3mdc: Difference between revisions

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[[Image:3mdc.png|left|200px]]


{{STRUCTURE_3mdc|  PDB=3mdc  |  SCENE=  }}
==DNA polymerase lambda in complex with dFdCTP==
 
<StructureSection load='3mdc' size='340' side='right'caption='[[3mdc]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
===DNA polymerase lambda in complex with dFdCTP===
== Structural highlights ==
 
<table><tr><td colspan='2'>[[3mdc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MDC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MDC FirstGlance]. <br>
{{ABSTRACT_PUBMED_20348107}}
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.999&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTF:2-DEOXY-2,2-DIFLUOROCYTIDINE+5-(TETRAHYDROGEN+TRIPHOSPHATE)'>GTF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
==About this Structure==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3mdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mdc OCA], [https://pdbe.org/3mdc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3mdc RCSB], [https://www.ebi.ac.uk/pdbsum/3mdc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3mdc ProSAT]</span></td></tr>
[[3mdc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MDC OCA].  
</table>
== Function ==
[https://www.uniprot.org/uniprot/DPOLL_HUMAN DPOLL_HUMAN] Repair polymerase. Involved in base excision repair (BER) responsible for repair of lesions that give rise to abasic (AP) sites in DNA. Has both DNA polymerase and terminal transferase activities. Has a 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity.<ref>PMID:11457865</ref> <ref>PMID:15537631</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/md/3mdc_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=3mdc ConSurf].
<div style="clear:both"></div>


==See Also==
==See Also==
*[[DNA polymerase|DNA polymerase]]
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 
== References ==
==Reference==
<references/>
<ref group="xtra">PMID:020348107</ref><references group="xtra"/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Chou, K M.]]
[[Category: Large Structures]]
[[Category: Garcia-Diaz, M.]]
[[Category: Chou KM]]
[[Category: Kunkel, T.]]
[[Category: Garcia-Diaz M]]
[[Category: Murray, M.]]
[[Category: Kunkel T]]
[[Category: Lyase]]
[[Category: Murray M]]
[[Category: Protein-dna complex]]
[[Category: Transferase-dna complex]]

Latest revision as of 13:24, 21 February 2024

DNA polymerase lambda in complex with dFdCTPDNA polymerase lambda in complex with dFdCTP

Structural highlights

3mdc is a 4 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.999Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DPOLL_HUMAN Repair polymerase. Involved in base excision repair (BER) responsible for repair of lesions that give rise to abasic (AP) sites in DNA. Has both DNA polymerase and terminal transferase activities. Has a 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity.[1] [2]

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. ↑ Garcia-Diaz M, Bebenek K, Kunkel TA, Blanco L. Identification of an intrinsic 5'-deoxyribose-5-phosphate lyase activity in human DNA polymerase lambda: a possible role in base excision repair. J Biol Chem. 2001 Sep 14;276(37):34659-63. Epub 2001 Jul 16. PMID:11457865 doi:10.1074/jbc.M106336200
  2. ↑ Maga G, Ramadan K, Locatelli GA, Shevelev I, Spadari S, Hubscher U. DNA elongation by the human DNA polymerase lambda polymerase and terminal transferase activities are differentially coordinated by proliferating cell nuclear antigen and replication protein A. J Biol Chem. 2005 Jan 21;280(3):1971-81. Epub 2004 Nov 10. PMID:15537631 doi:10.1074/jbc.M411650200

3mdc, resolution 2.00Å

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