2vld

From Proteopedia

(Difference between revisions)

Current revision

crystal structure of a repair endonuclease from Pyrococcus abyssi

Structural highlights

2vld is a 2 chain structure with sequence from Pyrococcus abyssi. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.6Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NUCS_PYRAB Cleaves both 3' and 5' ssDNA extremities of branched DNA structures. Binds to ssDNA.[HAMAP-Rule:MF_00722]^[1] ^[2]

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

We show that Pyrococcus abyssi PAB2263 (dubbed NucS (nuclease for ss DNA) is a novel archaeal endonuclease that interacts with the replication clamp PCNA. Structural determination of P. abyssi NucS revealed a two-domain dumbbell-like structure that in overall does not resemble any known protein structure. Biochemical and structural studies indicate that NucS orthologues use a non-catalytic ssDNA-binding domain to regulate the cleavage activity at another site, thus resulting into the specific cleavage at double-stranded DNA (dsDNA)/ssDNA junctions on branched DNA substrates. Both 3' and 5' extremities of the ssDNA can be cleaved at the nuclease channel that is too narrow to accommodate duplex DNA. Altogether, our data suggest that NucS proteins constitute a new family of structure-specific DNA endonucleases that are widely distributed in archaea and in bacteria, including Mycobacterium tuberculosis.

Structure and function of a novel endonuclease acting on branched DNA substrates.,Ren B, Kuhn J, Meslet-Cladiere L, Briffotaux J, Norais C, Lavigne R, Flament D, Ladenstein R, Myllykallio H EMBO J. 2009 Aug 19;28(16):2479-89. Epub 2009 Jul 16. PMID:19609302^[3]

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

References

↑ Ren B, Kuhn J, Meslet-Cladiere L, Briffotaux J, Norais C, Lavigne R, Flament D, Ladenstein R, Myllykallio H. Structure and function of a novel endonuclease acting on branched DNA substrates. EMBO J. 2009 Aug 19;28(16):2479-89. Epub 2009 Jul 16. PMID:19609302 doi:10.1038/emboj.2009.192
↑ Creze C, Ligabue A, Laurent S, Lestini R, Laptenok SP, Khun J, Vos MH, Czjzek M, Myllykallio H, Flament D. Modulation of the Pyrococcus abyssi NucS endonuclease activity by replication clamp at functional and structural levels. J Biol Chem. 2012 May 4;287(19):15648-60. doi: 10.1074/jbc.M112.346361. Epub 2012, Mar 19. PMID:22431731 doi:http://dx.doi.org/10.1074/jbc.M112.346361
↑ Ren B, Kuhn J, Meslet-Cladiere L, Briffotaux J, Norais C, Lavigne R, Flament D, Ladenstein R, Myllykallio H. Structure and function of a novel endonuclease acting on branched DNA substrates. EMBO J. 2009 Aug 19;28(16):2479-89. Epub 2009 Jul 16. PMID:19609302 doi:10.1038/emboj.2009.192

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 1: / Line 1: @@
 ==crystal structure of a repair endonuclease from Pyrococcus abyssi==
-<StructureSection load='2vld' size='340' side='right' caption='[[2vld]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+<StructureSection load='2vld' size='340' side='right'caption='[[2vld]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2vld]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VLD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VLD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2vld]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VLD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VLD 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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</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=2vld FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vld OCA], [http://pdbe.org/2vld PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vld RCSB], [http://www.ebi.ac.uk/pdbsum/2vld PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vld ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=2vld FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vld OCA], [https://pdbe.org/2vld PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vld RCSB], [https://www.ebi.ac.uk/pdbsum/2vld PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vld ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NUCS_PYRAB NUCS_PYRAB]] Cleaves both 3' and 5' ssDNA extremities of branched DNA structures. Binds to ssDNA.[HAMAP-Rule:MF_00722]<ref>PMID:19609302</ref> <ref>PMID:22431731</ref>
+[https://www.uniprot.org/uniprot/NUCS_PYRAB NUCS_PYRAB] Cleaves both 3' and 5' ssDNA extremities of branched DNA structures. Binds to ssDNA.[HAMAP-Rule:MF_00722]<ref>PMID:19609302</ref> <ref>PMID:22431731</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 14: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vl/2vld_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 32: / Line 33: @@
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Pyrococcus abyssi]]
-[[Category: Briffotaux, J]]
+[[Category: Briffotaux J]]
-[[Category: Flament, D]]
+[[Category: Flament D]]
-[[Category: Kuhn, J]]
+[[Category: Kuhn J]]
-[[Category: Ladenstein, R]]
+[[Category: Ladenstein R]]
-[[Category: Lavigne, R]]
+[[Category: Lavigne R]]
-[[Category: Meslet-Cladiere, L]]
+[[Category: Meslet-Cladiere L]]
-[[Category: Myllykallio, H]]
+[[Category: Myllykallio H]]
-[[Category: Norais, C]]
+[[Category: Norais C]]
-[[Category: Ren, B]]
+[[Category: Ren B]]
-[[Category: Endonuclease]]
-[[Category: Hydrolase]]

2vld

From Proteopedia

Current revision

crystal structure of a repair endonuclease from Pyrococcus abyssi

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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