2ihm

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (14:54, 20 September 2023) (edit) (undo)
 
(17 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2ihm.gif|left|200px]]<br /><applet load="2ihm" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="2ihm, resolution 2.4&Aring;" />
 
-
'''Polymerase mu in ternary complex with gapped 11mer DNA duplex and bound incoming nucleotide'''<br />
 
-
==Overview==
+
==Polymerase mu in ternary complex with gapped 11mer DNA duplex and bound incoming nucleotide==
-
DNA polymerase mu (Pol mu) is a family X enzyme with unique substrate, specificity that contributes to its specialized role in nonhomologous DNA, end joining (NHEJ). To investigate Pol mu's unusual substrate specificity, we describe the 2.4 A crystal structure of the polymerase domain of murine, Pol mu bound to gapped DNA with a correct dNTP at the active site. This, structure reveals substrate interactions with side chains in Pol mu that, differ from other family X members. For example, a single amino acid, substitution, H329A, has little effect on template-dependent synthesis by, Pol mu from a paired primer terminus, but it reduces both, template-independent and template-dependent synthesis during NHEJ of, intermediates whose 3' ends lack complementary template strand, nucleotides. These results provide insight into the substrate specificity, and differing functions of four closely related mammalian family X DNA, polymerases.
+
<StructureSection load='2ihm' size='340' side='right'caption='[[2ihm]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[2ihm]] is a 8 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=2IHM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IHM 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]] 2.4&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=D3T:2,3-DIDEOXY-THYMIDINE-5-TRIPHOSPHATE'>D3T</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=2ihm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ihm OCA], [https://pdbe.org/2ihm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ihm RCSB], [https://www.ebi.ac.uk/pdbsum/2ihm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ihm ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/DPOLM_MOUSE DPOLM_MOUSE] Gap-filling polymerase involved in repair of DNA double-strand breaks by non-homologous end joining (NHEJ). Participates in immunoglobulin (Ig) light chain gene rearrangement in V(D)J recombination.<ref>PMID:16860755</ref> <ref>PMID:17483519</ref>
 +
== 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/ih/2ihm_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=2ihm ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
DNA polymerase mu (Pol mu) is a family X enzyme with unique substrate specificity that contributes to its specialized role in nonhomologous DNA end joining (NHEJ). To investigate Pol mu's unusual substrate specificity, we describe the 2.4 A crystal structure of the polymerase domain of murine Pol mu bound to gapped DNA with a correct dNTP at the active site. This structure reveals substrate interactions with side chains in Pol mu that differ from other family X members. For example, a single amino acid substitution, H329A, has little effect on template-dependent synthesis by Pol mu from a paired primer terminus, but it reduces both template-independent and template-dependent synthesis during NHEJ of intermediates whose 3' ends lack complementary template strand nucleotides. These results provide insight into the substrate specificity and differing functions of four closely related mammalian family X DNA polymerases.
-
==About this Structure==
+
Structural insight into the substrate specificity of DNA Polymerase mu.,Moon AF, Garcia-Diaz M, Bebenek K, Davis BJ, Zhong X, Ramsden DA, Kunkel TA, Pedersen LC Nat Struct Mol Biol. 2007 Jan;14(1):45-53. Epub 2006 Dec 10. PMID:17159995<ref>PMID:17159995</ref>
-
2IHM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=NA:'>NA</scene> and <scene name='pdbligand=D3T:'>D3T</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IHM OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
Structural insight into the substrate specificity of DNA Polymerase mu., Moon AF, Garcia-Diaz M, Bebenek K, Davis BJ, Zhong X, Ramsden DA, Kunkel TA, Pedersen LC, Nat Struct Mol Biol. 2007 Jan;14(1):45-53. Epub 2006 Dec 10. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17159995 17159995]
+
</div>
-
[[Category: DNA-directed DNA polymerase]]
+
<div class="pdbe-citations 2ihm" style="background-color:#fffaf0;"></div>
-
[[Category: Mus musculus]]
+
-
[[Category: Single protein]]
+
-
[[Category: Kunkel, T.A.]]
+
-
[[Category: Moon, A.F.]]
+
-
[[Category: Pedersen, L.C]]
+
-
[[Category: D3T]]
+
-
[[Category: MG]]
+
-
[[Category: NA]]
+
-
[[Category: helix-turn-helix]]
+
-
[[Category: polymerase]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 14:37:50 2008''
+
==See Also==
 +
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
 +
[[Category: Mus musculus]]
 +
[[Category: Kunkel TA]]
 +
[[Category: Moon AF]]
 +
[[Category: Pedersen LC]]

Current revision

Polymerase mu in ternary complex with gapped 11mer DNA duplex and bound incoming nucleotide

PDB ID 2ihm

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/2ihm"
Personal tools