2fcc
From Proteopedia
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|PDB= 2fcc |SIZE=350|CAPTION= <scene name='initialview01'>2fcc</scene>, resolution 2.30Å | |PDB= 2fcc |SIZE=350|CAPTION= <scene name='initialview01'>2fcc</scene>, resolution 2.30Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=BRU:5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Deoxyribonuclease_(pyrimidine_dimer) Deoxyribonuclease (pyrimidine dimer)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.25.1 3.1.25.1] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_(pyrimidine_dimer) Deoxyribonuclease (pyrimidine dimer)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.25.1 3.1.25.1] </span> |
| - | |GENE= denV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= | + | |GENE= denV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4]) |
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2fcc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fcc OCA], [http://www.ebi.ac.uk/pdbsum/2fcc PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2fcc RCSB]</span> | ||
}} | }} | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2FCC is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ | + | 2FCC is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FCC OCA]. |
==Reference== | ==Reference== | ||
Structure of T4 pyrimidine dimer glycosylase in a reduced imine covalent complex with abasic site-containing DNA., Golan G, Zharkov DO, Grollman AP, Dodson ML, McCullough AK, Lloyd RS, Shoham G, J Mol Biol. 2006 Sep 15;362(2):241-58. Epub 2006 Jul 7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16916523 16916523] | Structure of T4 pyrimidine dimer glycosylase in a reduced imine covalent complex with abasic site-containing DNA., Golan G, Zharkov DO, Grollman AP, Dodson ML, McCullough AK, Lloyd RS, Shoham G, J Mol Biol. 2006 Sep 15;362(2):241-58. Epub 2006 Jul 7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16916523 16916523] | ||
| - | [[Category: Bacteriophage t4]] | ||
[[Category: Deoxyribonuclease (pyrimidine dimer)]] | [[Category: Deoxyribonuclease (pyrimidine dimer)]] | ||
| + | [[Category: Enterobacteria phage t4]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Dodson, M L.]] | [[Category: Dodson, M L.]] | ||
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[[Category: Shoham, G.]] | [[Category: Shoham, G.]] | ||
[[Category: Zharkov, D O.]] | [[Category: Zharkov, D O.]] | ||
| - | [[Category: GOL]] | ||
| - | [[Category: SO4]] | ||
[[Category: covalent intermediate]] | [[Category: covalent intermediate]] | ||
[[Category: dna repair]] | [[Category: dna repair]] | ||
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[[Category: t4-pdg]] | [[Category: t4-pdg]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:00:47 2008'' |
Revision as of 00:00, 31 March 2008
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| , resolution 2.30Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , | ||||||
| Gene: | denV (Enterobacteria phage T4) | ||||||
| Activity: | Deoxyribonuclease (pyrimidine dimer), with EC number 3.1.25.1 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with a DNA Substrate Containing Abasic Site
Overview
The base excision repair (BER) pathway for ultraviolet light (UV)-induced cyclobutane pyrimidine dimers is initiated by DNA glycosylases that also possess abasic (AP) site lyase activity. The prototypical enzyme known to catalyze these reactions is the T4 pyrimidine dimer glycosylase (T4-Pdg). The fundamental chemical reactions and the critical amino acids that lead to both glycosyl and phosphodiester bond scission are known. Catalysis proceeds via a protonated imine covalent intermediate between the alpha-amino group of the N-terminal threonine residue and the C1' of the deoxyribose sugar of the 5' pyrimidine at the dimer site. This covalent complex can be trapped as an irreversible, reduced cross-linked DNA-protein complex by incubation with a strong reducing agent. This active site trapping reaction is equally efficient on DNA substrates containing pyrimidine dimers or AP sites. Herein, we report the co-crystal structure of T4-Pdg as a reduced covalent complex with an AP site-containing duplex oligodeoxynucleotide. This high-resolution structure reveals essential precatalytic and catalytic features, including flipping of the nucleotide opposite the AP site, a sharp kink (approximately 66 degrees ) in the DNA at the dimer site and the covalent bond linking the enzyme to the DNA. Superposition of this structure with a previously published co-crystal structure of a catalytically incompetent mutant of T4-Pdg with cyclobutane dimer-containing DNA reveals new insights into the structural requirements and the mechanisms involved in DNA bending, nucleotide flipping and catalytic reaction.
About this Structure
2FCC is a Single protein structure of sequence from Enterobacteria phage t4. Full crystallographic information is available from OCA.
Reference
Structure of T4 pyrimidine dimer glycosylase in a reduced imine covalent complex with abasic site-containing DNA., Golan G, Zharkov DO, Grollman AP, Dodson ML, McCullough AK, Lloyd RS, Shoham G, J Mol Biol. 2006 Sep 15;362(2):241-58. Epub 2006 Jul 7. PMID:16916523
Page seeded by OCA on Mon Mar 31 03:00:47 2008
Categories: Deoxyribonuclease (pyrimidine dimer) | Enterobacteria phage t4 | Single protein | Dodson, M L. | Fernandes, A S. | Golan, G. | Grollman, A P. | Lloyd, R S. | McCullough, A K. | Shoham, G. | Zharkov, D O. | Covalent intermediate | Dna repair | Endonuclease | Enzyme-dna complex | Pyrimidine dimer | T4-pdg
