2j6t
From Proteopedia
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|PDB= 2j6t |SIZE=350|CAPTION= <scene name='initialview01'>2j6t</scene>, resolution 2.60Å | |PDB= 2j6t |SIZE=350|CAPTION= <scene name='initialview01'>2j6t</scene>, resolution 2.60Å | ||
|SITE= <scene name='pdbsite=AC1:Ca+Binding+Site+For+Chain+A'>AC1</scene> | |SITE= <scene name='pdbsite=AC1:Ca+Binding+Site+For+Chain+A'>AC1</scene> | ||
| - | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> | + | |LIGAND= <scene name='pdbligand=6OG:6-O-METHYL+GUANOSINE-5'-MONOPHOSPHATE'>6OG</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=DTP:2'-DEOXYADENOSINE+5'-TRIPHOSPHATE'>DTP</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] | + | |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> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2j6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j6t OCA], [http://www.ebi.ac.uk/pdbsum/2j6t PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2j6t RCSB]</span> | ||
}} | }} | ||
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[[Category: Guengerich, F P.]] | [[Category: Guengerich, F P.]] | ||
[[Category: Irimia, A.]] | [[Category: Irimia, A.]] | ||
| - | [[Category: CA]] | ||
| - | [[Category: DTP]] | ||
[[Category: dna damage]] | [[Category: dna damage]] | ||
[[Category: dna polymerase]] | [[Category: dna polymerase]] | ||
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[[Category: translesion dna synthesis]] | [[Category: translesion dna synthesis]] | ||
| - | ''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 03:53:50 2008'' |
Revision as of 00:53, 31 March 2008
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| , resolution 2.60Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | |||||||
| Ligands: | , , , , , , | ||||||
| Activity: | DNA-directed DNA polymerase, with EC number 2.7.7.7 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6-METHYLGUANINE MODIFIED DNA, AND DATP.
Overview
We examined the effect of a single O6-methylguanine (O6-MeG) template residue on catalysis by a model Y family polymerase, Dpo4 from Sulfolobus solfataricus. Mass spectral analysis of Dpo4-catalyzed extension products revealed that the enzyme accurately bypasses O6-MeG, with C being the major product (approximately 70%) and T or A being the minor species (approximately 20% or approximately 10%, respectively), consistent with steady-state kinetic parameters. Transient-state kinetic experiments revealed that kpol, the maximum forward rate constant describing polymerization, for dCTP incorporation opposite O6-MeG was approximately 6-fold slower than observed for unmodified G, and no measurable product was observed for dTTP incorporation in the pre-steady state. The lack of any structural information regarding how O6-MeG paired in a polymerase active site led us to perform x-ray crystallographic studies, which show that "wobble" pairing occurs between C and O6-MeG. A structure containing T opposite O6-MeG was solved, but much of the ribose and pyrimidine base density was disordered, in accordance with a much higher Km,dTTP that drives the difference in efficiency between C and T incorporation. The more stabilized C:O6-MeG pairing reinforces the importance of hydrogen bonding with respect to nucleotide selection within a geometrically tolerant polymerase active site.
About this Structure
2J6T is a Single protein structure of sequence from Sulfolobus solfataricus. Full crystallographic information is available from OCA.
Reference
Sulfolobus solfataricus DNA polymerase Dpo4 is partially inhibited by "wobble" pairing between O6-methylguanine and cytosine, but accurate bypass is preferred., Eoff RL, Irimia A, Egli M, Guengerich FP, J Biol Chem. 2007 Jan 12;282(2):1456-67. Epub 2006 Nov 14. PMID:17105728
Page seeded by OCA on Mon Mar 31 03:53:50 2008
Categories: DNA-directed DNA polymerase | Single protein | Sulfolobus solfataricus | Egli, M. | Eoff, R L. | Guengerich, F P. | Irimia, A. | Dna damage | Dna polymerase | Dna repair | Dna replication | Dna-binding | Dna-directed dna polymerase | Dpo4 | Magnesium | Metal-binding | Mutator protein | Nucleotidyltransferase | O6-methylguanine | Transferase | Transferase/dna complex | Translesion dna synthesis
