PDBsum entry: 1bpy

Transferase/DNA

PDB-id

1bpy


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Description

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Protein chain

DNA/RNA

Ligands

DCT

Metal ions

_MG ×2

_NA ×2

Waters ×321

* Residue conservation analysis

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PDB id:

1bpy

Name:

Transferase/DNA

Title:

Human DNA polymerase beta complexed with gapped DNA and ddctp

Structure:

DNA (5'- d( Cp Cp Gp Ap Cp Gp Gp Cp Gp Cp Ap Tp Cp Ap Gp C)-3'). Chain: t. Engineered: yes. DNA (5'-d( Gp Cp Tp Gp Ap Tp Gp Cp Gp Doc)-3'). Chain: p. Engineered: yes. DNA (5'-d( Gp Tp Cp Gp G)-3'). Chain: d.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Cellular_location: nucleus. Expressed in: escherichia coli. Expression_system_taxid: 562

UniProt:

P06746 (DPOLB_HUMAN)

Seq:

Struc:

Seq:

335 a.a.

Struc:

326 a.a.

Key:		PfamA domain
		Secondary structure			CATH domain

Enzyme class:

E.C.2.7.7.7 [IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

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

Resolution:

2.20Å

R-factor:

0.227

R-free:

0.330

Authors:

H.Pelletier M.R.Sawaya,R.Prasad,S.H.Wilson,J.Kraut

Key ref:

M.R.Sawaya et al. (1997). Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism.. Biochemistry, 36, 11205-11215. [PubMed id: 9287163] [DOI: 10.1021/bi9703812]

Date:

15-Apr-97

Release date:

16-Jun-97

Related entries:

1bpx
1bpz

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Surface

Enzyme reaction for E.C.2.7.7.7

N deoxynucleoside triphosphate
Bound ligand (Het Group name = DCT)
matches with 65.00% similarity

N diphosphate

{DNA}(N)

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

Key reference

DOI no: 10.1021/bi9703812 Biochemistry 36:11205-11215 (1997)

PubMed id: 9287163

Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism.

M.R.Sawaya, R.Prasad, S.H.Wilson, J.Kraut, H.Pelletier.

ABSTRACT

DNA polymerase beta (pol beta) fills single nucleotide (nt) gaps in DNA produced by the base excision repair pathway of mammalian cells. Crystal structures have been determined representing intermediates in the 1 nt gap-filling reaction of pol beta: the binary complex with a gapped DNA substrate (2.4 A resolution), the ternary complex including ddCTP (2.2 A), and the binary product complex containing only nicked DNA (2.6 A). Upon binding ddCTP to the binary gap complex, the thumb subdomain rotates into the closed conformation to contact the otherwise solvent-exposed ddCTP-template base pair. Thumb movement triggers further conformational changes which poise catalytic residue Asp192, dNTP, and template for nucleotidyl transfer, effectively assembling the active site. In the product nicked DNA complex, the thumb returns to the open conformation as in the gapped binary DNA complex, facilitating dissociation of the product. These findings suggest that pol beta may enhance fidelity by an induced fit mechanism in which correct base pairing between template and incoming dNTP induces alignment of catalytic groups for catalysis (via thumb closure), but incorrect base pairing will not. The structures also reveal that pol beta binds both gapped and nicked DNA with a 90 degrees kink occurring precisely at the 5'-phosphodiester linkage of the templating residue. If the DNA were not kinked in this way, contact between the thumb and dNTP-template base pair, presumably important for the checking mechanism, would be impossible, especially when the gap is but a single nucleotide. Such a 90 degrees kink may be a mechanistic feature employed by any polymerase involved in filling gaps to completion.

Literature references that cite this PDB file's key reference

PubMed id Reference

19151724 C.Castro, E.D.Smidansky, J.J.Arnold, K.R.Maksimchuk, I.Moustafa, A.Uchida, M.Götte, W.Konigsberg, and C.E.Cameron (2009).
Nucleic acid polymerases use a general acid for nucleotidyl transfer.

Nat Struct Mol Biol, 16, 212-218.

19331672 E.Arehart, S.Gleim, B.White, J.Hwa, and J.H.Moore (2009).
Multifactor dimensionality reduction analysis identifies specific nucleotide patterns promoting genetic polymorphisms.

BioData Min, 2, 2.

19502493 F.Romain, I.Barbosa, J.Gouge, F.Rougeon, and M.Delarue (2009).
Conferring a template-dependent polymerase activity to terminal deoxynucleotidyltransferase by mutations in the Loop1 region.

Nucleic Acids Res, 37, 4642-4656.

19306280 K.A.Donigan, and J.B.Sweasy (2009).
Sequence context-specific mutagenesis and base excision repair.

Mol Carcinog, 48, 362-368.

19088981 M.A.van Bochove, M.Swart, and F.M.Bickelhaupt (2009).
Stepwise walden inversion in nucleophilic substitution at phosphorus.

Phys Chem Chem Phys, 11, 259-267.

19701199 M.Garcia-Diaz, K.Bebenek, A.A.Larrea, J.M.Havener, L.Perera, J.M.Krahn, L.C.Pedersen, D.A.Ramsden, and T.A.Kunkel (2009).
Template strand scrunching during DNA gap repair synthesis by human polymerase lambda.

Nat Struct Mol Biol, 16, 967-972.

19251692 N.Leulliot, L.Cladière, F.Lecointe, D.Durand, U.Hübscher, and H.van Tilbeurgh (2009).
The Family X DNA Polymerase from Deinococcus radiodurans Adopts a Non-standard Extended Conformation.

J Biol Chem, 284, 11992-11999.

PDB code: 2w9m

18623241 N.M.Makridakis, L.F.Caldas Ferraz, and J.K.Reichardt (2009).
Genomic analysis of cancer tissue reveals that somatic mutations commonly occur in a specific motif.

Hum Mutat, 30, 39-48.

19281452 P.B.Balbo, and A.Bohm (2009).
Proton transfer in the mechanism of polyadenylate polymerase.

Biochem J, 420, 229-238.

18704949 S.Biswas, M.Guharoy, and P.Chakrabarti (2009).
Dissection, residue conservation, and structural classification of protein-DNA interfaces.

Proteins, 74, 643-654.

18437203 A.Abyzov, A.Uzun, P.R.Strauss, and V.A.Ilyin (2008).
An AP endonuclease 1-DNA polymerase beta complex: theoretical prediction of interacting surfaces.

PLoS Comput Biol, 4, e1000066.

18776221 B.Baños, J.M.Lázaro, L.Villar, M.Salas, and M.de Vega (2008).
Editing of misaligned 3'-termini by an intrinsic 3'-5' exonuclease activity residing in the PHP domain of a family X DNA polymerase.

Nucleic Acids Res, 36, 5736-5749.

18391035 G.Yang, J.Wang, Y.Cheng, G.E.Dutschman, H.Tanaka, M.Baba, and Y.C.Cheng (2008).
Mechanism of inhibition of human immunodeficiency virus type 1 reverse transcriptase by a stavudine analogue, 4'-ethynyl stavudine triphosphate.

Antimicrob Agents Chemother, 52, 2035-2042.

18984592 J.W.Beckman, Q.Wang, and F.P.Guengerich (2008).
Kinetic Analysis of Correct Nucleotide Insertion by a Y-family DNA Polymerase Reveals Conformational Changes Both Prior to and following Phosphodiester Bond Formation as Detected by Tryptophan Fluorescence.

J Biol Chem, 283, 36711-36723.

18393274 K.H.Tang, and M.D.Tsai (2008).
Structure and function of 2:1 DNA polymerase.DNA complexes.

J Cell Physiol, 216, 315-320.

18084022 K.H.Tang, M.Niebuhr, A.Aulabaugh, and M.D.Tsai (2008).
Solution structures of 2 : 1 and 1 : 1 DNA polymerase-DNA complexes probed by ultracentrifugation and small-angle X-ray scattering.

Nucleic Acids Res, 36, 849-860.

18385153 K.H.Tang, M.Niebuhr, C.S.Tung, H.C.Chan, C.C.Chou, and M.D.Tsai (2008).
Mismatched dNTP incorporation by DNA polymerase beta does not proceed via globally different conformational pathways.

Nucleic Acids Res, 36, 2948-2957.

PDB code: 2van

18185993 V.N.Vyjayanti, N.S.Chary, and K.S.Rao (2008).
On the inhibitory affect of some dementia drugs on DNA polymerase Beta activity.

Neurochem Res, 33, 2187-2196.

17671961 Y.Xiang, M.F.Goodman, W.A.Beard, S.H.Wilson, and A.Warshel (2008).
Exploring the role of large conformational changes in the fidelity of DNA polymerase beta.

Proteins, 70, 231-247.

17159995 A.F.Moon, M.Garcia-Diaz, K.Bebenek, B.J.Davis, X.Zhong, D.A.Ramsden, T.A.Kunkel, and L.C.Pedersen (2007).
Structural insight into the substrate specificity of DNA Polymerase mu.

Nat Struct Mol Biol, 14, 45-53.

PDB code: 2ihm

17267485 D.R.Langley, A.W.Walsh, C.J.Baldick, B.J.Eggers, R.E.Rose, S.M.Levine, A.J.Kapur, R.J.Colonno, and D.J.Tenney (2007).
Inhibition of hepatitis B virus polymerase by entecavir.

J Virol, 81, 3992-4001.

17439962 G.C.Lin, J.Jaeger, and J.B.Sweasy (2007).
Loop II of DNA polymerase beta is important for polymerization activity and fidelity.

Nucleic Acids Res, 35, 2924-2935.

17872511 G.Martin, and W.Keller (2007).
RNA-specific ribonucleotidyl transferases.

RNA, 13, 1834-1849.

17410550 I.Bougie, and M.Bisaillon (2007).
Characterization of the RNA binding energetics of the Candida albicans poly(A) polymerase.

Yeast, 24, 431-446.

17259182 K.Singh, A.Srivastava, S.S.Patel, and M.J.Modak (2007).
Participation of the fingers subdomain of Escherichia coli DNA polymerase I in the strand displacement synthesis of DNA.

J Biol Chem, 282, 10594-10604.

17990249 M.A.van Bochove, M.Swart, and F.M.Bickelhaupt (2007).
Nucleophilic substitution at phosphorus centers (SN2@p).

Chemphyschem, 8, 2452-2463.

17911108 M.Sajish, D.Tiwari, D.Rananaware, V.K.Nandicoori, and B.Prakash (2007).
A charge reversal differentiates (p)ppGpp synthesis by monofunctional and bifunctional Rel proteins.

J Biol Chem, 282, 34977-34983.

17850751 P.B.Balbo, and A.Bohm (2007).
Mechanism of poly(A) polymerase: structure of the enzyme-MgATP-RNA ternary complex and kinetic analysis.

Structure, 15, 1117-1131.

PDB code: 2q66

17174326 P.Oelschlaeger, M.Klahn, W.A.Beard, S.H.Wilson, and A.Warshel (2007).
Magnesium-cationic dummy atom molecules enhance representation of DNA polymerase beta in molecular dynamics simulations: improved accuracy in studies of structural features and mutational effects.

J Mol Biol, 366, 687-701.

17400246 P.R.Meyer, W.Rutvisuttinunt, S.E.Matsuura, A.G.So, and W.A.Scott (2007).
Stable complexes formed by HIV-1 reverse transcriptase at distinct positions on the primer-template controlled by binding deoxynucleoside triphosphates or foscarnet.

J Mol Biol, 369, 41-54.

17576677 P.Xu, L.Oum, L.S.Beese, N.E.Geacintov, and S.Broyde (2007).
Following an environmental carcinogen N2-dG adduct through replication: elucidating blockage and bypass in a high-fidelity DNA polymerase.

Nucleic Acids Res, 35, 4275-4288.

17090533 R.A.Perlow-Poehnelt, I.Likhterov, L.Wang, D.A.Scicchitano, N.E.Geacintov, and S.Broyde (2007).
Increased flexibility enhances misincorporation: temperature effects on nucleotide incorporation opposite a bulky carcinogen-DNA adduct by a Y-family DNA polymerase.

J Biol Chem, 282, 1397-1408.

17701034 S.Beetz, D.Diekhoff, and L.A.Steiner (2007).
Characterization of terminal deoxynucleotidyl transferase and polymerase mu in zebrafish.

Immunogenetics, 59, 735-744.

17055529 S.J.Garforth, T.W.Kim, M.A.Parniak, E.T.Kool, and V.R.Prasad (2007).
Site-directed mutagenesis in the fingers subdomain of HIV-1 reverse transcriptase reveals a specific role for the beta3-beta4 hairpin loop in dNTP selection.

J Mol Biol, 365, 38-49.

17576692 S.Nakanishi, R.Prasad, S.H.Wilson, and M.Smerdon (2007).
Different structural states in oligonucleosomes are required for early versus late steps of base excision repair.

Nucleic Acids Res, 35, 4313-4321.

17520027 Y.Savir, and T.Tlusty (2007).
Conformational proofreading: the impact of conformational changes on the specificity of molecular recognition.

PLoS ONE, 2, e468.

17293403 Y.Wang, S.Reddy, W.A.Beard, S.H.Wilson, and T.Schlick (2007).
Differing conformational pathways before and after chemistry for insertion of dATP versus dCTP opposite 8-oxoG in DNA polymerase beta.

Biophys J, 92, 3063-3070.

17313689 Y.Wang, and T.Schlick (2007).
Distinct energetics and closing pathways for DNA polymerase beta with 8-oxoG template and different incoming nucleotides.

BMC Struct Biol, 7, 7.

16831866 A.M.DeLucia, S.Chaudhuri, O.Potapova, N.D.Grindley, and C.M.Joyce (2006).
The properties of steric gate mutants reveal different constraints within the active sites of Y-family and A-family DNA polymerases.

J Biol Chem, 281, 27286-27291.

16214865 B.A.Sampoli Benítez, K.Arora, and T.Schlick (2006).
In silico studies of the African swine fever virus DNA polymerase X support an induced-fit mechanism.

Biophys J, 90, 42-56.

16446439 H.Zhu, J.Nandakumar, J.Aniukwu, L.K.Wang, M.S.Glickman, C.D.Lima, and S.Shuman (2006).
Atomic structure and nonhomologous end-joining function of the polymerase component of bacterial DNA ligase D.

Proc Natl Acad Sci U S A, 103, 1711-1716.

PDB codes: 2fao 2faq 2far

16506094 I.Jagannathan, H.A.Cole, and J.J.Hayes (2006).
Base excision repair in nucleosome substrates.

Chromosome Res, 14, 27-37.

16675458 K.A.Fiala, W.W.Duym, J.Zhang, and Z.Suo (2006).
Up-regulation of the fidelity of human DNA polymerase lambda by its non-enzymatic proline-rich domain.

J Biol Chem, 281, 19038-19044.

16707660 L.V.Gening, S.A.Klincheva, A.Reshetnjak, A.P.Grollman, and H.Miller (2006).
RNA aptamers selected against DNA polymerase beta inhibit the polymerase activities of DNA polymerases beta and kappa.

Nucleic Acids Res, 34, 2579-2586.

16920835 M.C.Foley, K.Arora, and T.Schlick (2006).
Sequential side-chain residue motions transform the binary into the ternary state of DNA polymerase lambda.

Biophys J, 91, 3182-3195.

16614066 N.Pourmand, M.Karhanek, H.H.Persson, C.D.Webb, T.H.Lee, A.Zahradníková, and R.W.Davis (2006).
Direct electrical detection of DNA synthesis.

Proc Natl Acad Sci U S A, 103, 6466-6470.

16379496 O.Rechkoblit, L.Malinina, Y.Cheng, V.Kuryavyi, S.Broyde, N.E.Geacintov, and D.J.Patel (2006).
Stepwise translocation of Dpo4 polymerase during error-free bypass of an oxoG lesion.

PLoS Biol, 4, e11.

PDB codes: 2asd 2asj 2asl 2atl 2au0

16938895 P.Lin, L.C.Pedersen, V.K.Batra, W.A.Beard, S.H.Wilson, and L.G.Pedersen (2006).
Energy analysis of chemistry for correct insertion by DNA polymerase beta.

Proc Natl Acad Sci U S A, 103, 13294-13299.

16963491 R.Juárez, J.F.Ruiz, S.A.Nick McElhinny, D.Ramsden, and L.Blanco (2006).
A specific loop in human DNA polymerase mu allows switching between creative and DNA-instructed synthesis.

Nucleic Acids Res, 34, 4572-4582.

17176036 R.Radhakrishnan, K.Arora, Y.Wang, W.A.Beard, S.H.Wilson, and T.Schlick (2006).
Regulation of DNA repair fidelity by molecular checkpoints: "gates" in DNA polymerase beta's substrate selection.

Biochemistry, 45, 15142-15156.

17022941 R.Radhakrishnan, and T.Schlick (2006).
Correct and incorrect nucleotide incorporation pathways in DNA polymerase beta.

Biochem Biophys Res Commun, 350, 521-529.

17079493 V.K.Batra, D.D.Shock, R.Prasad, W.A.Beard, E.W.Hou, L.C.Pedersen, J.M.Sayer, H.Yagi, S.Kumar, D.M.Jerina, and S.H.Wilson (2006).
Structure of DNA polymerase beta with a benzo[c]phenanthrene diol epoxide-adducted template exhibits mutagenic features.

Proc Natl Acad Sci U S A, 103, 17231-17236.

PDB code: 2i9g

16615916 V.K.Batra, W.A.Beard, D.D.Shock, J.M.Krahn, L.C.Pedersen, and S.H.Wilson (2006).
Magnesium-induced assembly of a complete DNA polymerase catalytic complex.

Structure, 14, 757-766.

PDB codes: 2fmp 2fmq 2fms

17005572 W.W.Duym, K.A.Fiala, N.Bhatt, and Z.Suo (2006).
Kinetic effect of a downstream strand and its 5'-terminal moieties on single nucleotide gap-filling synthesis catalyzed by human DNA polymerase lambda.

J Biol Chem, 281, 35649-35655.

16322565 Y.Wang, K.Arora, and T.Schlick (2006).
Subtle but variable conformational rearrangements in the replication cycle of Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) may accommodate lesion bypass.

Protein Sci, 15, 135-151.

16028221 C.Lehmann, S.Pullalarevu, W.Krajewski, M.A.Willis, A.Galkin, A.Howard, and O.Herzberg (2005).
Structure of HI0073 from Haemophilus influenzae, the nucleotide-binding domain of a two-protein nucleotidyl transferase.

Proteins, 60, 807-811.

PDB code: 1no5

16281058 J.Deng, N.L.Ernst, S.Turley, K.D.Stuart, and W.G.Hol (2005).
Structural basis for UTP specificity of RNA editing TUTases from Trypanosoma brucei.

EMBO J, 24, 4007-4017.

PDB codes: 2b4v 2b51 2b56

15608652 M.Garcia-Diaz, K.Bebenek, J.M.Krahn, T.A.Kunkel, and L.C.Pedersen (2005).
A closed conformation for the Pol lambda catalytic cycle.

Nat Struct Mol Biol, 12, 97-98.

PDB codes: 1xsl 1xsn 1xsp

16128805 N.Kasai, Y.Mizushina, H.Murata, T.Yamazaki, T.Ohkubo, K.Sakaguchi, and F.Sugawara (2005).
Sulfoquinovosylmonoacylglycerol inhibitory mode analysis of rat DNA polymerase beta.

FEBS J, 272, 4349-4361.

15952890 S.Prakash, R.E.Johnson, and L.Prakash (2005).
Eukaryotic translesion synthesis DNA polymerases: specificity of structure and function.

Annu Rev Biochem, 74, 317-353.

15339923 B.Tippin, S.Kobayashi, J.G.Bertram, and M.F.Goodman (2004).
To slip or skip, visualizing frameshift mutation dynamics for error-prone DNA polymerases.

J Biol Chem, 279, 45360-45368.

14742430 E.Matsui, J.Abe, H.Yokoyama, and I.Matsui (2004).
Aromatic residues located close to the active center are essential for the catalytic reaction of flap endonuclease-1 from hyperthermophilic archaeon Pyrococcus horikoshii.

J Biol Chem, 279, 16687-16696.

14730355 G.Lipps, A.O.Weinzierl, G.von Scheven, C.Buchen, and P.Cramer (2004).
Structure of a bifunctional DNA primase-polymerase.

Nat Struct Mol Biol, 11, 157-162.

PDB codes: 1rni 1ro0 1ro2

15146073 G.Martin, and W.Keller (2004).
Sequence motifs that distinguish ATP(CTP):tRNA nucleotidyl transferases from eubacterial poly(A) polymerases.

RNA, 10, 899-906.

15356290 H.P.Shanahan, M.A.Garcia, S.Jones, and J.M.Thornton (2004).
Identifying DNA-binding proteins using structural motifs and the electrostatic potential.

Nucleic Acids Res, 32, 4732-4741.

15258144 H.Y.Hu, J.K.Horton, M.R.Gryk, R.Prasad, J.M.Naron, D.A.Sun, S.M.Hecht, S.H.Wilson, and G.P.Mullen (2004).
Identification of small molecule synthetic inhibitors of DNA polymerase beta by NMR chemical shift mapping.

J Biol Chem, 279, 39736-39744.

15507687 K.Arora, and T.Schlick (2004).
In silico evidence for DNA polymerase-beta's substrate-induced conformational change.

Biophys J, 87, 3088-3099.

15297882 L.G.Brieba, B.F.Eichman, R.J.Kokoska, S.Doublié, T.A.Kunkel, and T.Ellenberger (2004).
Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase.

EMBO J, 23, 3452-3461.

PDB codes: 1t8e 1tk0 1tk5 1tk8 1tkd

15189842 L.Yang, W.A.Beard, S.H.Wilson, S.Broyde, and T.Schlick (2004).
Highly organized but pliant active site of DNA polymerase beta: compensatory mechanisms in mutant enzymes revealed by dynamics simulations and energy analyses.

Biophys J, 86, 3392-3408.

15479784 M.Akbari, M.Otterlei, J.Peña-Diaz, P.A.Aas, B.Kavli, N.B.Liabakk, L.Hagen, K.Imai, A.Durandy, G.Slupphaug, and H.E.Krokan (2004).
Repair of U/G and U/A in DNA by UNG2-associated repair complexes takes place predominantly by short-patch repair both in proliferating and growth-arrested cells.

Nucleic Acids Res, 32, 5486-5498.

15090549 M.E.Stauffer, and W.J.Chazin (2004).
Structural mechanisms of DNA replication, repair, and recombination.

J Biol Chem, 279, 30915-30918.

15057283 M.Hogg, S.S.Wallace, and S.Doublié (2004).
Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site.

EMBO J, 23, 1483-1493.

PDB codes: 1rv2 2p5o

15333632 M.Pandey, S.Patel, and A.Gabriel (2004).
Insights into the role of an active site aspartate in Ty1 reverse transcriptase polymerization.

J Biol Chem, 279, 47840-47848.

15131111 Q.Guo, Y.Shen, N.L.Zhukovskaya, J.Florián, and W.J.Tang (2004).
Structural and kinetic analyses of the interaction of anthrax adenylyl cyclase toxin with reaction products cAMP and pyrophosphate.

J Biol Chem, 279, 29427-29435.

PDB code: 1sk6

15210693 R.A.Perlow-Poehnelt, I.Likhterov, D.A.Scicchitano, N.E.Geacintov, and S.Broyde (2004).
The spacious active site of a Y-family DNA polymerase facilitates promiscuous nucleotide incorporation opposite a bulky carcinogen-DNA adduct: elucidating the structure-function relationship through experimental and computational approaches.

J Biol Chem, 279, 36951-36961.

15069184 R.Radhakrishnan, and T.Schlick (2004).
Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase beta's closing.

Proc Natl Acad Sci U S A, 101, 5970-5975.

14563842 S.Dalal, J.L.Kosa, and J.B.Sweasy (2004).
The D246V mutant of DNA polymerase beta misincorporates nucleotides: evidence for a role for the flexible loop in DNA positioning within the active site.

J Biol Chem, 279, 577-584.

15295113 S.Fox-Erlich, T.O.Martyn, H.J.Ellis, and M.R.Gryk (2004).
Delineation and analysis of the conceptual data model implied by the "IUPAC Recommendations for Biochemical Nomenclature".

Protein Sci, 13, 2559-2563.

14871898 V.J.Cannistraro, and J.S.Taylor (2004).
DNA-thumb interactions and processivity of T7 DNA polymerase in comparison to yeast polymerase eta.

J Biol Chem, 279, 18288-18295.

15145936 W.A.Beard, D.D.Shock, and S.H.Wilson (2004).
Influence of DNA structure on DNA polymerase beta active site function: extension of mutagenic DNA intermediates.

J Biol Chem, 279, 31921-31929.

12799467 B.C.Beard, S.H.Wilson, and M.J.Smerdon (2003).
Suppressed catalytic activity of base excision repair enzymes on rotationally positioned uracil in nucleosomes.

Proc Natl Acad Sci U S A, 100, 7465-7470.

12941707 D.S.Shin, L.Pellegrini, D.S.Daniels, B.Yelent, L.Craig, D.Bates, D.S.Yu, M.K.Shivji, C.Hitomi, A.S.Arvai, N.Volkmann, H.Tsuruta, T.L.Blundell, A.R.Venkitaraman, and J.A.Tainer (2003).
Full-length archaeal Rad51 structure and mutants: mechanisms for RAD51 assembly and control by BRCA2.

EMBO J, 22, 4566-4576.

PDB code: 1pzn

14602897 E.A.Worthey, A.Schnaufer, I.S.Mian, K.Stuart, and R.Salavati (2003).
Comparative analysis of editosome proteins in trypanosomatids.

Nucleic Acids Res, 31, 6392-6408.

14527324 G.L.Verdine, and D.P.Norman (2003).
Covalent trapping of protein-DNA complexes.

Annu Rev Biochem, 72, 337-366.

12644712 H.Guo, and T.D.Tullius (2003).
Gapped DNA is anisotropically bent.

Proc Natl Acad Sci U S A, 100, 3743-3747.

14627824 I.Shevelev, G.Blanca, G.Villani, K.Ramadan, S.Spadari, U.Hübscher, and G.Maga (2003).
Mutagenesis of human DNA polymerase lambda: essential roles of Tyr505 and Phe506 for both DNA polymerase and terminal transferase activities.

Nucleic Acids Res, 31, 6916-6925.

12601790 J.Florián, M.F.Goodman, and A.Warshel (2003).
Computer simulation studies of the fidelity of DNA polymerases.

Biopolymers, 68, 286-299.

14500881 K.Matsuda, T.Nishioka, K.Kinoshita, T.Kawabata, and N.Go (2003).
Finding evolutionary relations beyond superfamilies: fold-based superfamilies.

Protein Sci, 12, 2239-2251.

12692307 M.T.Washington, W.T.Wolfle, T.E.Spratt, L.Prakash, and S.Prakash (2003).
Yeast DNA polymerase eta makes functional contacts with the DNA minor groove only at the incoming nucleoside triphosphate.

Proc Natl Acad Sci U S A, 100, 5113-5118.

14654693 N.Kojima, K.Inoue, R.Nakajima-Shibata, S.Kawahara, and E.Ohtsuka (2003).
A new, but old, nucleoside analog: the first synthesis of 1-deaza-2'-deoxyguanosine and its properties as a nucleoside and as oligodeoxynucleotides.

Nucleic Acids Res, 31, 7175-7188.

14579358 R.C.Rittenhouse, W.K.Apostoluk, J.H.Miller, and T.P.Straatsma (2003).
Characterization of the active site of DNA polymerase beta by molecular dynamics and quantum chemical calculation.

Proteins, 53, 667-682.

12649320 S.J.Johnson, J.S.Taylor, and L.S.Beese (2003).
Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations.

Proc Natl Acad Sci U S A, 100, 3895-3900.

PDB codes: 1l3s 1l3t 1l3u 1l3v 1l5u 1lv5

12458221 S.J.Kim, W.A.Beard, J.Harvey, D.D.Shock, J.R.Knutson, and S.H.Wilson (2003).
Rapid segmental and subdomain motions of DNA polymerase beta.

J Biol Chem, 278, 5072-5081.

12186540 A.K.Showalter, and M.D.Tsai (2002).
A reexamination of the nucleotide incorporation fidelity of DNA polymerases.

Biochemistry, 41, 10571-10576.

11790128 A.M.Woodside, and F.P.Guengerich (2002).
Misincorporation and stalling at O(6)-methylguanine and O(6)-benzylguanine: evidence for inactive polymerase complexes.

Biochemistry, 41, 1039-1050.

12473094 A.V.Cherepanov, and S.de Vries (2002).
Dynamic mechanism of nick recognition by DNA ligase.

Eur J Biochem, 269, 5993-5999.

12220188 C.A.Dunlap, and M.D.Tsai (2002).
Use of 2-aminopurine and tryptophan fluorescence as probes in kinetic analyses of DNA polymerase beta.

Biochemistry, 41, 11226-11235.

12414710 H.H.Gan, R.A.Perlow, S.Roy, J.Ko, M.Wu, J.Huang, S.Yan, A.Nicoletta, J.Vafai, D.Sun, L.Wang, J.E.Noah, S.Pasquali, and T.Schlick (2002).
Analysis of protein sequence/structure similarity relationships.

Biophys J, 83, 2781-2791.

12411511 H.Nilsen, T.Lindahl, and A.Verreault (2002).
DNA base excision repair of uracil residues in reconstituted nucleosome core particles.

EMBO J, 21, 5943-5952.

11823435 M.Delarue, J.B.Boulé, J.Lescar, N.Expert-Bezançon, N.Jourdan, N.Sukumar, F.Rougeon, and C.Papanicolaou (2002).
Crystal structures of a template-independent DNA polymerase: murine terminal deoxynucleotidyltransferase.

EMBO J, 21, 427-439.

PDB codes: 1jms 1kdh 1kej

11821417 M.García-Díaz, K.Bebenek, R.Sabariegos, O.Domínguez, J.Rodríguez, T.Kirchhoff, E.García-Palomero, A.J.Picher, R.Juárez, J.F.Ruiz, T.A.Kunkel, and L.Blanco (2002).
DNA polymerase lambda, a novel DNA repair enzyme in human cells.

J Biol Chem, 277, 13184-13191.

12121998 M.Maitra, A.Gudzelak, S.X.Li, Y.Matsumoto, K.A.Eckert, J.Jager, and J.B.Sweasy (2002).
Threonine 79 is a hinge residue that governs the fidelity of DNA polymerase beta by helping to position the DNA within the active site.

J Biol Chem, 277, 35550-35560.

12210533 P.Cramer (2002).
Common structural features of nucleic acid polymerases.

Bioessays, 24, 724-729.

12063248 P.S.Kedar, S.J.Kim, A.Robertson, E.Hou, R.Prasad, J.K.Horton, and S.H.Wilson (2002).
Direct interaction between mammalian DNA polymerase beta and proliferating cell nuclear antigen.

J Biol Chem, 277, 31115-31123.

11914087 S.S.Mandal, E.Fidalgo da Silva, and L.J.Reha-Krantz (2002).
Using 2-aminopurine fluorescence to detect base unstacking in the template strand during nucleotide incorporation by the bacteriophage T4 DNA polymerase.

Biochemistry, 41, 4399-4406.

11948182 T.S.Fisher, and V.R.Prasad (2002).
Substitutions of Phe61 located in the vicinity of template 5'-overhang influence polymerase fidelity and nucleoside analog sensitivity of HIV-1 reverse transcriptase.

J Biol Chem, 277, 22345-22352.

12370169 W.A.Beard, D.D.Shock, B.J.Vande Berg, and S.H.Wilson (2002).
Efficiency of correct nucleotide insertion governs DNA polymerase fidelity.

J Biol Chem, 277, 47393-47398.

11756435 W.A.Beard, D.D.Shock, X.P.Yang, S.F.DeLauder, and S.H.Wilson (2002).
Loss of DNA polymerase beta stacking interactions with templating purines, but not pyrimidines, alters catalytic efficiency and fidelity.

J Biol Chem, 277, 8235-8242.

11861910 Z.Morávek, S.Neidle, and B.Schneider (2002).
Protein and drug interactions in the minor groove of DNA.

Nucleic Acids Res, 30, 1182-1191.

11685239 A.K.Showalter, I.J.Byeon, M.I.Su, and M.D.Tsai (2001).
Solution structure of a viral DNA polymerase X and evidence for a mutagenic function.

Nat Struct Biol, 8, 942-946.

PDB code: 1jqr

11376161 A.Skandalis, and L.A.Loeb (2001).
Enzymatic properties of rat DNA polymerase beta mutants obtained by randomized mutagenesis.

Nucleic Acids Res, 29, 2418-2426.

11504869 C.Rocher, R.Dalibart, T.Letellier, G.Précigoux, and P.Lestienne (2001).
Initiation of DNA replication by DNA polymerases from primers forming a triple helix.

Nucleic Acids Res, 29, 3320-3326.

11205337 J.F.Ruiz, O.Domínguez, T.Laín de Lera, M.Garcia-Díaz, A.Bernad, and L.Blanco (2001).
DNA polymerase mu, a candidate hypermutase?

Philos Trans R Soc Lond B Biol Sci, 356, 99.

11330999 J.W.Arndt, W.Gong, X.Zhong, A.K.Showalter, J.Liu, C.A.Dunlap, Z.Lin, C.Paxson, M.D.Tsai, and M.K.Chan (2001).
Insight into the catalytic mechanism of DNA polymerase beta: structures of intermediate complexes.

Biochemistry, 40, 5368-5375.

PDB codes: 1huo 1huz

11340626 K.W.Caldecott (2001).
Mammalian DNA single-strand break repair: an X-ra(y)ted affair.

Bioessays, 23, 447-455.

11812826 M.Gutiérrez-Rivas, and L.Menéndez-Arias (2001).
A mutation in the primer grip region of HIV-1 reverse transcriptase that confers reduced fidelity of DNA synthesis.

Nucleic Acids Res, 29, 4963-4972.

11685238 M.W.Maciejewski, R.Shin, B.Pan, A.Marintchev, A.Denninger, M.A.Mullen, K.Chen, M.R.Gryk, and G.P.Mullen (2001).
Solution structure of a viral DNA repair polymerase.

Nat Struct Biol, 8, 936-941.

PDB code: 1jaj

11557814 S.Taladriz, T.Hanke, M.J.Ramiro, M.García-Díaz, M.García De Lacoba, L.Blanco, and V.Larraga (2001).
Nuclear DNA polymerase beta from Leishmania infantum. Cloning, molecular analysis and developmental regulation.

Nucleic Acids Res, 29, 3822-3834.

11258875 T.E.Spratt (2001).
Identification of hydrogen bonds between Escherichia coli DNA polymerase I (Klenow fragment) and the minor groove of DNA by amino acid substitution of the polymerase and atomic substitution of the DNA.

Biochemistry, 40, 2647-2652.

11685231 W.A.Beard, and S.H.Wilson (2001).
DNA polymerases lose their grip.

Nat Struct Biol, 8, 915-917.

10773072 A.Marintchev, A.Robertson, E.K.Dimitriadis, R.Prasad, S.H.Wilson, and G.P.Mullen (2000).
Domain specific interaction in the XRCC1-DNA polymerase beta complex.

Nucleic Acids Res, 28, 2049-2059.

10944102 G.Martin, W.Keller, and S.Doublié (2000).
Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP.

EMBO J, 19, 4193-4203.

PDB code: 1f5a

10653647 H.Miller, R.Prasad, S.H.Wilson, F.Johnson, and A.P.Grollman (2000).
8-oxodGTP incorporation by DNA polymerase beta is modified by active-site residue Asn279.

Biochemistry, 39, 1029-1033.

10958780 J.Bard, A.M.Zhelkovsky, S.Helmling, T.N.Earnest, C.L.Moore, and A.Bohm (2000).
Structure of yeast poly(A) polymerase alone and in complex with 3'-dATP.

Science, 289, 1346-1349.

PDB code: 1fa0

11041863 J.C.Morales, and E.T.Kool (2000).
Functional hydrogen-bonding map of the minor groove binding tracks of six DNA polymerases.

Biochemistry, 39, 12979-12988.

10744736 L.J.Deterding, R.Prasad, G.P.Mullen, S.H.Wilson, and K.B.Tomer (2000).
Mapping of the 5'-2-deoxyribose-5-phosphate lyase active site in DNA polymerase beta by mass spectrometry.

J Biol Chem, 275, 10463-10471.

11087416 L.Sun, M.Wang, E.T.Kool, and J.S.Taylor (2000).
Pyrene nucleotide as a mechanistic probe: evidence for a transient abasic site-like intermediate in the bypass of dipyrimidine photoproducts by T7 DNA polymerase.

Biochemistry, 39, 14603-14610.

11092939 N.Sukumar, J.B.Boulé, N.Expert-Bezançon, N.Jourdan, J.Lescar, F.Rougeon, C.Papanicolaou, and M.Delarue (2000).
Crystallization of the catalytic domain of murine terminal deoxynucleotidyl transferase.

Acta Crystallogr D Biol Crystallogr, 56, 1662-1664.

10985785 P.L.Opresko, R.Shiman, and K.A.Eckert (2000).
Hydrophobic interactions in the hinge domain of DNA polymerase beta are important but not sufficient for maintaining fidelity of DNA synthesis.

Biochemistry, 39, 11399-11407.

11052676 S.Hoenke, M.Schmid, and P.Dimroth (2000).
Identification of the active site of phosphoribosyl-dephospho-coenzyme A transferase and relationship of the enzyme to an ancient class of nucleotidyltransferases.

Biochemistry, 39, 13233-13240.

10694411 S.R.Starck, J.Z.Deng, and S.M.Hecht (2000).
Naturally occurring alkylresorcinols that mediate DNA damage and inhibit its repair.

Biochemistry, 39, 2413-2419.

10631001 S.S.Daube, G.Arad, and Z.Livneh (2000).
Translesion replication by DNA polymerase beta is modulated by sequence context and stimulated by fork-like flap structures in DNA.

Biochemistry, 39, 397-405.

10966467 T.A.Kunkel, and K.Bebenek (2000).
DNA replication fidelity.

Annu Rev Biochem, 69, 497-529.

11123928 V.S.Kraynov, A.K.Showalter, J.Liu, X.Zhong, and M.D.Tsai (2000).
DNA polymerase beta: contributions of template-positioning and dNTP triphosphate-binding residues to catalysis and fidelity.

Biochemistry, 39, 16008-16015.

10734184 W.G.Krebs, and M.Gerstein (2000).
The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework.

Nucleic Acids Res, 28, 1665-1675.

10908318 X.Shao, and N.V.Grishin (2000).
Common fold in helix-hairpin-helix proteins.

Nucleic Acids Res, 28, 2643-2650.

11027140 Y.Mizushina, T.Ohkubo, F.Sugawara, and K.Sakaguchi (2000).
Structure of lithocholic acid binding to the N-terminal 8-kDa domain of DNA polymerase beta.

Biochemistry, 39, 12606-12613.

10022845 C.Isel, E.Westhof, C.Massire, S.F.Le Grice, B.Ehresmann, C.Ehresmann, and R.Marquet (1999).
Structural basis for the specificity of the initiation of HIV-1 reverse transcription.

EMBO J, 18, 1038-1048.

10447680 C.Roll, C.Ketterl, G.V.Fazakerley, and Y.Boulard (1999).
Solution structures of a duplex containing an adenine opposite a gap (absence of one nucleotide). An NMR study and molecular dynamic simulations with explicit water molecules.

Eur J Biochem, 264, 120-131.

10595540 G.Martin, P.Jenö, and W.Keller (1999).
Mapping of ATP binding regions in poly(A) polymerases by photoaffinity labeling and by mutational analysis identifies a domain conserved in many nucleotidyltransferases.

Protein Sci, 8, 2380-2391.

10048314 H.Kobayashi, K.Sato, Y.Komatsu, H.Morioka, J.D.Stewart, T.Tsurimoto, and E.Ohtsuka (1999).
Effects of a high-affinity antibody fragment on DNA polymerase reactions near a (6-4) photoproduct site.

Photochem Photobiol, 69, 226-230.

10075642 J.H.Hurley (1999).
Structure, mechanism, and regulation of mammalian adenylyl cyclase.

J Biol Chem, 274, 7599-7602.

10585471 J.L.Kosa, and J.B.Sweasy (1999).
The E249K mutator mutant of DNA polymerase beta extends mispaired termini.

J Biol Chem, 274, 35866-35872.

9920940 J.L.Kosa, and J.B.Sweasy (1999).
3'-Azido-3'-deoxythymidine-resistant mutants of DNA polymerase beta identified by in vivo selection.

J Biol Chem, 274, 3851-3858.

10026283 K.Nadassy, S.J.Wodak, and J.Janin (1999).
Structural features of protein-nucleic acid recognition sites.

Biochemistry, 38, 1999-2017.

10200170 L.L.Furge, and F.P.Guengerich (1999).
Explanation of pre-steady-state kinetics and decreased burst amplitude of HIV-1 reverse transcriptase at sites of modified DNA bases with an additional, nonproductive enzyme-DNA-nucleotide complex.

Biochemistry, 38, 4818-4825.

10464285 S.N.Sarkar, A.Ghosh, H.W.Wang, S.S.Sung, and G.C.Sen (1999).
The nature of the catalytic domain of 2'-5'-oligoadenylate synthetases.

J Biol Chem, 274, 25535-25542.

10200168 S.X.Li, J.A.Vaccaro, and J.B.Sweasy (1999).
Involvement of phenylalanine 272 of DNA polymerase beta in discriminating between correct and incorrect deoxynucleoside triphosphates.

Biochemistry, 38, 4800-4808.

10364165 T.A.Steitz (1999).
DNA polymerases: structural diversity and common mechanisms.

J Biol Chem, 274, 17395-17398.

10438542 T.E.Wilson, and M.R.Lieber (1999).
Efficient processing of DNA ends during yeast nonhomologous end joining. Evidence for a DNA polymerase beta (Pol4)-dependent pathway.

J Biol Chem, 274, 23599-23609.

9920913 W.P.Osheroff, H.K.Jung, W.A.Beard, S.H.Wilson, and T.A.Kunkel (1999).
The fidelity of DNA polymerase beta during distributive and processive DNA synthesis.

J Biol Chem, 274, 3642-3650.

10409611 W.P.Osheroff, W.A.Beard, S.H.Wilson, and T.A.Kunkel (1999).
Base substitution specificity of DNA polymerase beta depends on interactions in the DNA minor groove.

J Biol Chem, 274, 20749-20752.

10464295 Y.Mizushina, T.Ohkubo, T.Date, T.Yamaguchi, M.Saneyoshi, F.Sugawara, and K.Sakaguchi (1999).
Mode analysis of a fatty acid molecule binding to the N-terminal 8-kDa domain of DNA polymerase beta. A 1:1 complex and binding surface.

J Biol Chem, 274, 25599-25607.

9685411 E.K.Dimitriadis, R.Prasad, M.K.Vaske, L.Chen, A.E.Tomkinson, M.S.Lewis, and S.H.Wilson (1998).
Thermodynamics of human DNA ligase I trimerization and association with DNA polymerase beta.

J Biol Chem, 273, 20540-20550.

9831551 H.Huang, R.Chopra, G.L.Verdine, and S.C.Harrison (1998).
Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance.

Science, 282, 1669-1675.

PDB code: 1rtd

9657672 J.A.Feng, C.J.Crasto, and Y.Matsumoto (1998).
Deoxyribose phosphate excision by the N-terminal domain of the polymerase beta: the mechanism revisited.

Biochemistry, 37, 9605-9611.

9556598 R.Prasad, W.A.Beard, J.Y.Chyan, M.W.Maciejewski, G.P.Mullen, and S.H.Wilson (1998).
Functional analysis of the amino-terminal 8-kDa domain of DNA polymerase beta as revealed by site-directed mutagenesis. DNA binding and 5'-deoxyribose phosphate lyase activities.

J Biol Chem, 273, 11121-11126.

9614142 R.Prasad, W.A.Beard, P.R.Strauss, and S.H.Wilson (1998).
Human DNA polymerase beta deoxyribose phosphate lyase. Substrate specificity and catalytic mechanism.

J Biol Chem, 273, 15263-15270.

9461069 T.A.Kunkel, and S.H.Wilson (1998).
DNA polymerases on the move.

Nat Struct Biol, 5, 95-99.

9765248 Z.Suo, and K.A.Johnson (1998).
Selective inhibition of HIV-1 reverse transcriptase by an antiviral inhibitor, (R)-9-(2-Phosphonylmethoxypropyl)adenine.

J Biol Chem, 273, 27250-27258.

9765249 Z.Suo, and K.A.Johnson (1998).
DNA secondary structure effects on DNA synthesis catalyzed by HIV-1 reverse transcriptase.

J Biol Chem, 273, 27259-27267.

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.