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[[Image:2iry.gif|left|200px]]<br /><applet load="2iry" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2iry, resolution 1.78&Aring;" />
'''Crystal Structure of the Polymerase Domain from Mycobacterium tuberculosis Ligase D with dGTP and Manganese.'''<br />


==Overview==
==Crystal Structure of the Polymerase Domain from Mycobacterium tuberculosis Ligase D with dGTP and Manganese.==
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='2iry' size='340' side='right'caption='[[2iry]], [[Resolution|resolution]] 1.78&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2iry]] 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=2IRY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IRY 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]] 1.78&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=2iry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iry OCA], [https://pdbe.org/2iry PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2iry RCSB], [https://www.ebi.ac.uk/pdbsum/2iry PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2iry ProSAT], [https://www.topsan.org/Proteins/TBSGC/2iry TOPSAN]</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/2iry_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=2iry ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2IRY is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] with <scene name='pdbligand=MN:'>MN</scene> and <scene name='pdbligand=DGT:'>DGT</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IRY 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: DGT]]
[[Category: Pitcher RS]]
[[Category: MN]]
[[Category: dgtp]]
[[Category: ligase]]
[[Category: nhej]]
[[Category: polymerase]]
[[Category: primase]]
[[Category: transferase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:55:17 2008''

Latest revision as of 12:04, 21 February 2024

Crystal Structure of the Polymerase Domain from Mycobacterium tuberculosis Ligase D with dGTP and Manganese.Crystal Structure of the Polymerase Domain from Mycobacterium tuberculosis Ligase D with dGTP and Manganese.

Structural highlights

2iry is a 2 chain structure with sequence from Mycobacterium tuberculosis H37Rv. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.78Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

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).[1] [2] [3] [4] 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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Della M, Palmbos PL, Tseng HM, Tonkin LM, Daley JM, Topper LM, Pitcher RS, Tomkinson AE, Wilson TE, Doherty AJ. Mycobacterial Ku and ligase proteins constitute a two-component NHEJ repair machine. Science. 2004 Oct 22;306(5696):683-5. doi: 10.1126/science.1099824. PMID:15499016 doi:http://dx.doi.org/10.1126/science.1099824
  2. ↑ Pitcher RS, Brissett NC, Picher AJ, Andrade P, Juarez R, Thompson D, Fox GC, Blanco L, Doherty AJ. Structure and function of a mycobacterial NHEJ DNA repair polymerase. J Mol Biol. 2007 Feb 16;366(2):391-405. Epub 2006 Oct 20. PMID:17174332 doi:http://dx.doi.org/10.1016/j.jmb.2006.10.046
  3. ↑ Brissett NC, Pitcher RS, Juarez R, Picher AJ, Green AJ, Dafforn TR, Fox GC, Blanco L, Doherty AJ. Structure of a NHEJ polymerase-mediated DNA synaptic complex. Science. 2007 Oct 19;318(5849):456-9. PMID:17947582 doi:318/5849/456
  4. ↑ Brissett NC, Martin MJ, Pitcher RS, Bianchi J, Juarez R, Green AJ, Fox GC, Blanco L, Doherty AJ. Structure of a Preternary Complex Involving a Prokaryotic NHEJ DNA Polymerase. Mol Cell. 2011 Jan 21;41(2):221-31. PMID:21255731 doi:10.1016/j.molcel.2010.12.026

2iry, resolution 1.78Å

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