1ryr: Difference between revisions

Revision as of 08:04, 3 May 2008

REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION

OverviewOverview

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.

About this StructureAbout this Structure

1RYR is a Single protein structure of sequence from Sulfolobus solfataricus. This structure supersedes the now removed PDB entry 1pm0. Full crystallographic information is available from OCA.

ReferenceReference

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:12904819 Page seeded by OCA on Sat May 3 08:04:29 2008

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OCA

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 [[Image:1ryr.gif|left|200px]]
- {{Structure
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+The line below this paragraph, containing "STRUCTURE_1ryr", creates the "Structure Box" on the page.
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+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=ATP:ADENOSINE-5&#39;-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
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-|ACTIVITY= <span class='plainlinks'>[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] </span>
+or leave the SCENE parameter empty for the default display.
-|GENE= DPO4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 Sulfolobus solfataricus])
+-->
-|DOMAIN=
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-|RELATEDENTRY=[[1rys|1RYS]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ryr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ryr OCA], [http://www.ebi.ac.uk/pdbsum/1ryr PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ryr RCSB]</span>
-}}
 '''REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION'''
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 ==About this Structure==
-RYR 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].
+RYR 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 [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].
 ==Reference==
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 [[Category: Woodgate, R.]]
 [[Category: Yang, W.]]
-[[Category: lesion bypass]]
+[[Category: Lesion bypass]]
-[[Category: polymerase]]
+[[Category: Polymerase]]
-[[Category: tt-dimer]]
+[[Category: Tt-dimer]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 08:04:29 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:34:55 2008''