Primary Citation PubMed: 23599895
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Mechanism for priming DNA synthesis by yeast DNA Polymerase ?.
(2013) Elife 2
PubMed: 23599895 | PubMedCentral: PMC3628110 | DOI: 10.7554/eLife.00482
Coordinates and structure factors have been deposited with the Protein Data Bank under accession codes 4FVM (apo), 4FXD (binary complex) and 4FYD (ternary complex).
Perera RL , Torella R , Klinge S , Kilkenny ML , Maman JD , Pellegrini L , 2012 , Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA and dGTP , 4FYD ; http://www.rcsb.org/pdb/search/structidSearch.do?structureId=4FYD , Publicly available at the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ ).
Publication Year: 2013
Structural insights into eukaryotic DNA replication.
(2014) Front Microbiol 5
PubMed: 25202305 | PubMedCentral: PMC4142720 | DOI: 10.3389/fmicb.2014.00444
Number of amino acids Protein construct crystallized PDB ID code and reference Pol α POL1 Asp864 N/A P13382 S. cerevisiae 1 [4Fe-4S] 1468 aa 349–1258 4FYD Asp998 Cys1348,1353,1367,1372... 3.1 Å Perera et al., 2013 Asp996 Pol δ POL3 Asp608 Asp321 P15436 S. cerevisiae 1 [4Fe-4S] 1097 aa 67–985 3IAY Asp764 Glu323 Cys1056,1059,1069,1074 2.0 Å Asp762 Asp407 Swan et al., 2009 Asp520 Pol ε POL2 Asp640 Asp290 P21951 S. cerevisiae 2 [4Fe-4S] 2222 aa 1-1228 4M8O 2.2 Å Asp877 Glu292 Cys665,667,668,763 1-1187 (Hogg et al., 2014 ) Asp875 Asp383 Cys2164,2167,2179,2181 4PTF 2.8 Å Asp477 Jain et al., 2014a RB69 gp43 Asp411 Asp114 Q38087 Bacteriophage RB69 None 903 aa 1-903 1IG9 Asp623 Glu116 2.6 Å Asp621 Asp222 Franklin et al., 2001 Asp327 E. coli Pol II Asp419 Asp156 P21189 Escherichia coli None 783 aa 1-780 3K57 Asp547 Glu158 2.08 Å Asp545 Asp229 Wang and Yang, 2009 Asp315 Archaeal Tgo Asp404 Asp141 P56689 Thermococcus gorgonarius None 773 aa 1-757 2VWJ Asp542 Glu143 2.78 Å Asp540 Asp215 Firbank et al., 2008 Asp335 A mechanism of disengagement of the polymerase The RNA/DNA oligonucleotide captured in the crystals adopts an A-form conformation, as expected.
(A) Polymerase α (PDBID 4FYD) binds an RNA/DNA hybrid, where the wide, shallow minor groove of A-form DNA is apparent near the thumb.
Publication Year: 2014
The arabidopsis DNA polymerase ? has a role in the deposition of transcriptionally active epigenetic marks, development and flowering.
(2015) PLoS Genet 11
PubMed: 25693187 | PubMedCentral: PMC4334202 | DOI: 10.1371/journal.pgen.1004975
Protein Modeling Protein structures 3IAY, that correspond to the crystal structure of the catalytic subunit of yeast Polδ in ternary complex with a template primer and an incoming nucleotide (... losed conformation), 4FVM, that correspond to the catalytic subunit of yeast Polα in ternary complex with the template primer and the incoming nucleotide (closed conformation) and 4FYD, that correspond to the catalytic subunit of yeast Polα alone (open conformation), were used as templates and were obtained from the PDB website ( http://www.rcsb.org/pdb/home/home.do ).
The program “Modeller” [ 62 ] was used to construct the model using the X-ray structure of the yeast DNA Polymerase a catalytic subunit in its substrate-bound form (4FYD model,colored in light blue) and free form (4FVM model,colored in light brown).
As the yeast Polδ conformation changes upon substrate binding [ 29 ], we modeled POLD1 in both substrate-free (4FVM) and bound (4FYD) conformations using X-Ray models from POLA1 (29% identity) as references ( S1C Fig .)
Publication Year: 2015
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