Primary Citation PubMed: 8679562
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Kinetics of error generation in homologous B-family DNA polymerases.
(2006) Nucleic Acids Res 34
PubMed: 16687658 | PubMedCentral: PMC1459414 | DOI: 10.1093/nar/gkl300
2002 CA, USA DeLano Scientific, San Carlos Figures and Tables Figure 1 Exonuclease active site of T4 DNA polymerase ( 21 ) (PDB: 1NOY).
Publication Year: 2006
Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families.
(2008) BMC Struct Biol 8
PubMed: 19111067 | PubMedCentral: PMC2628669 | DOI: 10.1186/1472-6807-8-55
SCOP Family PDB code of Proteins Cysteine positions of the SS bond Sequence Similarity % Reason for non-conservation Comment Ref with SS without SS Rubisco, large subunit (c.1.14.1) 3rub 8ruc 172... 13;192 94.7 Crystallographic artifact Not clear if functionally significant or formed during crystallization period [ 83 ] Purple acid phosphatase (d.159.1.1) 1ute 1qhw 163–221 84.7 Crystallographic artifact No indication crosslink in electron density map [ 84 ] VHS domain (a.118.9.2) 1ujk 1juq 33–76 72.7 Crystallographic artifact Not favorable to accommodate cross link - DnaQ-like 3'-5' exonuclase (c.55.3.5) 1noy 1ih7 41–55 63.9 Crystallographic artifact Not favorable to accommodate cross link - Transferrin (c.94.1.2) - 1gv8 2tmp - - Fragments of domains 1gv8 – fragment of N-terminal domain of the intact protein, ovotransferrin 2tmp – only 1–122 residues of N-terminal domain of TIMP [ 85 ] Annexin (a.65.1.1) - 1scf - - Fragments of domains Partial structure - G proteins (c.37.1.8) - 1ryh 1mh1 1dsb - - Fragments of domains Partial structure - Glutathione S-transferase, N-terminal domain (c.47.1.5) 1k0m 1rk4 24–59 98.6 Structural transition A typical glutathione S-transferase but with a glutaredoxin-like active site.
Publication Year: 2008
Structural analysis of bacteriophage T4 DNA replication: a review in the Virology Journal series on bacteriophage T4 and its relatives.
(2010) Virol J 7
PubMed: 21129204 | PubMedCentral: PMC3012046 | DOI: 10.1186/1743-422X-7-359
T4 and Related Phage T7 Phage E. coli Eukaryotes Replicative DNA polymerase gp43 polymerase (pdb 1ig9 , 1clq , 1noy , 1ih7 ) Gene 5 Polymerase (pdb 1t7p , 1skr , 1t8e , 1x9m ) Pol III (α... 5;θ) (pdb 2hnh , 1ido ) Pol δ (subunits p125, p50, p66, p12) (pdb 3e0j ) Sliding clamp gp45 protein (pdb 1czd , 1b8h ) E. coli Thioredoxin (pdb 1t7p , 1skr ) β (pdb 2pol ) PCNA (pdb 1plr , 1axc , 1ul1 ) Clamp loader gp44/62 protein γ complex (γδδ'ψχ) (pdb 1jr3 , 1jqj , 3glf ) RF-C (subunits p140, p40, p38, p37, p36) (pdb 1sxj ) ssDNA binding protein gp32 protein (pdb 1gpc ) Gene 2.5 protein (pdb 1je5 ) SSB (pdb 1qvc ) RP-A (subunits p14, p32, p70) (pdb 1fgu , 2b29 , 1jmc , 1l1o , 2pi2 ) Replicative helicase gp41 helicase Gene 4 helicase (pdb 1e0j , 1e0k , 1q57 ) DnaB (pdb 1b79 , 2r6a ) MCM (pdb 3f9v , 1ltl ) helicase assembly protein gp59 protein (pdb 1c1k ) DnaC, PriA (pdb 3ec2 ) primase gp61 primase Gene 4 primase (pdb 1nui , 1q57 ) DnaG (pdb 1dd9 , 3b39 , 2r6c ) Pol α/primase (pdb 3flo ) 5' to 3' Exonuclease RNase H (pdb 1tfr , 2ihn ) Pol I N-domain FEN-1, RNase H1 (pdb 1ul1 , 2qk9 ) DNA ligase 1 T4 ligase (gp30) T7 ligase (pdb 1a0i ) DNA ligase (pdb 2owo ) DNA ligase I Figure 2 The molecular models, rendered to scale, of a DNA replication fork .
Publication Year: 2010
DNA polymerase ? and ? exonuclease domain mutations in endometrial cancer.
(2013) Hum Mol Genet 22
PubMed: 23528559 | PubMedCentral: PMC3690967 | DOI: 10.1093/hmg/ddt131
( C ) Structural assessment of POLE EDMs using a composite of the conserved yeast Pol δ structure (PDB 3IAY) and the ssDNA component of the T4 polymerase complex (PDB 1NOY).
Structural analysis Human mutations in both POLE and POLD1 were visualized in PyMOL ( http://pymol.org ) on the catalytic subunit of the yeast DNA polymerase δ [PDB ID: 3IAY ( 30 )] with the ssDNA component of the T4 polymerase complex [PDBID: 1NOY ( 31 )] modelled into the exonuclease active site.
Publication Year: 2013
Germline and somatic polymerase ? and ? mutations define a new class of hypermutated colorectal and endometrial cancers.
(2013) J Pathol 230
PubMed: 23447401 | PubMedCentral: PMC3709119 | DOI: 10.1002/path.4185
Figure 3 Pymol-generated image of POLE and POLD1 EDMs on a composite structure of yeast Polδ (PDB 3IAY) and the ssDNA component (yellow) of the T4 polymerase complex (PDB 1NOY).
Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas.
(2013) Nat Genet 45
PubMed: 23263490 | PubMedCentral: PMC3785128 | DOI: 10.1038/ng.2503
Structural analysis Human mutations in both POLE and POLD1 were visualised in PyMOL ( http://pymol.org ) on the catalytic subunit of the yeast DNA polymerase δ [PDB ID: 3IAY]), with the ssDNA ... omponent of the T4 polymerase complex [PDBID: 1NOY], modelled into the exonuclease active site.
Figure 2 Modelling of the germline and exonuclease domain mutations a) Composite model of the catalytic subunit of the yeast DNA polymerase δ (in ternary complex with DNA and an incoming nucleotide [PDB ID: 3IAY]) and the ssDNA component of the T4 polymerase complex [PDBID: 1NOY], modeled into the exonuclease active site.
The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification.
(2014) Nucleic Acids Res 42
PubMed: 24464998 | PubMedCentral: PMC3985635 | DOI: 10.1093/nar/gkt1414
In the structures of the exonuclease domains of DNA polymerase type B (1noy and 1xhx), there are two and three additional β-strands present, respectively, formed by an insertion between the se... ond α-helix and the fifth β-strand of the core.
Publication Year: 2014
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