1rys: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
New page: left|200px<br /> <applet load="1rys" size="450" color="white" frame="true" align="right" spinBox="true" caption="1rys, resolution 2.03Å" /> '''REPLICATION OF A CI...
 
No edit summary
 
(17 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1rys.gif|left|200px]]<br />
<applet load="1rys" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1rys, resolution 2.03&Aring;" />
'''REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION'''<br />


==Overview==
==REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION==
Ultraviolet light damages DNA by catalysing covalent bond formation, between adjacent pyrimidines, generating cis-syn cyclobutane pyrimidine, dimers (CPDs) as the most common lesion. CPDs block DNA replication by, high-fidelity DNA polymerases, but they can be efficiently bypassed by the, Y-family DNA polymerase pol eta. Mutations in POLH encoding pol eta are, implicated in nearly 20% of xeroderma pigmentosum, a human disease, characterized by extreme sensitivity to sunlight and predisposition to, skin cancer. Here we have determined two crystal structures of Dpo4, an, archaeal pol eta homologue, complexed with CPD-containing DNA, where the, 3' and 5' thymine of the CPD separately serves as a templating base. The, 3' thymine of the CPD forms a Watson-Crick base pair with the incoming, dideoxyATP, but the 5' thymine forms a Hoogsteen base pair with the, dideoxyATP in syn conformation. Dpo4 retains a similar tertiary structure, but each unusual DNA structure is individually fitted into the active site, for catalysis. A model of the pol eta-CPD complex built from the crystal, structures of Saccharomyces cerevisiae apo-pol eta and the Dpo4-CPD, complex suggests unique features that allow pol eta to efficiently bypass, CPDs.
<StructureSection load='1rys' size='340' side='right'caption='[[1rys]], [[Resolution|resolution]] 2.03&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1rys]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus Saccharolobus solfataricus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1pm8 1pm8]. The July 2007 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Thymine Dimers''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2007_7 10.2210/rcsb_pdb/mom_2007_7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RYS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RYS 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]] 2.03&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=1rys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rys OCA], [https://pdbe.org/1rys PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rys RCSB], [https://www.ebi.ac.uk/pdbsum/1rys PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rys ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DPO4_SACS2 DPO4_SACS2] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. It is involved in translesional synthesis.
== 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/ry/1rys_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=1rys ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1RYS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus] with CA, NA, ATP and EDO as [http://en.wikipedia.org/wiki/ligands ligands]. This structure superseeds the now removed PDB entry 1PM8. The following page contains interesting information on the relation of 1RYS with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb91_1.html Thymine Dimers]]. 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1RYS OCA].
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Replication of a cis-syn thymine dimer at atomic resolution., Ling H, Boudsocq F, Plosky BS, Woodgate R, Yang W, Nature. 2003 Aug 28;424(6952):1083-7. Epub 2003 Aug 6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12904819 12904819]
[[Category: Large Structures]]
[[Category: DNA-directed DNA polymerase]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Single protein]]
[[Category: Saccharolobus solfataricus]]
[[Category: Sulfolobus solfataricus]]
[[Category: Thymine Dimers]]
[[Category: Thymine Dimers]]
[[Category: Boudsocq, F.]]
[[Category: Boudsocq F]]
[[Category: Ling, H.]]
[[Category: Ling H]]
[[Category: Plosky, B.]]
[[Category: Plosky B]]
[[Category: Woodgate, R.]]
[[Category: Woodgate R]]
[[Category: Yang, W.]]
[[Category: Yang W]]
[[Category: ATP]]
[[Category: CA]]
[[Category: EDO]]
[[Category: NA]]
[[Category: cpd dimer]]
[[Category: lesion bypass]]
[[Category: polymerase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 18 09:05:51 2007''

Latest revision as of 11:26, 14 February 2024

REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTIONREPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION

Structural highlights

1rys is a 6 chain structure with sequence from Saccharolobus solfataricus. This structure supersedes the now removed PDB entry 1pm8. The July 2007 RCSB PDB Molecule of the Month feature on Thymine Dimers by David S. Goodsell is 10.2210/rcsb_pdb/mom_2007_7. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.03Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DPO4_SACS2 Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. It is involved in translesional synthesis.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1rys, resolution 2.03Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1rys&oldid=4054647"