1ryr: Difference between revisions

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[[Image:1ryr.gif|left|200px]]


{{Structure
==REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION==
|PDB= 1ryr |SIZE=350|CAPTION= <scene name='initialview01'>1ryr</scene>, resolution 2.28&Aring;
<StructureSection load='1ryr' size='340' side='right'caption='[[1ryr]], [[Resolution|resolution]] 2.28&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> and <scene name='pdbligand=ATP:ADENOSINE-5'-TRIPHOSPHATE'>ATP</scene>
<table><tr><td colspan='2'>[[1ryr]] is a 3 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=1pm0 1pm0]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RYR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RYR FirstGlance]. <br>
|ACTIVITY= [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]  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.28&#8491;</td></tr>
|GENE= DPO4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 Sulfolobus solfataricus])
<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></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=1ryr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ryr OCA], [https://pdbe.org/1ryr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ryr RCSB], [https://www.ebi.ac.uk/pdbsum/1ryr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ryr 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/1ryr_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=1ryr ConSurf].
<div style="clear:both"></div>


'''REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION'''
==See Also==
 
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
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.
[[Category: Large Structures]]
 
[[Category: Saccharolobus solfataricus]]
==About this Structure==
[[Category: Boudsocq F]]
1RYR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. This structure supersedes the now removed PDB entry 1PM0. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RYR OCA].
[[Category: Ling H]]
 
[[Category: Plosky B]]
==Reference==
[[Category: Woodgate R]]
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://www.ncbi.nlm.nih.gov/pubmed/12904819 12904819]
[[Category: Yang W]]
[[Category: DNA-directed DNA polymerase]]
[[Category: Single protein]]
[[Category: Sulfolobus solfataricus]]
[[Category: Boudsocq, F.]]
[[Category: Ling, H.]]
[[Category: Plosky, B.]]
[[Category: Woodgate, R.]]
[[Category: Yang, W.]]
[[Category: ATP]]
[[Category: CA]]
[[Category: lesion bypass]]
[[Category: polymerase]]
[[Category: tt-dimer]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:58:04 2008''

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

1ryr is a 3 chain structure with sequence from Saccharolobus solfataricus. This structure supersedes the now removed PDB entry 1pm0. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.28Å
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

1ryr, resolution 2.28Å

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OCA
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