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).
Additional files Major datasets The following datasets were generated: Perera RL , Torella R , Klinge S , Kilkenny ML , Maman JD , Pellegrini L , 2012 , Crystal structure of yeast DNA polymerase alpha , 4FVM ; http://www.rcsb.org/pdb/search/structidSearch.do?structureId=4FVM , Publicly available at the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ ).
Publication Year: 2013
An archaeal family-B DNA polymerase variant able to replicate past DNA damage: occurrence of replicative and translesion synthesis polymerases within the B family.
(2014) Nucleic Acids Res 42
PubMed: 25063297 | PubMedCentral: PMC4150786 | DOI: 10.1093/nar/gku683
( A )–( C ) Structural superimposition of the fingers regions from: ( A ) Saccharomyces cerevisiae Sce-Pol α (gray: pdb, 4FVM), Sce-Pol δ (black: pdb, 3IAY) and Sce-Pol ;... ; (orange: ‘Phyre2’ model); ( B ) Pyrococcus furiosus Pfu-Pol (blue: pdb, 2JGU) and Pfu-Pol (D473G) (red: ‘Phyre2’ model); ( C ) Thermococcus gorgonarius Tgo-Pol (purple: pdb, 1Tgo) and Tgo-Pol Z1 (green: ‘Phyre2’ model).
Hydrogen bonds formed between the fingers domain loop aspartic acid or its equivalent (the amino acid shown in green and arrowed in Figure 1 ) and amino acids (shown in blue) in the subsequent α-helix DNA polymerase Data source Number of H bonds Hydrogen bonding partners a Sce-Pol α pdb, 4FVM 3 D929-H931 D929-K932 D929-R933 Sce-Pol δ pdb, 3IAY 3 D686-F688 D686-K689 D686-R690 Sce-Pol ϵ b pdb, 4M8O 1 D807-K811 Sce-Pol ζ b ‘Phyre2’ model 2 D1070-T1073 D1070-K1075 Pfu-Pol pdb, 2JGU 2 D473-I475 D473-K477 Pfu-Pol D473G b ‘Phyre2’ model 1 G473-K477 Tgo-Pol pdb, 1TGO 3 D472-I474 D472-E475 D472-K476 Tgo-Pol Z1 b ‘Phyre2’ model 3 D473-T476 D473-K478 D473-R479 Eco-Pol II c pdb, 3K5O 3 N485-L488 N485-S489 N485-A491 a The first residue shown is the aspartic acid (asparagine in the case of Eco-Pol II) in the loop region, the second the amino acids in the following α-helix.
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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