2iru: Difference between revisions

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-[[Image:2iru.gif|left|200px]]<br /><applet load="2iru" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2iru, resolution 1.65&Aring;" />
-'''Crystal Structure of the Polymerase Domain from Mycobacterium tuberculosis Ligase D'''<br />
-==Overview==
+==Crystal Structure of the Polymerase Domain from Mycobacterium tuberculosis Ligase D==
-Non homologous end-joining (NHEJ)-mediated repair of DNA double-strand breaks in prokaryotes requires Ku and a specific multidomain DNA ligase (LigD). We present crystal structures of the primase/polymerisation domain (PolDom) of Mycobacterium tuberculosis LigD, alone and complexed with nucleotides. The PolDom structure combines the general fold of the archaeo-eukaryotic primase (AEP) superfamily with additional loops and domains that together form a deep cleft on the surface, likely used for DNA binding. Enzymatic analysis indicates that the PolDom of LigD, even in the absence of accessory domains and Ku proteins, has the potential to recognise DNA end-joining intermediates. Strikingly, one of the main signals for the specific and efficient binding of PolDom to DNA is the presence of a 5'-phosphate group, located at the single/double-stranded junction at both gapped and 3'-protruding DNA molecules. Although structurally unrelated, Pol lambda and Pol mu, the two eukaryotic DNA polymerases involved in NHEJ, are endowed with a similar capacity to bind a 5'-phosphate group. Other properties that are beneficial for NHEJ, such as the ability to generate template distortions and realignments of the primer, displayed by Pol lambda and Pol mu, are shared by the PolDom of bacterial LigD. In addition, PolDom can perform non-mutagenic translesion synthesis on termini containing modified bases. Significantly, ribonucleotide insertion appears to be a recurrent theme associated with NHEJ, maximised in this case by the deployment of a dedicated primase, although its in vivo relevance is unknown.
+<StructureSection load='2iru' size='340' side='right'caption='[[2iru]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2iru]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IRU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IRU FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.65&#8491;</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=2iru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iru OCA], [https://pdbe.org/2iru PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2iru RCSB], [https://www.ebi.ac.uk/pdbsum/2iru PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2iru ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/LIGD_MYCTU LIGD_MYCTU] With Ku forms a non-homologous end joining (NHEJ) repair enzyme which repairs DNA double-strand breaks (DSB) with reduced fidelity. Recognizes, processes and reseals DSBs, including repairs on incompatible DSB which require 3'-resection, gap filling and ligation. Anneals the 3' overhanging strands from opposing breaks to form a gapped intermediate, which then can be extended in trans by using the termini as primers for extension of the annealed break. Binds to the recessed 5'-phosphate moiety of the downstream DNA strand forming a stable synaptic complex even when the 3'-protruding ends of the template DNA strands are not complementary. Has numerous activities; gap filling copies the template strand, and prefers a 5'-phosphate in the gap and rNTPS (PubMed:17174332, PubMed:17947582), DNA-directed DNA or RNA polymerase on 5'-overhangs, terminal transferase (extending ssDNA or blunt dsDNA in a non-templated fashion, preferentially with rNTPs), DNA-dependent RNA primase (synthesizes short RNAs on unprimed closed ssDNA) and 3'- to 5'-exonuclease on ssDNA (PubMed:15499016). Isolated Pol domain (and presumably the holoenzyme) is able to form complexes between 2 noncompatible protruding 3'-ends DNA ends via microhomologous DNA strands, in a end-bridging function to which it adds a templated nucleotide (PubMed:17947582). Minimal primer length is 2 nucleotides (PubMed:21255731).<ref>PMID:15499016</ref> <ref>PMID:17174332</ref> <ref>PMID:17947582</ref> <ref>PMID:21255731</ref>   The preference of the polymerase domain for rNTPs over dNTPs may be advantageous in dormant cells, where the dNTP pool is limiting.  In conjunction with endogenous or Mycobacterium phage Omega Ku (AC Q853W0) can reconstitute NHEJ in Saccharomyces cerevisiae.
+== 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/ir/2iru_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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/main_output.php?pdb_ID=2iru ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-IRU is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IRU OCA].
+*[[DNA ligase 3D structures|DNA ligase 3D structures]]
+== References ==
-==Reference==
+<references/>
-Structure and function of a mycobacterial NHEJ DNA repair polymerase., Pitcher RS, Brissett NC, Picher AJ, Andrade P, Juarez R, Thompson D, Fox GC, Blanco L, Doherty AJ, J Mol Biol. 2007 Feb 16;366(2):391-405. Epub 2006 Oct 20. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17174332 17174332]
+__TOC__
-[[Category: Mycobacterium tuberculosis]]
+</StructureSection>
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Brissett, N C.]]
+[[Category: Mycobacterium tuberculosis H37Rv]]
-[[Category: Doherty, A J.]]
+[[Category: Brissett NC]]
-[[Category: Pitcher, R S.]]
+[[Category: Doherty AJ]]
-[[Category: ligase]]
+[[Category: Pitcher RS]]
-[[Category: nhej]]
-[[Category: polymerase]]
-[[Category: primase]]
-[[Category: transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:55:12 2008''