PDBsum entry: 2p5o

Transferase/DNA

PDB-id

2p5o


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Description

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Protein chains

DNA/RNA

Waters ×495

* Residue conservation analysis

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PDB id:

2p5o

Name:

Transferase/DNA

Title:

Crystal structure of rb69 gp43 in complex with DNA containing an abasic site analog

Structure:

Template DNA. Chain: e, g, i, k. Engineered: yes. Primer DNA. Chain: f, h, j, l. Engineered: yes. DNA polymerase. Chain: a, b, c, d. Synonym: gp43.

Source:

Synthetic: yes. Other_details: commercially produced. Enterobacteria phage rb69. Organism_taxid: 12353. Gene: 43. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

UniProt:

Chains A, C: Q38087 (DPOL_BPR69)

Seq:

Struc:


Seq:

Struc:


Seq:

Struc:


Seq:				903 a.a.

Struc:				856 a.a.*

Chain B: Q38087 (DPOL_BPR69)

Seq:

Struc:


Seq:

Struc:


Seq:

Struc:


Seq:				903 a.a.

Struc:				771 a.a.*

Chain D: Q38087 (DPOL_BPR69)

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

903 a.a.

Struc:

671 a.a.*

Key:

PfamA domain

Secondary structure

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

Enzyme class:

Chains A, B, C, D: E.C.2.7.7.7 [IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1) (see diagram below)

Resolution:

2.80Å

R-factor:

0.245

R-free:

0.290

Authors:

M.Hogg,S.S.Wallace,S.Doublie

Key ref:

M.Hogg et al. (2004). Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site.. EMBO J, 23, 1483-1493. [PubMed id: 15057283] [DOI: 10.1038/sj.emboj.7600150]

Date:

15-Mar-07

Release date:

03-Apr-07

Supersedes:

1rv2

Related entries:

1ig9
1clq
2dy4
2dtu
1q9y

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Enzyme reaction for E.C.2.7.7.7

N deoxynucleoside triphosphate	=	N diphosphate	+	{DNA}(N)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site.

Key reference

DOI no: 10.1038/sj.emboj.7600150 EMBO J 23:1483-1493 (2004)

PubMed id: 15057283

Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site.

M.Hogg, S.S.Wallace, S.Doublié.

ABSTRACT

Abasic sites are common DNA lesions, which are strong blocks to replicative polymerases and are potentially mutagenic when bypassed. We report here the 2.8 A structure of the bacteriophage RB69 replicative DNA polymerase attempting to process an abasic site analog. Four different complexes were captured in the crystal asymmetric unit: two have DNA in the polymerase active site whereas the other two molecules are in the exonuclease mode. When compared to complexes with undamaged DNA, the DNA surrounding the abasic site reveals distinct changes suggesting why the lesion is so poorly bypassed: the DNA in the polymerase active site has not translocated and is therefore stalled, precluding extension. All four molecules exhibit conformations that differ from the previously published structures. The polymerase incorporates dAMP across the lesion under crystallization conditions, indicating that the different conformations observed in the crystal may be part of the active site switching reaction pathway.

Selected figure(s)

Figure 2.
Figure 2 Protein/DNA contacts in polymerizing and editing conformations. (A) Polymerase mode. Hydrogen bond contacts less than 2.8 � are represented by solid lines and those greater than 2.8 and less than 3.5 � are shown with dashed lines. Residues in parentheses represent charge interactions longer than 3.5 �. Wavy lines represent water-mediated contacts. Hydrophobic interactions are symbolized by dashed arcs. Contacts mediated by a nitrogen main-chain atom are indicated by the suffix 'N'. Protein residues are colored according to their domain location: exonuclease (cyan), N-terminal domain (orange), palm (red), thumb (green) and fingers (blue). Underlined residues are contacts in Pol1 that are absent in Pol2. (B) Exonuclease mode. All descriptions as above. Figure 4.
Figure 4 Minor groove interactions are lost in furan-containing DNA. (A) Minor groove interactions in the active site of ternary complex (1IG9; Franklin et al, 2001). Hydrogen bonds are shown as dashed red lines. For clarity only the bases of the primer strand are shown. (B) Pol1, in the same orientation as the ternary complex in (A). All minor groove interactions seen in the ternary complex are lost. (C) Pol2, in the same orientation as in (A) and (B). The DNA shifts further away from the palm domain.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2004, 23, 1483-1493) copyright 2004.

Figures were selected by the author.

Literature references that cite this PDB file's key reference

PubMed id Reference

19661923 B.Ibarra, Y.R.Chemla, S.Plyasunov, S.B.Smith, J.M.Lázaro, M.Salas, and C.Bustamante (2009).
Proofreading dynamics of a processive DNA polymerase.

EMBO J, 28, 2794-2802.

19718023 M.K.Swan, R.E.Johnson, L.Prakash, S.Prakash, and A.K.Aggarwal (2009).
Structural basis of high-fidelity DNA synthesis by yeast DNA polymerase delta.

Nat Struct Mol Biol, 16, 979-986.

PDB code: 3iay

19124465 S.M.Sherrer, J.A.Brown, L.R.Pack, V.P.Jasti, J.D.Fowler, A.K.Basu, and Z.Suo (2009).
Mechanistic Studies of the Bypass of a Bulky Single-base Lesion Catalyzed by a Y-family DNA Polymerase.

J Biol Chem, 284, 6379-6388.

19074196 X.Meng, Y.Zhou, S.Zhang, E.Y.Lee, D.N.Frick, and M.Y.Lee (2009).
DNA damage alters DNA polymerase delta to a form that exhibits increased discrimination against modified template bases and mismatched primers.

Nucleic Acids Res, 37, 647-657.

17975836 B.Sharma, E.Crespan, G.Villani, and G.Maga (2008).
The balance between the rates of incorporation and pyrophosphorolytic removal influences the HIV-1 reverse transcriptase bypass of an abasic site with deoxy-, dideoxy-, and ribonucleotides.

Proteins, 71, 715-727.

18845683 G.Serrano-Heras, A.Bravo, and M.Salas (2008).
Phage phi29 protein p56 prevents viral DNA replication impairment caused by uracil excision activity of uracil-DNA glycosylase.

Proc Natl Acad Sci U S A, 105, 19044-19049.

18166979 S.D.McCulloch, and T.A.Kunkel (2008).
The fidelity of DNA synthesis by eukaryotic replicative and translesion synthesis polymerases.

Cell Res, 18, 148-161.

18596099 W.Tian, Y.T.Hwang, and C.B.Hwang (2008).
The enhanced DNA replication fidelity of a mutant herpes simplex virus type 1 DNA polymerase is mediated by an improved nucleotide selectivity and reduced mismatch extension ability.

J Virol, 82, 8937-8941.

18503083 X.Zhong, L.C.Pedersen, and T.A.Kunkel (2008).
Characterization of a replicative DNA polymerase mutant with reduced fidelity and increased translesion synthesis capacity.

Nucleic Acids Res, 36, 3892-3904.

PDB code: 3cq8

17607682 A.J.Berdis, and D.McCutcheon (2007).
The use of non-natural nucleotides to probe template-independent DNA synthesis.

Chembiochem, 8, 1399-1408.

17702757 E.Fidalgo da Silva, and L.J.Reha-Krantz (2007).
DNA polymerase proofreading: active site switching catalyzed by the bacteriophage T4 DNA polymerase.

Nucleic Acids Res, 35, 5452-5463.

17446402 E.G.Kovaleva, and J.D.Lipscomb (2007).
Crystal structures of Fe2+ dioxygenase superoxo, alkylperoxo, and bound product intermediates.

Science, 316, 453-457.

PDB codes: 2ig9 2iga

17766250 H.Zhang, W.Cao, E.Zakharova, W.Konigsberg, and E.M.De La Cruz (2007).
Fluorescence of 2-aminopurine reveals rapid conformational changes in the RB69 DNA polymerase-primer/template complexes upon binding and incorporation of matched deoxynucleoside triphosphates.

Nucleic Acids Res, 35, 6052-6062.

17210571 K.A.Fiala, C.D.Hypes, and Z.Suo (2007).
Mechanism of abasic lesion bypass catalyzed by a Y-family DNA polymerase.

J Biol Chem, 282, 8188-8198.

17234630 K.A.Fiala, and Z.Suo (2007).
Sloppy bypass of an abasic lesion catalyzed by a Y-family DNA polymerase.

J Biol Chem, 282, 8199-8206.

17098747 M.Hogg, P.Aller, W.Konigsberg, S.S.Wallace, and S.Doublié (2007).
Structural and biochemical investigation of the role in proofreading of a beta hairpin loop found in the exonuclease domain of a replicative DNA polymerase of the B family.

J Biol Chem, 282, 1432-1444.

PDB code: 2dtu

17210917 P.Aller, M.A.Rould, M.Hogg, S.S.Wallace, and S.Doublié (2007).
A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol.

Proc Natl Acad Sci U S A, 104, 814-818.

PDB code: 2dy4

17183508 S.Melissis, N.E.Labrou, and Y.D.Clonis (2007).
One-step purification of Taq DNA polymerase using nucleotide-mimetic affinity chromatography.

Biotechnol J, 2, 121-132.

16415021 E.P.Tchesnokov, C.Gilbert, G.Boivin, and M.Götte (2006).
Role of helix P of the human cytomegalovirus DNA polymerase in resistance and hypersusceptibility to the antiviral drug foscarnet.

J Virol, 80, 1440-1450.

17091513 I.Lee, and A.Berdis (2006).
Fluorescent analysis of translesion DNA synthesis by using a novel, non-natural nucleotide analogue.

Chembiochem, 7, 1990-1997.

16687658 M.Hogg, W.Cooper, L.Reha-Krantz, and S.S.Wallace (2006).
Kinetics of error generation in homologous B-family DNA polymerases.

Nucleic Acids Res, 34, 2528-2535.

16705640 R.Shi, A.Azzi, C.Gilbert, G.Boivin, and S.X.Lin (2006).
Three-dimensional modeling of cytomegalovirus DNA polymerase and preliminary analysis of drug resistance.

Proteins, 64, 301-307.

15764597 D.Picard, C.C.Kao, and K.A.Hudak (2005).
Pokeweed antiviral protein inhibits brome mosaic virus replication in plant cells.

J Biol Chem, 280, 20069-20075.

15385534 G.W.Hsu, J.R.Kiefer, D.Burnouf, O.J.Becherel, R.P.Fuchs, and L.S.Beese (2004).
Observing translesion synthesis of an aromatic amine DNA adduct by a high-fidelity DNA polymerase.

J Biol Chem, 279, 50280-50285.

PDB codes: 1ua0 1ua1

15528277 S.Dutta, Y.Li, D.Johnson, L.Dzantiev, C.C.Richardson, L.J.Romano, and T.Ellenberger (2004).
Crystal structures of 2-acetylaminofluorene and 2-aminofluorene in complex with T7 DNA polymerase reveal mechanisms of mutagenesis.

Proc Natl Acad Sci U S A, 101, 16186-16191.

PDB codes: 1x9m 1x9s 1x9w

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.