Primary Citation PubMed: 9287163
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A specific loop in human DNA polymerase mu allows switching between creative and DNA-instructed synthesis.
(2006) Nucleic Acids Res 34
PubMed: 16963491 | PubMedCentral: PMC1636348 | DOI: 10.1093/nar/gkl457
In this figure, represented by using the Swiss PDB Viewer program ( ), a gapped DNA has been also modelled based on a Polβ ternary complex (PDB id: 1BPY).
Publication Year: 2006
Distinct energetics and closing pathways for DNA polymerase beta with 8-oxoG template and different incoming nucleotides.
(2007) BMC Struct Biol 7
PubMed: 17313689 | PubMedCentral: PMC1819382 | DOI: 10.1186/1472-6807-7-7
Methods Systems preparation We construct open and closed models of the pol β/DNA substrate complexes from the binary (PDB ID code 1BPX) and ternary (PDB ID code 1BPY) crystal structures [ 41 ]... respectively.
Publication Year: 2007
The Leu22Pro tumor-associated variant of DNA polymerase beta is dRP lyase deficient.
(2008) Nucleic Acids Res 36
PubMed: 18039710 | PubMedCentral: PMC2241857 | DOI: 10.1093/nar/gkm1053
The N-terminal helix of the wild-type pol β; crystal structure (PDB code 1bpy) is overlaid in gray (semi-transparent rendering).
Publication Year: 2008
Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis.
(2008) Acta Crystallogr D Biol Crystallogr 64
PubMed: 18094466 | PubMedCentral: PMC2394787 | DOI: 10.1107/S0907444907053516
A direct application to MR was presented in the case of polymerase β (PDB codes 1bpx and 1bpy ), which showed that when replacing the rigid-body fitting program after the translation function ... y the normal-mode amplitude refinement ( NOMAD-Ref ; Lindahl et al. , 2006 ▶ ), the score of the list of potential solutions was modified in such a way that false positives were down-weighted and the true solution now emerged as that with the highest score (Delarue & Dumas, 2004 ▶ ).
Mismatched dNTP incorporation by DNA polymerase beta does not proceed via globally different conformational pathways.
PubMed: 18385153 | PubMedCentral: PMC2396427 | DOI: 10.1093/nar/gkn138
As crystal structures are unavailable for complexes of I260Q, the coordinates of the binary (1BPX) and matched ternary (1BPY) complexes of the WT were used for the homology modeling approach ( 28 ).
Figure 4 A (inset) shows a set of four intercalated structures (gray) between the open crystal structure (1BPX, blue) and the G:C matched ternary complex crystal structure (1BPY, red).
Molecular modeling in the ternary complex of Pol β While the overall root mean square difference (RMSD) is over 2 Å between the two sets of corresponding C α atoms from the conformations of the binary (1BPX) and the matched ternary complex (1BPY), the pairwise RMSDs for the subdomain regions are all <1 Å.
Based on the crystal structures of the binary (1BPX) and matched ternary (1BPY) complex of Pol β, the modification of Ile by Gln at residue 260 should not interfere with the dNTP-binding subdomain closure.
( A ) Binding of DNA to free Pol β (1BPD, blue) causes rotation of the N-terminal 8 kDa domain in the Pol β·DNA binary complex (1BPX, red) (left), while subsequent binding of matched nucleotide (dNTP) induces the ‘open-to-closed’ conformational change of the dNTP-binding subdomain in the matched Pol β·DNA·dNTP ternary complex (1BPY, green) (right).
Nucleic acid polymerases use a general acid for nucleotidyl transfer.
(2009) Nat Struct Mol Biol 16
PubMed: 19151724 | PubMedCentral: PMC2728625 | DOI: 10.1038/nsmb.1540
DdDp (X-Family): Pol β polymerase with the ddCTP bound to the active site in the presence of Mg 2+ ions (pdb 1BPY) 50 .
Publication Year: 2009
Re-visiting protein-centric two-tier classification of existing DNA-protein complexes.
(2012) BMC Bioinformatics 13
PubMed: 22800292 | PubMedCentral: PMC3472317 | DOI: 10.1186/1471-2105-13-165
Table 1 Representatives for previous families 54 existing families (Thornton classification) representatives were selected and were validated using Jack-knifing Group Families Representative(s) HTH ... 000a0; Cro & repressor 1LMB Homeodomain 1FJL, 1HDD, 6PAX LacI repressor 1WET Endonuclease Fok1 1FOK Gamma Delta resolvase 1GDT Hin recombinase 1HCR RAP1 family 1IGN Prd paired domain 1PDN Tc3 transposase 1TC3 Trp repressor 1TRR Diptheria tox repressor 1DDN Transcription factor IIB 1D3U Interferon regulatory 2IRF Catabolite gene activator protein 1RUO Transcription factor 1CF7, 3HTS Ets domain 1BC8 Zinc Co-ordinating β-β-α zinc finger 1ZAA Harmone Nuclear Receptor 2NLL Loop sheet helix 1TSR GAL4 type 1ZME Zipper type Leucine Zipper 1YSA Helix loop helix 1AN2 Other-α Helix Pappilomavirus 1 E2 2BOP Histone 1AOI EBNA1 nuclear protein 1B3T Skn-1 transcription factor 1SKN Cre Recombinase 1CRX High Mobility Group 1QRV MADS box 1MNM β-Sheet TATA box binding 1YTB β-Hairpin/Ribbon MetJ repressor 1CMA Tus replication terminator 1ECR Integration host factor 1IHF Transcription Factor T-domain 1XBR Hyperthermophile DNA 1AZP Arc repressor 1PAR Other ReI homology 1SVC Stat protein 1BF5 Enzyme Methyltransferase 6MHT Endonuclease PvuII 3PVI Endonuclease ecorV 1RVA Endonuclease ecorI 1QPS Endonuclease BamHI 3BAM Enonuclease V 1VAS Dnase I 2DNJ DNA mismatch endonuclease 1CW0 DNA polymerase β 1BPY DNA Polymerase I 2BDP DNA Polymerase T7 1T7P,1CLQ HIV Reverse Transcriptase 2HMI Uracil DNA glycosylase 1SSP 3-Methyladenine DNA glycosylase 1BNK Homing endonuclease 1A73, 1BP7 TopoisomeraseI 1A31 For all the 59 selected representatives, PSI-BLAST profiles were again built against dummy database using the earlier profile creation parameters (as described in Methods).
Publication Year: 2012
DNA stabilization at the Bacillus subtilis PolX core--a binding model to coordinate polymerase, AP-endonuclease and 3'-5' exonuclease activities.
(2012) Nucleic Acids Res 40
PubMed: 22844091 | PubMedCentral: PMC3479172 | DOI: 10.1093/nar/gks702
Palm subdomains of modelled PolXBs and Polβ ternary complex (PDB 1BPY) ( 39 ) were further structurally aligned.
DNA-binding determinants promoting NHEJ by human Pol?.
PubMed: 23034807 | PubMedCentral: PMC3526283 | DOI: 10.1093/nar/gks896
Ternary complex formation in solution Analysis of the 3D information available shows structural differences in Polβ when forming binary (E:DNA; PDB ID: 1BPX) versus ternary (E:DNA:dNTP; PDB ID... 1BPY) complexes.
Moreover, these footprints are fully compatible with the 3D structural information available for the ternary complexes of both DNA polymerases (PDB IDs: 2IHM for Polµ and 1BPY for Polβ; Supplementary Figure S1 ).
In the ternary structures of Polβ (PDB ID: 1BPY), Polλ (PDB ID: 1XSN) and Polµ (PDB ID: 2IHM), the 5′-P moiety is located at a positively charged pocket in this domain, where binding is mediated by several hydrogen bonding interactions with basic side chains.
A specific N-terminal extension of the 8 kDa domain is required for DNA end-bridging by human Pol? and Pol?.
(2013) Nucleic Acids Res 41
PubMed: 23935073 | PubMedCentral: PMC3799444 | DOI: 10.1093/nar/gkt681
This fact could well explain the 5-fold difference in K m observed between the full-length Polλ and the crystallized form of the enzyme ( 16 ) and also the conformation adopted by the 8 kDa do... ain in this Polλ structure, which is intermediate between the open and closed conformation of Polß (PDB IDs: 1BPZ, 1BPY).
Publication Year: 2013
PubMed ID is not available.
Published in 2014
The polβ gapped binary complex structure and the ternary complex structures were solved by molecular replacement 36 using published binary (PDB ID 1BPX) and ternary (PDB ID 1BPY) structures as... the search models, respectively.
Publication Year: 2014
Table 1 Crystallographic Structures of Pol β Catalytic Intermediates intermediate (conformation) a ligand PDB entry refs I (O) none 1BPD, 3UXN ( 18 ), ( 78 ) II (O) DNA 1BPX, 3ISB ( 30 ), ( 66... ) III (O) DNA, dNTP 4F5N, 4F5O, 4F5P b ( 34 ) IV (C) DNA, dNTP 2BPF, 1BPY, 2FMS, 1HUO, 4KLD, 4KLE, 4KLF, 3C2L, b 3C2M, b 4KLP, 4KLQ, b 4KLS b ( 30 ), ( 36 ), ( 37 ), ( 39 ), ( 46 ), ( 65 ) V (C) DNA +1 , PP i 1HUZ, 4KLG, 4KLH, 4KLI, 4KLJ, 4KLL, 4KLM, 4KLO, 4KLT b ( 39 ), ( 46 ) VI (O) DNA +1 , PP i – – VII (O) DNA +1 1BPZ, 1TV9, b 1TVA, b 4KLU b ( 30 ), ( 39 ), ( 79 ) a The global conformation is specified as open (O) or closed (C).
The length of the scissile P α –O lg bond in the unprotonated methyl triphosphate complexes varies from 1.616 to 1.632 Å; these distances agree reasonably well with the distanc... of 1.608 Å observed in the ternary complex of pol β (PDB code 1BPY).
Structure and mechanism of an intramembrane liponucleotide synthetase central for phospholipid biosynthesis.
(2014) Nat Commun 5
PubMed: 24968740 | PubMedCentral: PMC4083444 | DOI: 10.1038/ncomms5244
PDB code: 1BPY.
Transition-state destabilization reveals how human DNA polymerase ? proceeds across the chemically unstable lesion N7-methylguanine.
(2014) Nucleic Acids Res 42
PubMed: 24966350 | PubMedCentral: PMC4117778 | DOI: 10.1093/nar/gku554
Structures were solved by molecular replacement using a gapped binary complex structure with an open conformation (PDB ID: 1BPX) and a ternary complex structure with a closed conformation (PDB ID: 1BP... ) as the search models.
ACCESSION NUMBERS PDB IDs: 4O5C, 4O5K, 4O5E , 4P2H, 1BPX, 1BPY, 2FMS, 3C2L, 3C2M and 4PGX.
The spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase ?.
PubMed: 25200079 | PubMedCentral: PMC4176172 | DOI: 10.1093/nar/gku789
( E ) Published polβ structure with dG•dCTP* and the active-site Mg 2+ (PDB ID 1BPY).
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