1rys: Difference between revisions

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[[Image:1rys.gif|left|200px]]<br /><applet load="1rys" size="350" color="white" frame="true" align="right" spinBox="true"
[[Image:1rys.gif|left|200px]]
caption="1rys, resolution 2.03&Aring;" />
 
'''REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION'''<br />
{{Structure
|PDB= 1rys |SIZE=350|CAPTION= <scene name='initialview01'>1rys</scene>, resolution 2.03&Aring;
|SITE=
|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ATP:ADENOSINE-5'-TRIPHOSPHATE'>ATP</scene> and <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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==
==Overview==
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==About this Structure==
==About this Structure==
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 <scene name='pdbligand=CA:'>CA</scene>, <scene name='pdbligand=NA:'>NA</scene>, <scene name='pdbligand=ATP:'>ATP</scene> and <scene name='pdbligand=EDO:'>EDO</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. This structure supersedes 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1RYS OCA].  
1RYS 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 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]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RYS OCA].  


==Reference==
==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: DNA-directed DNA polymerase]]
[[Category: Single protein]]
[[Category: Single protein]]
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[[Category: polymerase]]
[[Category: polymerase]]


''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:56:04 2008''
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:58:05 2008''

Revision as of 11:58, 20 March 2008

File:1rys.gif


Drag the structure with the mouse to rotate
1rys, resolution 2.03Å
Ligands: CA, NA, ATP and EDO
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


Overview

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 Structure

1RYS is a Single protein structure of sequence from Sulfolobus solfataricus. This structure supersedes the now removed PDB entry 1PM8. The following page contains interesting information on the relation of 1RYS with [Thymine Dimers]. Full crystallographic information is available from 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:12904819

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