:37, 19 September 2018

Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair

Structural highlights

2w36 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.
NonStd Res:	,
Related:	2w35
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]

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.

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

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2w36"

@@ Line 1: / Line 1: @@
-==STRUCTURES OF ENDONUCLEASE V WITH DNA REVEAL INITIATION OF DEAMINATED ADENINE REPAIR==
+==Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair==
 <StructureSection load='2w36' size='340' side='right' caption='[[2w36]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
@@ Line 6: / Line 7: @@
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2w35|2w35]]</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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2w36 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w36 OCA], [http://pdbe.org/2w36 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2w36 RCSB], [http://www.ebi.ac.uk/pdbsum/2w36 PDBsum]</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=2w36 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w36 OCA], [http://pdbe.org/2w36 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2w36 RCSB], [http://www.ebi.ac.uk/pdbsum/2w36 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2w36 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 14: / Line 15: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/w3/2w36_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/w3/2w36_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

2w36

From Proteopedia

Revision as of 20:37, 19 September 2018

Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox