1ryr: Difference between revisions

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Revision as of 14:58, 20 March 2008

File:1ryr.gif

, resolution 2.28Å

Ligands:

and

Gene:

DPO4 (Sulfolobus solfataricus)

Activity:

DNA-directed DNA polymerase, with EC number 2.7.7.7

Coordinates:

save as pdb, mmCIF, xml

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 Thu Mar 20 13:58:04 2008

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

OCA

@@ Line 1: / Line 1: @@
-[[Image:1ryr.gif|left|200px]]<br /><applet load="1ryr" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:1ryr.gif|left|200px]]
-caption="1ryr, resolution 2.28&Aring;" />
-'''REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION'''<br />
+ {{Structure
+|PDB= 1ryr |SIZE=350|CAPTION= <scene name='initialview01'>1ryr</scene>, resolution 2.28&Aring;
+|SITE=
+|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> and <scene name='pdbligand=ATP:ADENOSINE-5'-TRIPHOSPHATE'>ATP</scene>
+|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]
+|GENE= DPO4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 Sulfolobus solfataricus])
+}}
+'''REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-RYR 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 <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=ATP:'>ATP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. This structure supersedes the now removed PDB entry 1PM0. 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=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 1PM0. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RYR OCA].
 ==Reference==
-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]
+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: DNA-directed DNA polymerase]]
 [[Category: Single protein]]
@@ Line 25: / Line 34: @@
 [[Category: tt-dimer]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:56:03 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:58:04 2008''