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PDB ID Mentions in PubMed Central Article count: 9

Citations in PubMed

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PDB ID Mentions in PubMed Central

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Mutagenic nucleotide incorporation and hindered translocation by a food carcinogen C8-dG adduct in Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): modeling and dynamics studies.

(2006) Nucleic Acids Res 34

PubMed: 16820532 | PubMedCentral: PMC1500869 | DOI: 10.1093/nar/gkl425

We therefore modeled it into the structure, using the conformation of an analogous terminal base in the Dpo4 type I structure (PDB ID: 1JX4).

Publication Year: 2006


The RAGNYA fold: a novel fold with multiple topological variants found in functionally diverse nucleic acid, nucleotide and peptide-binding proteins.

(2007) Nucleic Acids Res 35

PubMed: 17715145 | PubMedCentral: PMC2034487 | DOI: 10.1093/nar/gkm558

The PDBIDs of these structures are respectively 1JJ2, 1JX4, 1MZP and 1GSA.

As a result we identified 11 different domains containing an equivalent fold, namely: ( 1 ) L3-I (PDB: 1JJ2 chain B residues 80–190); ( 2 ) siRNA silencing repressor of Tombusviruses (CIRV p19; PDB: 1RPU, chain A); ( 3 ) The GYF domain (PDB 1L2Z, chain A; 1WH2); ( 4 ) Enhancer of rudimentary proteins (ER; PDB: 1WWQ); ( 5 ) one domain of the tRNA Wybutosine biosynthesis enzyme Tyw3p, typified by the SSO0622 protein from Sulfolobus solfataricus (PDB: 1TLJ, chain A, residues 53–102 and 147–172); ( 6 ) the two related globular domains of AMMECR1 (PDB: 1WSC, chain A); (7a) the N-terminal domain of ATP-grasp enzyme superfamily (PDB: 1WR2, chain A, residues 37–116) (7b) the related domain from the DNA/RNA ligase-type nucleotidyltransferases (1V9P chain B, residues 2085–2119 and 2255–2293); ( 8 ) C-terminal DNA-interacting domain of DinB-like (Y-family) DNA polymerases (PDB: 1JX4, Chain A, residues 241–341); ( 9 ) The DNA-recombination proteins of the NinB family from λ and other related caudate bacteriophages (PDB: 1PC6 A and B); ( 10 ) the ribosomal protein L1 (1DWU, chain B) ( Figure 1 ).

Publication Year: 2007


DNA conformations and their sequence preferences.

(2008) Nucleic Acids Res 36

PubMed: 18477633 | PubMedCentral: PMC2441783 | DOI: 10.1093/nar/gkn260

The PDB codes of the structures used in the analysis Structure Type PDB Codes Noncomplexed A-DNA ( 46 ) 118d, 137d, 138d, 160d, 1d78, 1d79, 1dnz, 1kgk, 1m77, 1ma8, 1mlx, 1nzg, 1vj4, 1xjx, 1z7i, 1zex, ... zey, 1zf1, 1zf6, 1zf8, 1zf9, 1zfa, 213d, 243d, 260d, 295d, 2d94, 317d, 338d, 344d, 345d, 348d, 349d, 368d, 369d, 370d, 371d, 395d, 396d, 399d, 414d, 440d, 9dna, dh010, adh012, adh034 Noncomplexed B-DNA ( 72 ) 122d, 123d, 158d, 183d, 196d, 1bd1, 1bna, 1cw9, 1d23, 1d3r, 1d49, 1d56, 1d61, 1d8g, 1d8x, 1dou, 1dpn, 1edr, 1ehv, 1en3, 1en8, 1en9, 1ene, 1enn, 1fq2, 1g75, 1i3t, 1ikk, 1j8l, 1jgr, 1l4j, 1l6b, 1m6g, 1n1o, 1nvn, 1nvy, 1p4y, 1p54, 1s23, 1s2r, 1sgs, 1sk5, 1ub8, 1ve8, 1zf0, 1zf3, 1zf4, 1zf5, 1zf7, 1zfb, 1zff, 1zfg, 232d, 251d, 2d25, 307d, 355d, 3dnb, 403d, 423d, 428d, 431d, 436d, 454d, 455d, 456d, 460d, 463d, 476d, 477d, 5dnb, 9bna DNA/drug and DNA/ protein complexes, Z-DNA, quadruplexes (329) 110d, 115d, 131d, 145d, 151d, 152d, 159d, 181d, 182d, 184d, 190d, 191d, 1a1g, 1a1h, 1a1i, 1a1k, 1a2e, 1a73, 1aay, 1ais, 1azp, 1b94, 1b97, 1bf4, 1bqj, 1brn, 1c8c, 1cdw, 1ckq, 1cl8, 1cn0, 1d02, 1d11, 1d14, 1d15, 1d21, 1d22, 1d2i, 1d32, 1d37, 1d38, 1d40, 1d41, 1d45, 1d48, 1d53, 1d54, 1d58, 1d67, 1d76, 1d90, 1d9r, 1da0, 1da2, 1da9, 1dc0, 1dc1, 1dcg, 1dcr, 1dcw, 1dfm, 1dj6, 1dl8, 1dn4, 1dn5, 1dn8, 1dnf, 1dp7, 1dsz, 1e3o, 1egw, 1em0, 1emh, 1eo4, 1eon, 1esg, 1eyu, 1f0v, 1fd5, 1fdg, 1fhz, 1fiu, 1fms, 1fn1, 1fn2, 1g2f, 1g9z, 1gtw, 1gu4, 1h6f, 1hcr, 1hlv, 1hwt, 1hzs, 1i0t, 1i3w, 1ick, 1ign, 1ih4, 1ih6, 1imr, 1ims, 1j59, 1j75, 1jb7, 1jes, 1jft, 1jh9, 1jk1, 1jk2, 1jpq, 1jtl, 1juc, 1jux, 1jx4, 1k3w, 1k3x, 1k9g, 1kbu, 1kci, 1kx3, 1kx5, 1l1h, 1l1t, 1l1z, 1l3l, 1l3s, 1l3t, 1l3u, 1l3v, 1lat, 1lau, 1ljx, 1llm, 1lmb, 1m07, 1m19, 1m3q, 1m5r, 1m69, 1m6f, 1mf5, 1mj2, 1mjm, 1mjo, 1mjq, 1mnn, 1mus, 1mw8, 1nh2, 1njw, 1njx, 1nk0, 1nk4, 1nk7, 1nk8, 1nk9, 1nkc, 1nke, 1nkp, 1nnj, 1nqs, 1nr8, 1nt8, 1nvp, 1o0k, 1omk, 1orn, 1p20, 1p3i, 1p3l, 1p71, 1per, 1pfe, 1ph4, 1ph6, 1ph8, 1pji, 1pjj, 1puf, 1pup, 1puy, 1q3f, 1qda, 1qn3, 1qn4, 1qn5, 1qn6, 1qn8, 1qn9, 1qna, 1qnb, 1qne, 1qum, 1qyk, 1qyl, 1qzg, 1r2z, 1r3z, 1r41, 1r68, 1rff, 1rh6, 1rnb, 1rpe, 1rqy, 1run, 1s1k, 1s1l, 1s32, 1ssp, 1suz, 1sx5, 1sxq, 1t9i, 1tdz, 1tez, 1tro, 1u1p, 1u1q, 1u1r, 1u4b, 1ue2, 1ue4, 1uhy, 1v3n, 1v3o, 1v3p, 1vzk, 1w0u, 1wd0, 1wte, 1wto, 1wtp, 1wtq, 1wtr, 1wtv, 1xa2, 1xam, 1xc9, 1xjv, 1xo0, 1xuw, 1xux, 1xvn, 1xvr, 1xyi, 1ytb, 1ytf, 1zez, 1zf2, 1zna, 200d, 210d, 211d, 212d, 215d, 221d, 224d, 234d, 235d, 236d, 241d, 242d, 244d, 245d, 254d, 258d, 276d, 277d, 278d, 279d, 284d, 288d, 292d, 293d, 2bdp, 2bop, 2cgp, 2crx, 2dcg, 2des, 2hap, 2hdd, 2nll, 2or1, 2pvi, 304d, 306d, 308d, 313d, 314d, 331d, 334d, 336d, 351d, 352d, 360d, 362d, 366d, 367d, 383d, 385d, 386d, 3bam, 3bdp, 3cro, 3crx, 3hts, 3pvi, 400d, 417d, 427d, 432d, 441d, 442d, 443d, 452d, 453d, 465d, 467d, 473d, 481d, 482d, 4bdp, adh013, zdf013, zdfb03, zdfb06 The DNA conformational space was investigated at the level of a dinucleotide unit with its 5′-end phosphate group removed; it was described by six backbone torsion angles between γ and δ + 1, plus two χ angles characterizing the glycosidic bond ( Figure 1 ).

Publication Year: 2008


Mechanistic Studies with DNA Polymerases Reveal Complex Outcomes following Bypass of DNA Damage.

(2010) J Nucleic Acids 2010

PubMed: 20936119 | PubMedCentral: PMC2948923 | DOI: 10.4061/2010/830473

The Y-family polymerase Dpo4 from S. solfataricus is also shown in ternary complex with 13/18-mer DNA (gray) and an incoming ddATP (pdb id code 1JX4; [ 43 ]).

Publication Year: 2010


MsDpo4-a DinB Homolog from Mycobacterium smegmatis-Is an Error-Prone DNA Polymerase That Can Promote G:T and T:G Mismatches.

(2012) J Nucleic Acids 2012

PubMed: 22523658 | PubMedCentral: PMC3317225 | DOI: 10.1155/2012/285481

Analysis of the MsDpo4 in the context of the available ssDpo4 structure (PDB code: 1JX4) revealed that D9, D107, and E108 should be the three residues critical for catalysis ( Figure 1 ).

Publication Year: 2012


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4018060

Table 1 Structures of Y-Family DNA Polymerases name species state PDB entry Structures of the Catalytic Region Dpo4 a Sulfolobus solfataricus apo 2RDI( 100 )     DNA binary complex 2RD... ( 100 )     ternary complex 1JX4, 2AGO; 95 , 136 2ATL 137     frameshift 3QZ7, 3QZ8( 39 )     CPD bypass 1RYR, 1RYS( 138 )     BPDE bypass 1S0M; 138 2IA6 and 2IBK( 37 )     abasic bypass 1S0N, 1S0O, 1S10( 105 )     [AF]G bypass 3KHG, 3KHH, 3KHL, 3KHR( 139 )     APG bypass 4FBU, 4FBT( 140 )     cisplatin bypass 3M9M, 3M9N, 3M9O( 141 )     DFT bypass 2VA2, 2V9W( 142 )     εdG (ε-G) 2BQR( 143 )     PdG bypass 2R8I( 144 )     8-oxo-G bypass 2ASD, 2ASJ, 2ASL; 137 2C2D, 2C2E( 66 )     8-oxo-G mispair 3GII, 3GIJ, 3GIK, 3GIL, 3GIM( 145 )     8-oxo-G (mutant Dpo4) 2UVR, 2UVU, 2UVV, 2UVW( 146 ) Dbh Sulfolobus acidocaldarius apo 1IM4; 93 1K1S 94     DNA binary complex 3BQ0, 3BQ2( 38 )     ternary complex 3BQ1( 38 ) Dpo4–Dbh chimera ternary 4F4W, 4F4X, 4F4Y, 4F4Z, 4F50( 86 ) pol η yeast apo 1JIH( 85 )   human ternary complex 3MFH( 67 )     CPD bypass 3MFI( 67 )     cisplatin bypass 2R8K( 96 )     8-oxo-G bypass 3OHA( 67 )     DNA binary complex 4J9P, 4J9Q, 4J9R, 4J9S( 99 )     ternary complex 4ED8( 127 )     CPD bypass 3MR2, 3MR3( 97 )     cisplatin bypass 4DL2, 4DL3, 4DL4, 4DL5, 4DL6, 4DL7; 98 4EEY 147     T:G mismatch 4J9K, 4J9L, 4J9M, 4J9N, 4J9O, 4J9P, 4J9Q, 4J9R, 4J9S( 98 ) pol ι human ternary complex 2ALZ; 115 3GV8 116     abasic bypass 3G6Y( 148 )     8-oxo-G bypass 3Q8R( 69 )     APG bypass 4EYI( 149 )     εdA (ε-A) 2DPJ( 150 )     T:G mismatch 3GV5, 3GV8; 116 3H4B, 3H4D( 118 ) pol κ human apo 1T94( 102 )     ternary complex 2OH2( 103 )     CPD (extension) 3PZP( 151 )     8-oxo-G bypass 2W7O, 2W7P; 152 3IN5 153 Rev1 yeast ternary complex 2AQ4( 106 )   human ternary complex 3GQC( 107 )         Structures of Regulatory Domains DinB E. coli (PolIV) LF (DinB) and β-clamp 1UNN( 154 ) Dpo4 S. solfataricus Dpo4 and PCNA 3FDS( 155 ) pol η, ι, and κ human PIP (η, ι, or κ) and PCNA 2ZVK, 2ZVM, 2ZVL( 156 ) pol η human apo-UBZ 2I5O( 157 ) pol ι human apo-UBM2 2KHU; 158 2L0G 159   mouse UBM2–Ub 2KHW; 158 2L0F 159     UBM1/2–Ub 2KWU, 2KWV( 160 ) Rev1 yeast BRCT 4ID3; 161 2M2I 73   mouse apo CTD 2LSG( 162 )   human CTD-κ (RIR) 2LSJ( 162 )     CTD-Rev3/7-κ (RIR) 4FJO( 77 )     apo CTD 2LSY( 163 )     CTD-η (RIR) 2LSK( 163 )     CTD-Rev3/7 3VU7( 76 )     CTD-Rev3/7-κ (RIR) 4GK5( 78 ) a There are additional structures in the PDB of Dpo4 complexed with DNA lesions beyond those listed here.

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4018064

Ternary structures of (A) Dpo4 (PDB entry 1JX4), (B) truncated hpol η (PDB entry 3MR2), (C) truncated hpol κ (PDB entry 2OH2), (D) truncated hpol ι (PDB entry 1T3N), and (E) tr... ncated hRev1 (PDB entry 3GQC).

Publication Year: 2014


Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase.

(2014) Nucleic Acids Res 42

PubMed: 25104018 | PubMedCentral: PMC4150803 | DOI: 10.1093/nar/gku709

MOLREP ( 37 ) was used for molecular replacement using PDB: 1JX4 as model ( 38 ).

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4471857

(C) Shown is a representative Y-family polymerase, Dpo4, an error-prone polymerase, bound to DNA (PDB entry 1JX4).

Publication Year: 2015