1yjm: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,332,843 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,332,843 edits
No edit summary
 
(9 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Seed}}
[[Image:1yjm.png|left|200px]]


<!--
==Crystal structure of the FHA domain of mouse polynucleotide kinase in complex with an XRCC4-derived phosphopeptide.==
The line below this paragraph, containing "STRUCTURE_1yjm", creates the "Structure Box" on the page.
<StructureSection load='1yjm' size='340' side='right'caption='[[1yjm]], [[Resolution|resolution]] 2.20&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'>[[1yjm]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YJM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YJM 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]] 2.2&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</scene></td></tr>
{{STRUCTURE_1yjm|  PDB=1yjm  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yjm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yjm OCA], [https://pdbe.org/1yjm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yjm RCSB], [https://www.ebi.ac.uk/pdbsum/1yjm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yjm ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PNKP_MOUSE PNKP_MOUSE] Plays a key role in the repair of DNA damage, functioning as part of both the non-homologous end-joining (NHEJ) and base excision repair (BER) pathways. Through its two catalytic activities, PNK ensures that DNA termini are compatible with extension and ligation by either removing 3'-phosphates from, or by phosphorylating 5'-hydroxyl groups on, the ribose sugar of the DNA backbone.
== 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/yj/1yjm_consurf.spt"</scriptWhenChecked>
    <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/main_output.php?pdb_ID=1yjm ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Mammalian polynucleotide kinase (PNK) is a key component of both the base excision repair (BER) and nonhomologous end-joining (NHEJ) DNA repair pathways. PNK acts as a 5'-kinase/3'-phosphatase to create 5'-phosphate/3'-hydroxyl termini, which are a necessary prerequisite for ligation during repair. PNK is recruited to repair complexes through interactions between its N-terminal FHA domain and phosphorylated components of either pathway. Here, we describe the crystal structure of intact mammalian PNK and a structure of the PNK FHA bound to a cognate phosphopeptide. The kinase domain has a broad substrate binding pocket, which preferentially recognizes double-stranded substrates with recessed 5' termini. In contrast, the phosphatase domain efficiently dephosphorylates single-stranded 3'-phospho termini as well as double-stranded substrates. The FHA domain is linked to the kinase/phosphatase catalytic domain by a flexible tether, and it exhibits a mode of target selection based on electrostatic complementarity between the binding surface and the phosphothreonine peptide.


===Crystal structure of the FHA domain of mouse polynucleotide kinase in complex with an XRCC4-derived phosphopeptide.===
The molecular architecture of the mammalian DNA repair enzyme, polynucleotide kinase.,Bernstein NK, Williams RS, Rakovszky ML, Cui D, Green R, Karimi-Busheri F, Mani RS, Galicia S, Koch CA, Cass CE, Durocher D, Weinfeld M, Glover JN Mol Cell. 2005 Mar 4;17(5):657-70. PMID:15749016<ref>PMID:15749016</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
<!--
</div>
The line below this paragraph, {{ABSTRACT_PUBMED_15749016}}, adds the Publication Abstract to the page
<div class="pdbe-citations 1yjm" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 15749016 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_15749016}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
1YJM is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YJM OCA].
 
==Reference==
The molecular architecture of the mammalian DNA repair enzyme, polynucleotide kinase., Bernstein NK, Williams RS, Rakovszky ML, Cui D, Green R, Karimi-Busheri F, Mani RS, Galicia S, Koch CA, Cass CE, Durocher D, Weinfeld M, Glover JN, Mol Cell. 2005 Mar 4;17(5):657-70. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15749016 15749016]
[[Category: Mus musculus]]
[[Category: Mus musculus]]
[[Category: Polynucleotide 5'-hydroxy-kinase]]
[[Category: Bernstein NK]]
[[Category: Single protein]]
[[Category: Cass CE]]
[[Category: Bernstein, N K.]]
[[Category: Cui D]]
[[Category: Cass, C E.]]
[[Category: Durocher D]]
[[Category: Cui, D.]]
[[Category: Galicia S]]
[[Category: Durocher, D.]]
[[Category: Glover JNM]]
[[Category: Galicia, S.]]
[[Category: Green R]]
[[Category: Glover, J N.M.]]
[[Category: Karimi-Busheri F]]
[[Category: Green, R.]]
[[Category: Koch CA]]
[[Category: Karimi-Busheri, F.]]
[[Category: Mani RS]]
[[Category: Koch, C A.]]
[[Category: Rakovszky ML]]
[[Category: Mani, R S.]]
[[Category: Weinfeld M]]
[[Category: Rakovszky, M L.]]
[[Category: Williams RS]]
[[Category: Weinfeld, M.]]
[[Category: Williams, R S.]]
[[Category: Fha domain]]
[[Category: Polynucleotide kinase]]
[[Category: Xrcc4 phosphopeptide]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 06:49:25 2008''
Retrieved from "https://proteopedia.org/1yjm"