Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 16

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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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 ▶ ).

Publication Year: 2008


Mismatched dNTP incorporation by DNA polymerase beta does not proceed via globally different conformational pathways.

(2008) Nucleic Acids Res 36

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).

Publication Year: 2008


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.

Publication Year: 2012


DNA-binding determinants promoting NHEJ by human Pol?.

(2012) Nucleic Acids Res 40

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.

Publication Year: 2012


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

PubMedCentral: PMC4004240

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


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4018062

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).

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4081047

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).

Publication Year: 2014


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.

Publication Year: 2014


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.

Publication Year: 2014


The spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase ?.

(2014) Nucleic Acids Res 42

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).

Publication Year: 2014