2q8u

From Proteopedia

(Difference between revisions)

Current revision

CRYSTAL STRUCTURE OF MRE11 FROM THERMOTOGA MARITIMA MSB8 (TM1635) AT 2.20 A RESOLUTION

Structural highlights

2q8u is a 2 chain structure with sequence from Thermotoga maritima MSB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.2Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

MRE11_THEMA Part of the Rad50/Mre11 complex, which is involved in the early steps of DNA double-strand break (DSB) repair (PubMed:21458667, PubMed:21937514, PubMed:24316220). The complex may facilitate opening of the processed DNA ends to aid in the recruitment of HerA and NurA (By similarity). Mre11 binds to DSB ends and has both double-stranded 3'-5' exonuclease activity and single-stranded endonuclease activity (Probable) (PubMed:20122942, PubMed:21458667, PubMed:24316220).[UniProtKB:Q8U1N9]^[1] ^[2] ^[3] ^[4]

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

Mre11 nuclease plays a central role in the repair of cytotoxic and mutagenic DNA double-strand breaks. As X-ray structural information has been available only for the Pyrococcus furiosus enzyme (PfMre11), the conserved and variable features of this nuclease across the domains of life have not been experimentally defined. Our crystal structure and biochemical studies demonstrate that TM1635 from Thermotoga maritima, originally annotated as a putative nuclease, is an Mre11 endo/exonuclease (TmMre11) and the first such structure from eubacteria. TmMre11 and PfMre11 display similar overall structures, despite sequence identity in the twilight zone of only approximately 20%. However, they differ substantially in their DNA-specificity domains and in their dimeric organization. Residues in the nuclease domain are highly conserved, but those in the DNA-specificity domain are not. The structural differences likely affect how Mre11 from different organisms recognize and interact with single-stranded DNA, double-stranded DNA and DNA hairpin structures during DNA repair. The TmMre11 nuclease active site has no bound metal ions, but is conserved in sequence and structure with the exception of a histidine that is important in PfMre11 nuclease activity. Nevertheless, biochemical characterization confirms that TmMre11 possesses both endonuclease and exonuclease activities on single-stranded and double-stranded DNA substrates, respectively.

Crystal structure of the first eubacterial Mre11 nuclease reveals novel features that may discriminate substrates during DNA repair.,Das D, Moiani D, Axelrod HL, Miller MD, McMullan D, Jin KK, Abdubek P, Astakhova T, Burra P, Carlton D, Chiu HJ, Clayton T, Deller MC, Duan L, Ernst D, Feuerhelm J, Grant JC, Grzechnik A, Grzechnik SK, Han GW, Jaroszewski L, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Marciano D, Morse AT, Nigoghossian E, Okach L, Paulsen J, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Tainer JA, Wilson IA J Mol Biol. 2010 Apr 2;397(3):647-63. Epub 2010 Feb 1. PMID:20122942^[5]

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

References

↑ Lammens K, Bemeleit DJ, Mockel C, Clausing E, Schele A, Hartung S, Schiller CB, Lucas M, Angermuller C, Soding J, Strasser K, Hopfner KP. The Mre11:Rad50 Structure Shows an ATP-Dependent Molecular Clamp in DNA Double-Strand Break Repair. Cell. 2011 Apr 1;145(1):54-66. PMID:21458667 doi:10.1016/j.cell.2011.02.038
↑ Mockel C, Lammens K, Schele A, Hopfner KP. ATP driven structural changes of the bacterial Mre11:Rad50 catalytic head complex. Nucleic Acids Res. 2011 Sep 21. PMID:21937514 doi:10.1093/nar/gkr749
↑ Shibata A, Moiani D, Arvai AS, Perry J, Harding SM, Genois MM, Maity R, van Rossum-Fikkert S, Kertokalio A, Romoli F, Ismail A, Ismalaj E, Petricci E, Neale MJ, Bristow RG, Masson JY, Wyman C, Jeggo PA, Tainer JA. DNA Double-Strand Break Repair Pathway Choice Is Directed by Distinct MRE11 Nuclease Activities. Mol Cell. 2013 Dec 3. pii: S1097-2765(13)00828-9. doi:, 10.1016/j.molcel.2013.11.003. PMID:24316220 doi:http://dx.doi.org/10.1016/j.molcel.2013.11.003
↑ Das D, Moiani D, Axelrod HL, Miller MD, McMullan D, Jin KK, Abdubek P, Astakhova T, Burra P, Carlton D, Chiu HJ, Clayton T, Deller MC, Duan L, Ernst D, Feuerhelm J, Grant JC, Grzechnik A, Grzechnik SK, Han GW, Jaroszewski L, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Marciano D, Morse AT, Nigoghossian E, Okach L, Paulsen J, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Tainer JA, Wilson IA. Crystal structure of the first eubacterial Mre11 nuclease reveals novel features that may discriminate substrates during DNA repair. J Mol Biol. 2010 Apr 2;397(3):647-63. Epub 2010 Feb 1. PMID:20122942 doi:10.1016/j.jmb.2010.01.049
↑ Das D, Moiani D, Axelrod HL, Miller MD, McMullan D, Jin KK, Abdubek P, Astakhova T, Burra P, Carlton D, Chiu HJ, Clayton T, Deller MC, Duan L, Ernst D, Feuerhelm J, Grant JC, Grzechnik A, Grzechnik SK, Han GW, Jaroszewski L, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Marciano D, Morse AT, Nigoghossian E, Okach L, Paulsen J, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Tainer JA, Wilson IA. Crystal structure of the first eubacterial Mre11 nuclease reveals novel features that may discriminate substrates during DNA repair. J Mol Biol. 2010 Apr 2;397(3):647-63. Epub 2010 Feb 1. PMID:20122942 doi:10.1016/j.jmb.2010.01.049

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/2q8u"

Categories: Large Structures | Thermotoga maritima MSB8

@@ Line 1: / Line 1: @@
 ==CRYSTAL STRUCTURE OF MRE11 FROM THERMOTOGA MARITIMA MSB8 (TM1635) AT 2.20 A RESOLUTION==
-<StructureSection load='2q8u' size='340' side='right' caption='[[2q8u]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+<StructureSection load='2q8u' size='340' side='right'caption='[[2q8u]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2q8u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima_msb8 Thermotoga maritima msb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q8U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q8U FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2q8u]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q8U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q8U 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]] 2.2&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TM_1635 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 Thermotoga maritima MSB8])</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q8u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q8u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q8u RCSB], [http://www.ebi.ac.uk/pdbsum/2q8u PDBsum], [http://www.topsan.org/Proteins/JCSG/2q8u TOPSAN]</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=2q8u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q8u OCA], [https://pdbe.org/2q8u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q8u RCSB], [https://www.ebi.ac.uk/pdbsum/2q8u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q8u ProSAT], [https://www.topsan.org/Proteins/JCSG/2q8u TOPSAN]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/MRE11_THEMA MRE11_THEMA] Part of the Rad50/Mre11 complex, which is involved in the early steps of DNA double-strand break (DSB) repair (PubMed:21458667, PubMed:21937514, PubMed:24316220). The complex may facilitate opening of the processed DNA ends to aid in the recruitment of HerA and NurA (By similarity). Mre11 binds to DSB ends and has both double-stranded 3'-5' exonuclease activity and single-stranded endonuclease activity (Probable) (PubMed:20122942, PubMed:21458667, PubMed:24316220).[UniProtKB:Q8U1N9]<ref>PMID:21458667</ref> <ref>PMID:21937514</ref> <ref>PMID:24316220</ref> <ref>PMID:20122942</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q8/2q8u_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q8/2q8u_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>
-</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/chain_selection.php?pdb_ID=2ata 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=2q8u ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 25: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2q8u" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Thermotoga maritima msb8]]
+[[Category: Large Structures]]
-[[Category: Structural genomic]]
+[[Category: Thermotoga maritima MSB8]]
-[[Category: Hydrolase]]
-[[Category: Jcsg]]
-[[Category: PSI, Protein structure initiative]]

2q8u

From Proteopedia

Current revision

CRYSTAL STRUCTURE OF MRE11 FROM THERMOTOGA MARITIMA MSB8 (TM1635) AT 2.20 A RESOLUTION

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox