2irx

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:04, 21 February 2024) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:2irx.png|left|200px]]
 
-
<!--
+
==Crystal Structure of the Polymerase Domain from Mycobacterium tuberculosis Ligase D with GTP and Manganese.==
-
The line below this paragraph, containing "STRUCTURE_2irx", creates the "Structure Box" on the page.
+
<StructureSection load='2irx' size='340' side='right'caption='[[2irx]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[2irx]] is a 1 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=2IRX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IRX FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-
{{STRUCTURE_2irx| PDB=2irx | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2irx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2irx OCA], [https://pdbe.org/2irx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2irx RCSB], [https://www.ebi.ac.uk/pdbsum/2irx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2irx 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/2irx_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=2irx ConSurf].
 +
<div style="clear:both"></div>
-
===Crystal Structure of the Polymerase Domain from Mycobacterium tuberculosis Ligase D with GTP and Manganese.===
+
==See Also==
-
 
+
*[[DNA ligase 3D structures|DNA ligase 3D structures]]
-
 
+
== References ==
-
<!--
+
<references/>
-
The line below this paragraph, {{ABSTRACT_PUBMED_17174332}}, adds the Publication Abstract to the page
+
__TOC__
-
(as it appears on PubMed at http://www.pubmed.gov), where 17174332 is the PubMed ID number.
+
</StructureSection>
-
-->
+
[[Category: Large Structures]]
-
{{ABSTRACT_PUBMED_17174332}}
+
[[Category: Mycobacterium tuberculosis H37Rv]]
-
 
+
[[Category: Brissett NC]]
-
==About this Structure==
+
[[Category: Doherty AJ]]
-
2IRX 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=2IRX OCA].
+
[[Category: Pitcher RS]]
-
 
+
-
==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]
+
-
[[Category: Mycobacterium tuberculosis]]
+
-
[[Category: Single protein]]
+
-
[[Category: Brissett, N C.]]
+
-
[[Category: Doherty, A J.]]
+
-
[[Category: Pitcher, R S.]]
+
-
[[Category: Gtp]]
+
-
[[Category: Ligase]]
+
-
[[Category: Nhej]]
+
-
[[Category: Polymerase]]
+
-
[[Category: Primase]]
+
-
[[Category: Transferase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 07:54:41 2008''
+

Current revision

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

PDB ID 2irx

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2irx"
Personal tools