2iry - Revision history

OCA at 09:04, 21 February 2024

2024-02-21T09:04:11Z

← Older revision		Revision as of 09:04, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='2iry' size='340' side='right'caption='[[2iry]], [[Resolution\|resolution]] 1.78Å' scene=''>		<StructureSection load='2iry' size='340' side='right'caption='[[2iry]], [[Resolution\|resolution]] 1.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2iry]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Myctu Myctu~~]. 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>		<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='~~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>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.78Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[2iru\|2iru]], [[2irx\|2irx]]~~</~~div~~><~~/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~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">Rv0938 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])~~</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>		<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>		</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 ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 20:
	</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].		</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>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	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.

	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:17174332<ref>PMID:17174332</ref>		==See Also==
			*[[DNA ligase 3D structures\|DNA ligase 3D structures]]
	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class~~=~~"pdbe-citations 2iry" style~~=~~"background-color:#fffaf0;"></div>~~
	== References ==		== References ==
	<references/>		<references/>
Line 33:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Myctu~~]]		[[Category: Mycobacterium tuberculosis H37Rv]]
	[[Category: Brissett~~, N C~~]]		[[Category: Brissett NC]]
	[[Category: Doherty~~, A J~~]]		[[Category: Doherty AJ]]
	[[Category: Pitcher~~, R S]]~~		[[Category: Pitcher RS]]
	~~[[Category: Dgtp]]~~
	~~[[Category: Ligase]]~~
	~~[[Category: Nhej]]~~
	~~[[Category: Polymerase]]~~
	~~[[Category: Primase]]~~
	~~[[Category: Transferase~~]]

OCA at 11:21, 31 March 2021

2021-03-31T11:21:16Z

← Older revision		Revision as of 11:21, 31 March 2021
Line 1:		Line 1:

	==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.==
	<StructureSection load='2iry' size='340' side='right' caption='[[2iry]], [[Resolution\|resolution]] 1.78Å' scene=''>		<StructureSection load='2iry' size='340' side='right'caption='[[2iry]], [[Resolution\|resolution]] 1.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2iry]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Myctu Myctu]. 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 [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2IRY FirstGlance]. <br>		<table><tr><td colspan='2'>[[2iry]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Myctu Myctu]. 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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2iru\|2iru]], [[2irx\|2irx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2iru\|2iru]], [[2irx\|2irx]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rv0938 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rv0938 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</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=2iry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iry OCA], [~~http~~://pdbe.org/2iry PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2iry RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2iry PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2iry ProSAT], [~~http~~://www.topsan.org/Proteins/TBSGC/2iry 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=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>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 32:		Line 32:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Myctu]]		[[Category: Myctu]]
	[[Category: Brissett, N C]]		[[Category: Brissett, N C]]

OCA at 08:36, 4 July 2018

2018-07-04T08:36:59Z

← Older revision		Revision as of 08:36, 4 July 2018
Line 1:		Line 1:

	==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.==
	<StructureSection load='2iry' size='340' side='right' caption='[[2iry]], [[Resolution\|resolution]] 1.78Å' scene=''>		<StructureSection load='2iry' size='340' side='right' caption='[[2iry]], [[Resolution\|resolution]] 1.78Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2iru\|2iru]], [[2irx\|2irx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2iru\|2iru]], [[2irx\|2irx]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rv0938 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rv0938 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</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=2iry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iry OCA], [http://pdbe.org/2iry PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2iry RCSB], [http://www.ebi.ac.uk/pdbsum/2iry PDBsum], [http://www.topsan.org/Proteins/TBSGC/2iry TOPSAN]</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=2iry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iry OCA], [http://pdbe.org/2iry PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2iry RCSB], [http://www.ebi.ac.uk/pdbsum/2iry PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2iry ProSAT], [http://www.topsan.org/Proteins/TBSGC/2iry TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ir/2iry_consurf.spt"</scriptWhenChecked>		<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>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 08:36, 8 February 2016

2016-02-08T08:36:06Z

← Older revision		Revision as of 08:36, 8 February 2016
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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=2iry ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:46, 10 September 2015

2015-09-10T09:46:45Z

← Older revision		Revision as of 09:46, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2iry' size='340' side='right' caption='[[2iry]], [[Resolution\|resolution]] 1.78Å' scene=''>		<StructureSection load='2iry' size='340' side='right' caption='[[2iry]], [[Resolution\|resolution]] 1.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2iry]] is a 2 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IRY FirstGlance]. <br>		<table><tr><td colspan='2'>[[2iry]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IRY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2iru\|2iru]], [[2irx\|2irx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2iru\|2iru]], [[2irx\|2irx]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rv0938 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 ~~Mycobacterium tuberculosis H37Rv~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rv0938 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</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=2iry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iry OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2iry RCSB], [http://www.ebi.ac.uk/pdbsum/2iry PDBsum], [http://www.topsan.org/Proteins/TBSGC/2iry TOPSAN]</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=2iry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iry OCA], [http://pdbe.org/2iry PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2iry RCSB], [http://www.ebi.ac.uk/pdbsum/2iry PDBsum], [http://www.topsan.org/Proteins/TBSGC/2iry TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 2iry" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Mycobacterium tuberculosis h37rv~~]]		[[Category: Myctu]]
	[[Category: Brissett, N C]]		[[Category: Brissett, N C]]
	[[Category: Doherty, A J]]		[[Category: Doherty, A J]]

OCA at 09:30, 16 January 2015

2015-01-16T09:30:11Z

← Older revision		Revision as of 09:30, 16 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2iry]] is a 2 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IRY FirstGlance]. <br>		<table><tr><td colspan='2'>[[2iry]] is a 2 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IRY FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2iru\|2iru]], [[2irx\|2irx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2iru\|2iru]], [[2irx\|2irx]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rv0938 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 Mycobacterium tuberculosis H37Rv])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rv0938 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 Mycobacterium tuberculosis H37Rv])</td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2iry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iry OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2iry RCSB], [http://www.ebi.ac.uk/pdbsum/2iry PDBsum], [http://www.topsan.org/Proteins/TBSGC/2iry TOPSAN]</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=2iry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iry OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2iry RCSB], [http://www.ebi.ac.uk/pdbsum/2iry PDBsum], [http://www.topsan.org/Proteins/TBSGC/2iry TOPSAN]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Mycobacterium tuberculosis h37rv]]		[[Category: Mycobacterium tuberculosis h37rv]]
	[[Category: Brissett, N C.]]		[[Category: Brissett, N C]]
	[[Category: Doherty, A J.]]		[[Category: Doherty, A J]]
	[[Category: Pitcher, R S.]]		[[Category: Pitcher, R S]]
	[[Category: Dgtp]]		[[Category: Dgtp]]
	[[Category: Ligase]]		[[Category: Ligase]]

OCA at 10:56, 30 September 2014

2014-09-30T10:56:31Z

← Older revision		Revision as of 10:56, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2iry~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal Structure of the Polymerase Domain from Mycobacterium tuberculosis Ligase D with dGTP and Manganese.==
			<StructureSection load='2iry' size='340' side='right' caption='[[2iry]], [[Resolution\|resolution]] 1.78Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2iry]] is a 2 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IRY FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2iru\|2iru]], [[2irx\|2irx]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rv0938 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 Mycobacterium tuberculosis H37Rv])</td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2iry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iry OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2iry RCSB], [http://www.ebi.ac.uk/pdbsum/2iry PDBsum], [http://www.topsan.org/Proteins/TBSGC/2iry TOPSAN]</span></td></tr>
			<table>
			== 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/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			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.

	~~{{STRUCTURE_2iry\| PDB=2iry \| SCENE= }}~~		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:17174332<ref>PMID:17174332</ref>

	~~===Crystal Structure~~ of the ~~Polymerase Domain from Mycobacterium tuberculosis Ligase D with dGTP and Manganese~~.~~===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_17174332}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2iry]] is a 2 chain structure with sequence from [http://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].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:017174332<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Mycobacterium tuberculosis h37rv]]		[[Category: Mycobacterium tuberculosis h37rv]]
	[[Category: Brissett, N C.]]		[[Category: Brissett, N C.]]

OCA: Protected "2iry" [edit=sysop:move=sysop]

2013-01-07T15:23:40Z

Protected "2iry" [edit=sysop:move=sysop]

← Older revision	Revision as of 15:23, 7 January 2013
(No difference)

OCA at 15:23, 7 January 2013

2013-01-07T15:23:34Z

← Older revision		Revision as of 15:23, 7 January 2013
Line 1:		Line 1:
	~~{{Seed}}~~
	[[Image:2iry.png\|left\|200px]]		[[Image:2iry.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2iry", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_2iry\| PDB=2iry \| SCENE= }}		{{STRUCTURE_2iry\| PDB=2iry \| SCENE= }}

	===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.===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_17174332}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 17174332 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_17174332}}		{{ABSTRACT_PUBMED_17174332}}

	==About this Structure==		==About this Structure==
	~~2IRY~~ is a 2 ~~chains~~ structure ~~of sequences~~ 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=2IRY OCA].		[[2iry]] is a 2 chain structure with sequence from [http://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].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~17174332~~</ref><references group="xtra"/>		<ref group="xtra">PMID:017174332</ref><references group="xtra"/>
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis h37rv]]
	[[Category: Brissett, N C.]]		[[Category: Brissett, N C.]]
	[[Category: Doherty, A J.]]		[[Category: Doherty, A J.]]
Line 34:		Line 22:
	[[Category: Primase]]		[[Category: Primase]]
	[[Category: Transferase]]		[[Category: Transferase]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 20:39:11 2009''~~

OCA at 18:39, 16 February 2009

2009-02-16T18:39:14Z

← Older revision		Revision as of 18:39, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	2IRY is a ~~[[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=2IRY OCA].		2IRY is a 2 chains structure of sequences 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=2IRY OCA].

	==Reference==		==Reference==
	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:~~//~~www.ncbi.nlm.nih.gov/pubmed/17174332 17174332]~~		<ref group="xtra">PMID:17174332</ref><references group="xtra"/>
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	~~[[Category: Single protein]]~~
	[[Category: Brissett, N C.]]		[[Category: Brissett, N C.]]
	[[Category: Doherty, A J.]]		[[Category: Doherty, A J.]]
Line 36:		Line 35:
	[[Category: Transferase]]		[[Category: Transferase]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon ~~Jul 28 00~~:49:~~25 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 20:39:11 2009''