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PDBsum entry 1bpe
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Nucleotidyltransferase PDB id
1bpe

 

 

 

 

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Contents
Protein chain
284 a.a. *
Ligands
DTP
* Residue conservation analysis
PDB id:
1bpe
Name: Nucleotidyltransferase
Title: Crystal structure of rat DNA polymerase beta; evidence for a common polymerase mechanism
Structure: DNA polymerase beta. Chain: a. Engineered: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116
Resolution:
2.90Å     R-factor:   0.199    
Authors: M.R.Sawaya,H.Pelletier,A.Kumar,S.H.Wilson,J.Kraut
Key ref: M.R.Sawaya et al. (1994). Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism. Science, 264, 1930-1935. PubMed id: 7516581 DOI: 10.1126/science.7516581
Date:
12-Apr-94     Release date:   31-Jul-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
P06766  (DPOLB_RAT) -  DNA polymerase beta from Rattus norvegicus
Seq:
Struc: 		335 a.a.
284 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class 1: E.C.2.7.7.7  - DNA-directed Dna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
DNA(n)
 + 2'-deoxyribonucleoside 5'-triphosphate
 = DNA(n+1)
 + diphosphate
   Enzyme class 2: E.C.4.2.99.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
   Enzyme class 3: E.C.4.2.99.18  - DNA-(apurinic or apyrimidinic site) lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)- 2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3- dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-phospho- 2'-deoxyribonucleoside-DNA + H+
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1126/science.7516581 Science 264:1930-1935 (1994)
PubMed id: 7516581  
 
 
Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism.
M.R.Sawaya, H.Pelletier, A.Kumar, S.H.Wilson, J.Kraut.
 
  ABSTRACT  
 
Structures of the 31-kilodalton catalytic domain of rat DNA polymerase beta (pol beta) and the whole 39-kilodalton enzyme were determined at 2.3 and 3.6 angstrom resolution, respectively. The 31-kilodalton domain is composed of fingers, palm, and thumb subdomains arranged to form a DNA binding channel reminiscent of the polymerase domains of the Klenow fragment of Escherichia coli DNA polymerase I, HIV-1 reverse transcriptase, and bacteriophage T7 RNA polymerase. The amino-terminal 8-kilodalton domain is attached to the fingers subdomain by a flexible hinge. The two invariant aspartates found in all polymerase sequences and implicated in catalytic activity have the same geometric arrangement within structurally similar but topologically distinct palms, indicating that the polymerases have maintained, or possibly re-evolved, a common nucleotidyl transfer mechanism. The location of Mn2+ and deoxyadenosine triphosphate in pol beta confirms the role of the invariant aspartates in metal ion and deoxynucleoside triphosphate binding.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22751018 L.A.Yates, S.Fleurdépine, O.S.Rissland, L.De Colibus, K.Harlos, C.J.Norbury, and R.J.Gilbert (2012).
Structural basis for the activity of a cytoplasmic RNA terminal uridylyl transferase.
  Nat Struct Mol Biol, 19, 782-787.
PDB codes: 4e7x 4e80 4e8f
22678295 X.Zhang, W.Ren, P.DeCaen, C.Yan, X.Tao, L.Tang, J.Wang, K.Hasegawa, T.Kumasaka, J.He, J.Wang, D.E.Clapham, and N.Yan (2012).
Crystal structure of an orthologue of the NaChBac voltage-gated sodium channel.
  Nature, 486, 130-134.
PDB code: 4dxw
21377475 P.Xie (2011).
A model for the dynamics of mammalian family X DNA polymerases.
  J Theor Biol, 277, 111-122.  
19596089 E.A.Motea, and A.J.Berdis (2010).
Terminal deoxynucleotidyl transferase: the story of a misguided DNA polymerase.
  Biochim Biophys Acta, 1804, 1151-1166.  
20108981 J.Yamtich, D.Starcevic, J.Lauper, E.Smith, I.Shi, S.Rangarajan, J.Jaeger, and J.B.Sweasy (2010).
Hinge residue I174 is critical for proper dNTP selection by DNA polymerase beta.
  Biochemistry, 49, 2326-2334.  
19631767 J.Yamtich, and J.B.Sweasy (2010).
DNA polymerase family X: function, structure, and cellular roles.
  Biochim Biophys Acta, 1804, 1136-1150.  
20376302 K.Singh, B.Marchand, K.A.Kirby, E.Michailidis, and S.G.Sarafianos (2010).
Structural Aspects of Drug Resistance and Inhibition of HIV-1 Reverse Transcriptase.
  Viruses, 2, 606-638.  
20351257 M.J.Cuneo, and R.E.London (2010).
Oxidation state of the XRCC1 N-terminal domain regulates DNA polymerase beta binding affinity.
  Proc Natl Acad Sci U S A, 107, 6805-6810.
PDB codes: 3k75 3k77 3lqc
20822442 M.Morar, and G.D.Wright (2010).
The genomic enzymology of antibiotic resistance.
  Annu Rev Genet, 44, 25-51.  
20844920 S.H.Wilson, W.A.Beard, D.D.Shock, V.K.Batra, N.A.Cavanaugh, R.Prasad, E.W.Hou, Y.Liu, K.Asagoshi, J.K.Horton, D.F.Stefanick, P.S.Kedar, M.J.Carrozza, A.Masaoka, and M.L.Heacock (2010).
Base excision repair and design of small molecule inhibitors of human DNA polymerase β.
  Cell Mol Life Sci, 67, 3633-3647.  
20080740 Y.Santoso, C.M.Joyce, O.Potapova, L.Le Reste, J.Hohlbein, J.P.Torella, N.D.Grindley, and A.N.Kapanidis (2010).
Conformational transitions in DNA polymerase I revealed by single-molecule FRET.
  Proc Natl Acad Sci U S A, 107, 715-720.  
20575136 Y.Santoso, J.P.Torella, and A.N.Kapanidis (2010).
Characterizing single-molecule FRET dynamics with probability distribution analysis.
  Chemphyschem, 11, 2209-2219.  
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.  
19013261 G.C.Lin, J.Jaeger, K.A.Eckert, and J.B.Sweasy (2009).
Loop II of DNA polymerase beta is important for discrimination during substrate binding.
  DNA Repair (Amst), 8, 182-189.  
19180449 K.S.Keating, S.C.Flores, M.B.Gerstein, and L.A.Kuhn (2009).
StoneHinge: hinge prediction by network analysis of individual protein structures.
  Protein Sci, 18, 359-371.  
20004168 M.Morar, K.Bhullar, D.W.Hughes, M.Junop, and G.D.Wright (2009).
Structure and mechanism of the lincosamide antibiotic adenylyltransferase LinB.
  Structure, 17, 1649-1659.
PDB codes: 3jyy 3jz0
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
19281452 P.B.Balbo, and A.Bohm (2009).
Proton transfer in the mechanism of polyadenylate polymerase.
  Biochem J, 420, 229-238.  
19759017 W.A.Beard, D.D.Shock, V.K.Batra, L.C.Pedersen, and S.H.Wilson (2009).
DNA polymerase beta substrate specificity: side chain modulation of the "A-rule".
  J Biol Chem, 284, 31680-31689.
PDB codes: 3isb 3isc 3isd
19336415 Z.Guo, L.Zheng, H.Dai, M.Zhou, H.Xu, and B.Shen (2009).
Human DNA polymerase beta polymorphism, Arg137Gln, impairs its polymerase activity and interaction with PCNA and the cellular base excision repair capacity.
  Nucleic Acids Res, 37, 3431-3441.  
18416825 C.Hazan, F.Boudsocq, V.Gervais, O.Saurel, M.Ciais, C.Cazaux, J.Czaplicki, and A.Milon (2008).
Structural insights on the pamoic acid and the 8 kDa domain of DNA polymerase beta complex: towards the design of higher-affinity inhibitors.
  BMC Struct Biol, 8, 22.  
18847263 G.T.Hwang, and F.E.Romesberg (2008).
Unnatural substrate repertoire of A, B, and X family DNA polymerases.
  J Am Chem Soc, 130, 14872-14882.  
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
18717589 M.P.Roettger, M.Bakhtina, and M.D.Tsai (2008).
Mismatched and matched dNTP incorporation by DNA polymerase beta proceed via analogous kinetic pathways.
  Biochemistry, 47, 9718-9727.  
18937502 S.Dalal, D.Starcevic, J.Jaeger, and J.B.Sweasy (2008).
The I260Q variant of DNA polymerase beta extends mispaired primer termini due to its increased affinity for deoxynucleotide triphosphate substrates.
  Biochemistry, 47, 12118-12125.  
18598057 S.Kumar, M.Bakhtina, and M.D.Tsai (2008).
Altered order of substrate binding by DNA polymerase X from African Swine Fever virus.
  Biochemistry, 47, 7875-7887.  
18004759 S.O.Yesylevskyy, V.N.Kharkyanen, and A.P.Demchenko (2008).
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  Proteins, 71, 831-843.  
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In situ proteolysis for protein crystallization and structure determination.
  Nat Methods, 4, 1019-1021.
PDB codes: 2p35 2pz9 2qni 2r8b 2r8w 2r9q 2ra5 2rc3
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
17631059 A.F.Moon, M.Garcia-Diaz, V.K.Batra, W.A.Beard, K.Bebenek, T.A.Kunkel, S.H.Wilson, and L.C.Pedersen (2007).
The X family portrait: structural insights into biological functions of X family polymerases.
  DNA Repair (Amst), 6, 1709-1725.  
17872511 G.Martin, and W.Keller (2007).
RNA-specific ribonucleotidyl transferases.
  RNA, 13, 1834-1849.  
17189640 J.Stagno, I.Aphasizheva, A.Rosengarth, H.Luecke, and R.Aphasizhev (2007).
UTP-bound and Apo structures of a minimal RNA uridylyltransferase.
  J Mol Biol, 366, 882-899.
PDB codes: 2ikf 2nom
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
17223131 P.B.Balbo, J.Toth, and A.Bohm (2007).
X-ray crystallographic and steady state fluorescence characterization of the protein dynamics of yeast polyadenylate polymerase.
  J Mol Biol, 366, 1401-1415.
PDB codes: 2hhp 2o1p
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.  
17701034 S.Beetz, D.Diekhoff, and L.A.Steiner (2007).
Characterization of terminal deoxynucleotidyl transferase and polymerase mu in zebrafish.
  Immunogenetics, 59, 735-744.  
16600869 N.El-Andaloussi, T.Valovka, M.Toueille, R.Steinacher, F.Focke, P.Gehrig, M.Covic, P.O.Hassa, P.Schär, U.Hübscher, and M.O.Hottiger (2006).
Arginine methylation regulates DNA polymerase beta.
  Mol Cell, 22, 51-62.  
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.  
16959569 S.Bailey, R.A.Wing, and T.A.Steitz (2006).
The structure of T. aquaticus DNA polymerase III is distinct from eukaryotic replicative DNA polymerases.
  Cell, 126, 893-904.
PDB codes: 2hpi 2hpm
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
15983981 B.H.Kim, R.Sadreyev, and N.V.Grishin (2005).
COG4849 is a novel family of nucleotidyltransferases.
  J Mol Recognit, 18, 422-425.  
16043633 E.Crespan, S.Zanoli, A.Khandazhinskaya, I.Shevelev, M.Jasko, L.Alexandrova, M.Kukhanova, G.Blanca, G.Villani, U.Hübscher, S.Spadari, and G.Maga (2005).
Incorporation of non-nucleoside triphosphate analogues opposite to an abasic site by human DNA polymerases beta and lambda.
  Nucleic Acids Res, 33, 4117-4127.  
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.  
16120966 S.González-Barrera, A.Sánchez, J.F.Ruiz, R.Juárez, A.J.Picher, G.Terrados, P.Andrade, and L.Blanco (2005).
Characterization of SpPol4, a unique X-family DNA polymerase in Schizosaccharomyces pombe.
  Nucleic Acids Res, 33, 4762-4774.  
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
15573140 K.Ramadan, I.Shevelev, and U.Hübscher (2004).
The DNA-polymerase-X family: controllers of DNA quality?
  Nat Rev Mol Cell Biol, 5, 1038-1043.  
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.  
14992725 M.Garcia-Diaz, K.Bebenek, J.M.Krahn, L.Blanco, T.A.Kunkel, and L.C.Pedersen (2004).
A structural solution for the DNA polymerase lambda-dependent repair of DNA gaps with minimal homology.
  Mol Cell, 13, 561-572.
PDB code: 1rzt
15065652 T.A.Steitz, and Y.W.Yin (2004).
Accuracy, lesion bypass, strand displacement and translocation by DNA polymerases.
  Philos Trans R Soc Lond B Biol Sci, 359, 17-23.  
12486719 C.Lehmann, K.Lim, V.R.Chalamasetty, W.Krajewski, E.Melamud, A.Galkin, A.Howard, Z.Kelman, P.T.Reddy, A.G.Murzin, and O.Herzberg (2003).
The HI0073/HI0074 protein pair from Haemophilus influenzae is a member of a new nucleotidyltransferase family: structure, sequence analyses, and solution studies.
  Proteins, 50, 249-260.
PDB code: 1jog
12869708 H.D.Cho, A.K.Oyelere, S.A.Strobel, and A.M.Weiner (2003).
Use of nucleotide analogs by class I and class II CCA-adding enzymes (tRNA nucleotidyltransferase): deciphering the basis for nucleotide selection.
  RNA, 9, 970-981.  
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.  
14592988 M.Okabe, K.Tomita, R.Ishitani, R.Ishii, N.Takeuchi, F.Arisaka, O.Nureki, and S.Yokoyama (2003).
Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure.
  EMBO J, 22, 5918-5927.
PDB codes: 1uet 1ueu 1uev
14750947 N.Ito, O.Nureki, M.Shirouzu, S.Yokoyama, and F.Hanaoka (2003).
Crystal structure of the Pyrococcus horikoshii DNA primase-UTP complex: implications for the mechanism of primer synthesis.
  Genes Cells, 8, 913-923.
PDB codes: 1v33 1v34
14636576 R.Hartmann, J.Justesen, S.N.Sarkar, G.C.Sen, and V.C.Yee (2003).
Crystal structure of the 2'-specific and double-stranded RNA-activated interferon-induced antiviral protein 2'-5'-oligoadenylate synthetase.
  Mol Cell, 12, 1173-1185.
PDB code: 1px5
12595556 Z.Sevilya, S.Loya, N.Adir, and A.Hizi (2003).
The ribonuclease H activity of the reverse transcriptases of human immunodeficiency viruses type 1 and type 2 is modulated by residue 294 of the small subunit.
  Nucleic Acids Res, 31, 1481-1487.  
12186540 A.K.Showalter, and M.D.Tsai (2002).
A reexamination of the nucleotide incorporation fidelity of DNA polymerases.
  Biochemistry, 41, 10571-10576.  
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.  
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
12478587 P.J.Hanic-Joyce, and P.B.Joyce (2002).
Characterization of a gene encoding tRNA nucleotidyltransferase from Candida glabrata.
  Yeast, 19, 1399-1411.  
12218190 R.L.Read, R.G.Martinho, S.W.Wang, A.M.Carr, and C.J.Norbury (2002).
Cytoplasmic poly(A) polymerases mediate cellular responses to S phase arrest.
  Proc Natl Acad Sci U S A, 99, 12079-12084.  
12453427 S.Hasan, N.El-Andaloussi, U.Hardeland, P.O.Hassa, C.Bürki, R.Imhof, P.Schär, and M.O.Hottiger (2002).
Acetylation regulates the DNA end-trimming activity of DNA polymerase beta.
  Mol Cell, 10, 1213-1222.  
12045093 U.Hubscher, G.Maga, and S.Spadari (2002).
Eukaryotic DNA polymerases.
  Annu Rev Biochem, 71, 133-163.  
  11861546 Z.Wang, I.B.Castaño, C.Adams, C.Vu, D.Fitzhugh, and M.F.Christman (2002).
Structure/function analysis of the Saccharomyces cerevisiae Trf4/Pol sigma DNA polymerase.
  Genetics, 160, 381-391.  
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
11727826 A.S.Reichert, D.L.Thurlow, and M.Mörl (2001).
A eubacterial origin for the human tRNA nucleotidyltransferase?
  Biol Chem, 382, 1431-1438.  
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.  
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.  
11685247 L.F.Silvian, E.A.Toth, P.Pham, M.F.Goodman, and T.Ellenberger (2001).
Crystal structure of a DinB family error-prone DNA polymerase from Sulfolobus solfataricus.
  Nat Struct Biol, 8, 984-989.
PDB codes: 1k1q 1k1s
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.  
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Domain specific interaction in the XRCC1-DNA polymerase beta complex.
  Nucleic Acids Res, 28, 2049-2059.  
11063578 C.I.Wooddell, and R.R.Burgess (2000).
Topology of yeast RNA polymerase II subunits in transcription elongation complexes studied by photoaffinity cross-linking.
  Biochemistry, 39, 13405-13421.  
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
11090167 H.Liu, J.H.Naismith, and R.T.Hay (2000).
Identification of conserved residues contributing to the activities of adenovirus DNA polymerase.
  J Virol, 74, 11681-11689.  
10684941 J.Tong, F.Barany, and W.Cao (2000).
Ligation reaction specificities of an NAD(+)-dependent DNA ligase from the hyperthermophile Aquifex aeolicus.
  Nucleic Acids Res, 28, 1447-1454.  
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Mutagenesis of E477 or K505 in the B' domain of human topoisomerase II beta increases the requirement for magnesium ions during strand passage.
  Biochemistry, 39, 1223-1233.  
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.  
10747040 O.Domínguez, J.F.Ruiz, T.Laín de Lera, M.García-Díaz, M.A.González, T.Kirchhoff, C.Martínez-A, A.Bernad, and L.Blanco (2000).
DNA polymerase mu (Pol mu), homologous to TdT, could act as a DNA mutator in eukaryotic cells.
  EMBO J, 19, 1731-1742.  
10757807 S.W.Wang, T.Toda, R.MacCallum, A.L.Harris, and C.Norbury (2000).
Cid1, a fission yeast protein required for S-M checkpoint control when DNA polymerase delta or epsilon is inactivated.
  Mol Cell Biol, 20, 3234-3244.  
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.  
10917598 Y.M.Hou (2000).
Unusual synthesis by the Escherichia coli CCA-adding enzyme.
  RNA, 6, 1031-1043.  
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.  
11042381 Y.Mizushina, T.Ueno, M.Oda, T.Yamaguchi, M.Saneyoshi, and K.Sakaguchi (2000).
The biochemical mode of inhibition of DNA polymerase beta by alpha-rubromycin.
  Biochim Biophys Acta, 1523, 172-181.  
10762083 Y.Yamamoto, D.Sono, and Y.Sokawa (2000).
Effects of specific mutations in active site motifs of 2',5'-oligoadenylate synthetase on enzymatic activity.
  J Interferon Cytokine Res, 20, 337-344.  
10387012 B.W.Kirk, and R.D.Kuchta (1999).
Arg304 of human DNA primase is a key contributor to catalysis and NTP binding: primase and the family X polymerases share significant sequence homology.
  Biochemistry, 38, 7727-7736.  
  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.  
10047577 J.Jäger, and J.D.Pata (1999).
Getting a grip: polymerases and their substrate complexes.
  Curr Opin Struct Biol, 9, 21-28.  
10097083 K.P.Hopfner, A.Eichinger, R.A.Engh, F.Laue, W.Ankenbauer, R.Huber, and B.Angerer (1999).
Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius.
  Proc Natl Acad Sci U S A, 96, 3600-3605.
PDB code: 1tgo
  10548040 M.Smalla, P.Schmieder, M.Kelly, A.Ter Laak, G.Krause, L.Ball, M.Wahl, P.Bork, and H.Oschkinat (1999).
Solution structure of the receptor tyrosine kinase EphB2 SAM domain and identification of two distinct homotypic interaction sites.
  Protein Sci, 8, 1954-1961.
PDB code: 1sgg
10557268 S.Bressanelli, L.Tomei, A.Roussel, I.Incitti, R.L.Vitale, M.Mathieu, R.De Francesco, and F.A.Rey (1999).
Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus.
  Proc Natl Acad Sci U S A, 96, 13034-13039.
PDB code: 1csj
10368292 S.Doublié, M.R.Sawaya, and T.Ellenberger (1999).
An open and closed case for all polymerases.
  Structure, 7, R31-R35.  
10450084 S.Hayward (1999).
Structural principles governing domain motions in proteins.
  Proteins, 36, 425-435.  
9590127 A.Ogawa, T.Murate, S.Izuta, M.Takemura, K.Furuta, J.Kobayashi, T.Kamikawa, Y.Nimura, and S.Yoshida (1998).
Sulfated glycoglycerolipid from archaebacterium inhibits eukaryotic DNA polymerase alpha, beta and retroviral reverse transcriptase and affects methyl methanesulfonate cytotoxicity.
  Int J Cancer, 76, 512-518.  
9521727 C.Roll, C.Ketterlé, V.Faibis, G.V.Fazakerley, and Y.Boulard (1998).
Conformations of nicked and gapped DNA structures by NMR and molecular dynamic simulations in water.
  Biochemistry, 37, 4059-4070.  
9747586 D.A.Connor, A.M.Falick, M.C.Young, and M.D.Shetlar (1998).
Probing the binding region of the single-stranded DNA-binding domain of rat DNA polymerase beta using nanosecond-pulse laser-induced cross-linking and mass spectrometry.
  Photochem Photobiol, 68, 299-308.  
9736621 J.Cavarelli, B.Delagoutte, G.Eriani, J.Gangloff, and D.Moras (1998).
L-arginine recognition by yeast arginyl-tRNA synthetase.
  EMBO J, 17, 5438-5448.
PDB code: 1bs2
9757823 K.Singh, and M.J.Modak (1998).
A unified DNA- and dNTP-binding mode for DNA polymerases.
  Trends Biochem Sci, 23, 277-281.  
  10082363 M.Bergdoll, L.D.Eltis, A.D.Cameron, P.Dumas, and J.T.Bolin (1998).
All in the family: structural and evolutionary relationships among three modular proteins with diverse functions and variable assembly.
  Protein Sci, 7, 1661-1670.  
10384295 N.A.Woychik (1998).
Fractions to functions: RNA polymerase II thirty years later.
  Cold Spring Harb Symp Quant Biol, 63, 311-317.  
9914251 S.Doublié, and T.Ellenberger (1998).
The mechanism of action of T7 DNA polymerase.
  Curr Opin Struct Biol, 8, 704-712.  
9479474 W.A.Beard, and S.H.Wilson (1998).
Structural insights into DNA polymerase beta fidelity: hold tight if you want it right.
  Chem Biol, 5, R7-13.  
9485450 W.S.Furey, C.M.Joyce, M.A.Osborne, D.Klenerman, J.A.Peliska, and S.Balasubramanian (1998).
Use of fluorescence resonance energy transfer to investigate the conformation of DNA substrates bound to the Klenow fragment.
  Biochemistry, 37, 2979-2990.  
9572863 Y.Matsumoto, K.Kim, D.S.Katz, and J.A.Feng (1998).
Catalytic center of DNA polymerase beta for excision of deoxyribose phosphate groups.
  Biochemistry, 37, 6456-6464.  
9164453 A.Wlodawer (1997).
Deposition of macromolecular coordinates resulting from crystallographic and NMR studies.
  Nat Struct Biol, 4, 173-174.  
9241233 B.B.Oude Essink, N.K.Back, and B.Berkhout (1997).
Increased polymerase fidelity of the 3TC-resistant variants of HIV-1 reverse transcriptase.
  Nucleic Acids Res, 25, 3212-3217.  
9050827 C.M.Joyce (1997).
Choosing the right sugar: how polymerases select a nucleotide substrate.
  Proc Natl Acad Sci U S A, 94, 1619-1622.  
  9371463 D.R.Smith, L.A.Doucette-Stamm, C.Deloughery, H.Lee, J.Dubois, T.Aldredge, R.Bashirzadeh, D.Blakely, R.Cook, K.Gilbert, D.Harrison, L.Hoang, P.Keagle, W.Lumm, B.Pothier, D.Qiu, R.Spadafora, R.Vicaire, Y.Wang, J.Wierzbowski, R.Gibson, N.Jiwani, A.Caruso, D.Bush, and J.N.Reeve (1997).
Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics.
  J Bacteriol, 179, 7135-7155.  
9012795 G.Gao, M.Orlova, M.M.Georgiadis, W.A.Hendrickson, and S.P.Goff (1997).
Conferring RNA polymerase activity to a DNA polymerase: a single residue in reverse transcriptase controls substrate selection.
  Proc Natl Acad Sci U S A, 94, 407-411.  
9354757 J.Ding, S.H.Hughes, and E.Arnold (1997).
Protein-nucleic acid interactions and DNA conformation in a complex of human immunodeficiency virus type 1 reverse transcriptase with a double-stranded DNA template-primer.
  Biopolymers, 44, 125-138.  
9309225 J.L.Hansen, A.M.Long, and S.C.Schultz (1997).
Structure of the RNA-dependent RNA polymerase of poliovirus.
  Structure, 5, 1109-1122.
PDB code: 1rdr
9215631 J.Wang, A.K.Sattar, C.C.Wang, J.D.Karam, W.H.Konigsberg, and T.A.Steitz (1997).
Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69.
  Cell, 89, 1087-1099.
PDB codes: 1waf 1wag 1wah 1wai 1waj
9060443 K.A.Eckert, S.E.Hile, and P.L.Vargo (1997).
Development and use of an in vitro HSV-tk forward mutation assay to study eukaryotic DNA polymerase processing of DNA alkyl lesions.
  Nucleic Acids Res, 25, 1450-1457.  
9062120 L.P.Gardner, K.A.Mookhtiar, and J.E.Coleman (1997).
Initiation, elongation, and processivity of carboxyl-terminal mutants of T7 RNA polymerase.
  Biochemistry, 36, 2908-2918.  
9287163 M.R.Sawaya, R.Prasad, S.H.Wilson, J.Kraut, and H.Pelletier (1997).
Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism.
  Biochemistry, 36, 11205-11215.
PDB codes: 1bpx 1bpy 1bpz
  9191022 R.Hindges, and U.Hübscher (1997).
DNA polymerase delta, an essential enzyme for DNA transactions.
  Biol Chem, 378, 345-362.  
8692686 A.J.Doherty, L.C.Serpell, and C.P.Ponting (1996).
The helix-hairpin-helix DNA-binding motif: a structural basis for non-sequence-specific recognition of DNA.
  Nucleic Acids Res, 24, 2488-2497.  
8555168 A.Y.Woody, S.S.Eaton, P.A.Osumi-Davis, and R.W.Woody (1996).
Asp537 and Asp812 in bacteriophage T7 RNA polymerase as metal ion-binding sites studied by EPR, flow-dialysis, and transcription.
  Biochemistry, 35, 144-152.  
8679529 B.G.Werneburg, J.Ahn, X.Zhong, R.J.Hondal, V.S.Kraynov, and M.D.Tsai (1996).
DNA polymerase beta: pre-steady-state kinetic analysis and roles of arginine-283 in catalysis and fidelity.
  Biochemistry, 35, 7041-7050.  
8794744 B.M.Moore, R.K.Jalluri, and M.B.Doughty (1996).
DNA polymerase photoprobe 2-[(4-azidophenacyl)thio]-2'-deoxyadenosine 5'-triphosphate labels an Escherichia coli DNA polymerase I Klenow fragment substrate binding site.
  Biochemistry, 35, 11642-11651.  
8619993 D.K.Srivastava, R.K.Evans, A.Kumar, W.A.Beard, and S.H.Wilson (1996).
dNTP binding site in rat DNA polymerase beta revealed by controlled proteolysis and azido photoprobe cross-linking.
  Biochemistry, 35, 3728-3734.  
8703921 F.M.Pisani, G.Manco, V.Carratore, and M.Rossi (1996).
Domain organization and DNA-induced conformational changes of an archaeal family B DNA polymerase.
  Biochemistry, 35, 9158-9166.  
  8665867 G.Martin, and W.Keller (1996).
Mutational analysis of mammalian poly(A) polymerase identifies a region for primer binding and catalytic domain, homologous to the family X polymerases, and to other nucleotidyltransferases.
  EMBO J, 15, 2593-2603.  
8841118 H.Pelletier, M.R.Sawaya, W.Wolfle, S.H.Wilson, and J.Kraut (1996).
Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, processivity, and fidelity.
  Biochemistry, 35, 12742-12761.
PDB codes: 9icm 9icw 9icx 9icy
8841119 H.Pelletier, M.R.Sawaya, W.Wolfle, S.H.Wilson, and J.Kraut (1996).
A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta.
  Biochemistry, 35, 12762-12777.
PDB codes: 1zqt 7ice 7icf 7icg 7ich 7ici 7icj 7ick 7icl 7icm 7icn 7ico 7icp 7icq 7icr 7ics 7ict 7icu 7icv 8icj 8ick 8icl 8icm 8icn 8ico 8icp 8icq 8icr 8ics 8ict 8icu 8icv 8icw 8icx 8icy 9icf 9ick 9icn 9ico 9icp 9icq 9icr 9ics 9ict 9icu 9icv
8841120 H.Pelletier, and M.R.Sawaya (1996).
Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis.
  Biochemistry, 35, 12778-12787.
PDB codes: 1nom 1zqa 1zqb 1zqc 1zqd 1zqe 1zqf 1zqg 1zqh 1zqi 1zqj 1zqk 1zql 1zqm 1zqn 1zqo 1zqp 1zqq 1zqr 1zqs 1zqu 1zqv 1zqw 1zqx 1zqy 1zqz 8ica 8icb 8icc 8ice 8icf 8icg 8ich 8ici 8icz 9ica 9icb 9icc 9ice 9icg 9ich 9ici 9icj 9icl
8646784 K.K.Leuther, D.A.Bushnell, and R.D.Kornberg (1996).
Two-dimensional crystallography of TFIIB- and IIE-RNA polymerase II complexes: implications for start site selection and initiation complex formation.
  Cell, 85, 773-779.  
8790389 M.Suzuki, D.Baskin, L.Hood, and L.A.Loeb (1996).
Random mutagenesis of Thermus aquaticus DNA polymerase I: concordance of immutable sites in vivo with the crystal structure.
  Proc Natl Acad Sci U S A, 93, 9670-9675.  
  8892891 N.Gargano, S.Biocca, A.Bradbury, and A.Cattaneo (1996).
Human recombinant antibody fragments neutralizing human immunodeficiency virus type 1 reverse transcriptase provide an experimental basis for the structural classification of the DNA polymerase family.
  J Virol, 70, 7706-7712.  
  8670908 N.K.Back, M.Nijhuis, W.Keulen, C.A.Boucher, B.O.Oude Essink, A.B.van Kuilenburg, A.H.van Gennip, and B.Berkhout (1996).
Reduced replication of 3TC-resistant HIV-1 variants in primary cells due to a processivity defect of the reverse transcriptase enzyme.
  EMBO J, 15, 4040-4049.  
8994974 P.Heikinheimo, J.Lehtonen, A.Baykov, R.Lahti, B.S.Cooperman, and A.Goldman (1996).
The structural basis for pyrophosphatase catalysis.
  Structure, 4, 1491-1508.
PDB codes: 1wgi 1wgj
8871404 R.Sousa (1996).
Structural and mechanistic relationships between nucleic acid polymerases.
  Trends Biochem Sci, 21, 186-190.  
  8627740 S.H.Hughes, Z.Hostomsky, S.F.Le Grice, K.Lentz, and E.Arnold (1996).
What is the orientation of DNA polymerases on their templates?
  J Virol, 70, 2679-2683.  
8811091 T.Yamaguchi, and M.Saneyoshi (1996).
A photolabile 2',3'-dideoxyuridylate analog bearing an aryl(trifluoromethyl)diazirine moiety: photoaffinity labeling of HIV-1 reverse transcriptase.
  Nucleic Acids Res, 24, 3364-3369.  
9016652 V.Mizrahi, and P.Huberts (1996).
Deoxy- and dideoxynucleotide discrimination and identification of critical 5' nuclease domain residues of the DNA polymerase I from Mycobacterium tuberculosis.
  Nucleic Acids Res, 24, 4845-4852.  
  8670845 V.Truniger, J.M.Lázaro, M.Salas, and L.Blanco (1996).
A DNA binding motif coordinating synthesis and degradation in proofreading DNA polymerases.
  EMBO J, 15, 3430-3441.  
8769567 Y.J.Chyan, P.R.Strauss, T.G.Wood, and S.H.Wilson (1996).
Identification of novel mRNA isoforms for human DNA polymerase beta.
  DNA Cell Biol, 15, 653-659.  
  7592405 C.M.Joyce, and T.A.Steitz (1995).
Polymerase structures and function: variations on a theme?
  J Bacteriol, 177, 6321-6329.  
7539708 E.Arnold, J.Ding, S.H.Hughes, and Z.Hostomsky (1995).
Structures of DNA and RNA polymerases and their interactions with nucleic acid substrates.
  Curr Opin Struct Biol, 5, 27-38.  
7784216 I.Husain, B.S.Morton, W.A.Beard, R.K.Singhal, R.Prasad, S.H.Wilson, and J.M.Besterman (1995).
Specific inhibition of DNA polymerase beta by its 14 kDa domain: role of single- and double-stranded DNA binding and 5'-phosphate recognition.
  Nucleic Acids Res, 23, 1597-1603.  
7777511 J.S.Hoffmann, M.J.Pillaire, G.Maga, V.Podust, U.Hübscher, and G.Villani (1995).
DNA polymerase beta bypasses in vitro a single d(GpG)-cisplatin adduct placed on codon 13 of the HRAS gene.
  Proc Natl Acad Sci U S A, 92, 5356-5360.  
8535782 M.M.Georgiadis, S.M.Jessen, C.M.Ogata, A.Telesnitsky, S.P.Goff, and W.A.Hendrickson (1995).
Mechanistic implications from the structure of a catalytic fragment of Moloney murine leukemia virus reverse transcriptase.
  Structure, 3, 879-892.
PDB code: 1mml
7753632 P.Chary, and R.S.Lloyd (1995).
In vitro replication by prokaryotic and eukaryotic polymerases on DNA templates containing site-specific and stereospecific benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide adducts.
  Nucleic Acids Res, 23, 1398-1405.  
  7556104 R.Sousa, and R.Padilla (1995).
A mutant T7 RNA polymerase as a DNA polymerase.
  EMBO J, 14, 4609-4621.  
  7853486 S.A.Jablonski, and C.D.Morrow (1995).
Mutation of the aspartic acid residues of the GDD sequence motif of poliovirus RNA-dependent RNA polymerase results in enzymes with altered metal ion requirements for activity.
  J Virol, 69, 1532-1539.  
  7862140 S.A.Shaaban, B.M.Krupp, and B.D.Hall (1995).
Termination-altering mutations in the second-largest subunit of yeast RNA polymerase III.
  Mol Cell Biol, 15, 1467-1478.  
7535923 S.F.Chao, V.L.Chan, P.Juranka, A.H.Kaplan, R.Swanstrom, and C.A.Hutchison (1995).
Mutational sensitivity patterns define critical residues in the palm subdomain of the reverse transcriptase of human immunodeficiency virus type 1.
  Nucleic Acids Res, 23, 803-810.  
7568114 S.Korolev, M.Nayal, W.M.Barnes, E.Di Cera, and G.Waksman (1995).
Crystal structure of the large fragment of Thermus aquaticus DNA polymerase I at 2.5-A resolution: structural basis for thermostability.
  Proc Natl Acad Sci U S A, 92, 9264-9268.
PDB code: 1ktq
8747457 S.Moréra, M.L.Lacombe, Y.Xu, G.LeBras, and J.Janin (1995).
X-ray structure of human nucleoside diphosphate kinase B complexed with GDP at 2 A resolution.
  Structure, 3, 1307-1314.
PDB code: 1nue
7816603 W.Zhu, and J.Ito (1994).
Family A and family B DNA polymerases are structurally related: evolutionary implications.
  Nucleic Acids Res, 22, 5177-5183.  
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 codes are shown on the right.

 

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