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PDBsum entry 4rnp

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protein links
Nucleotidyltransferase PDB id
4rnp
Jmol
Contents
Protein chains
780 a.a.* *
* Residue conservation analysis
* C-alpha coords only
PDB id:
4rnp
Name: Nucleotidyltransferase
Title: Bacteriophage t7 RNA polymerase, high salt crystal form, low temperature data, alpha-carbons only
Structure: RNA polymerase. Chain: a, b, c. Synonym: t7 rnap, DNA-directed RNA polymerase. Engineered: yes. Other_details: high salt form, low temperature data
Source: Enterobacteria phage t7. Organism_taxid: 10760. Cell_line: 293. Gene: t7 rnap. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
3.00Å     R-factor:   not given    
Authors: Z.J.Liu,R.Sousa,J.P.Rose,B.C.Wang
Key ref: R.Sousa et al. (1993). Crystal structure of bacteriophage T7 RNA polymerase at 3.3 A resolution. Nature, 364, 593-599. PubMed id: 7688864
Date:
11-Sep-97     Release date:   03-Dec-97    
Supersedes: 3rnp
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00573  (RPOL_BPT7) -  T7 RNA polymerase
Seq:
Struc:
 
Seq:
Struc:
883 a.a.
780 a.a.
Key:    PfamA domain  Secondary structure

 Enzyme reactions 
   Enzyme class: E.C.2.7.7.6  - DNA-directed Rna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Nucleoside triphosphate
+ RNA(n)
= diphosphate
+ RNA(n+1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     transcription, DNA-dependent   1 term 
  Biochemical function     transferase activity     4 terms  

 

 
    reference    
 
 
Nature 364:593-599 (1993)
PubMed id: 7688864  
 
 
Crystal structure of bacteriophage T7 RNA polymerase at 3.3 A resolution.
R.Sousa, Y.J.Chung, J.P.Rose, B.C.Wang.
 
  ABSTRACT  
 
The crystal structure of T7 RNA polymerase reveals a molecule organized around a cleft that can accommodate a double-stranded DNA template. A portion (approximately 45%) of the molecule displays extensive structural homology to the polymerase domain of Klenow fragment and more limited homology to the human immunodeficiency virus HIV-1 reverse transcriptase. A comparison of the structures and sequences of these polymerases identifies structural elements that may be responsible for discriminating between ribonucleotide and deoxyribonucleotide substrates, and RNA and DNA templates. The relative locations of the catalytic site and a specific promoter recognition residue allow the orientation of the polymerase on the template to be defined.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21134269 C.Yin, U.Richter, T.Börner, and A.Weihe (2010).
Evolution of plant phage-type RNA polymerases: the genome of the basal angiosperm Nuphar advena encodes two mitochondrial and one plastid phage-type RNA polymerases.
  BMC Evol Biol, 10, 379.  
  19744344 B.S.Andrade, A.G.Taranto, A.Góes-Neto, and A.A.Duarte (2009).
Comparative modeling of DNA and RNA polymerases from Moniliophthora perniciosa mitochondrial plasmid.
  Theor Biol Med Model, 6, 22.  
19854925 C.N.Lee, J.W.Lin, S.F.Weng, and Y.H.Tseng (2009).
Genomic characterization of the intron-containing T7-like phage phiL7 of Xanthomonas campestris.
  Appl Environ Microbiol, 75, 7828-7837.  
19407923 C.Yin, U.Richter, T.Börner, and A.Weihe (2009).
Evolution of phage-type RNA polymerases in higher plants: characterization of the single phage-type RNA polymerase gene from Selaginella moellendorffii.
  J Mol Evol, 68, 528-538.  
19861424 P.Le, P.R.Fisher, and C.Barth (2009).
Transcription of the Dictyostelium discoideum mitochondrial genome occurs from a single initiation site.
  RNA, 15, 2321-2330.  
18166198 D.Nayak, S.Siller, Q.Guo, and R.Sousa (2008).
Mechanism of T7 RNAP pausing and termination at the T7 concatemer junction: a local change in transcription bubble structure drives a large change in transcription complex architecture.
  J Mol Biol, 376, 541-553.  
18536012 H.J.Woo, Y.Liu, and R.Sousa (2008).
Molecular dynamics studies of the energetics of translocation in model T7 RNA polymerase elongation complexes.
  Proteins, 73, 1021-1036.  
18570883 H.Yu, and D.C.Schwartz (2008).
Imaging and analysis of transcription on large, surface-mounted single template DNA molecules.
  Anal Biochem, 380, 111-121.  
18025581 M.Khalaj-Kondori, M.Sadeghizadeh, K.Khajeh, H.Naderi-Manesh, A.M.Ahadi, and A.Emamzadeh (2007).
Cloning, sequence analysis and three-dimensional structure prediction of DNA pol I from thermophilic Geobacillus sp. MKK isolated from an Iranian hot spring.
  Appl Biochem Biotechnol, 142, 200-208.  
17392338 P.L.Polosa, S.Deceglie, M.Falkenberg, M.Roberti, B.Di Ponzio, M.N.Gadaleta, and P.Cantatore (2007).
Cloning of the sea urchin mitochondrial RNA polymerase and reconstitution of the transcription termination system.
  Nucleic Acids Res, 35, 2413-2427.  
17253774 R.S.Turingan, C.Liu, M.E.Hawkins, and C.T.Martin (2007).
Structural confirmation of a bent and open model for the initiation complex of T7 RNA polymerase.
  Biochemistry, 46, 1714-1723.  
17978174 S.Kaneko, C.Chu, A.J.Shatkin, and J.L.Manley (2007).
Human capping enzyme promotes formation of transcriptional R loops in vitro.
  Proc Natl Acad Sci U S A, 104, 17620-17625.  
16402203 M.L.Miller, T.J.Antes, F.Qian, and D.L.Miller (2006).
Identification of a putative mitochondrial RNA polymerase from Physarum polycephalum: characterization, expression, purification, and transcription in vitro.
  Curr Genet, 49, 259-271.  
16790422 P.Gong, and C.T.Martin (2006).
Mechanism of instability in abortive cycling by T7 RNA polymerase.
  J Biol Chem, 281, 23533-23544.  
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
17005565 V.S.Anand, and S.S.Patel (2006).
Transient state kinetics of transcription elongation by T7 RNA polymerase.
  J Biol Chem, 281, 35677-35685.  
15109812 A.R.Pavlov, N.V.Pavlova, S.A.Kozyavkin, and A.I.Slesarev (2004).
Recent developments in the optimization of thermostable DNA polymerases for efficient applications.
  Trends Biotechnol, 22, 253-260.  
15016373 D.Temiakov, V.Patlan, M.Anikin, W.T.McAllister, S.Yokoyama, and D.G.Vassylyev (2004).
Structural basis for substrate selection by t7 RNA polymerase.
  Cell, 116, 381-391.
PDB code: 1s0v
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
15016374 Y.W.Yin, and T.A.Steitz (2004).
The structural mechanism of translocation and helicase activity in T7 RNA polymerase.
  Cell, 116, 393-404.
PDB codes: 1s76 1s77
12441338 A.Kukarin, M.Rong, and W.T.McAllister (2003).
Exposure of T7 RNA polymerase to the isolated binding region of the promoter allows transcription from a single-stranded template.
  J Biol Chem, 278, 2419-2424.  
14657021 S.Mukherjee, L.G.Brieba, and R.Sousa (2003).
Discontinuous movement and conformational change during pausing and termination by T7 RNA polymerase.
  EMBO J, 22, 6483-6493.  
  12734553 S.Mukherjee, and R.Sousa (2003).
Use of Site-Specifically Tethered Chemical Nucleases to Study Macromolecular Reactions.
  Biol Proced Online, 5, 78-89.  
12351656 D.Temiakov, M.Anikin, and W.T.McAllister (2002).
Characterization of T7 RNA polymerase transcription complexes assembled on nucleic acid scaffolds.
  J Biol Chem, 277, 47035-47043.  
11859084 J.Grams, J.C.Morris, M.E.Drew, Z.Wang, P.T.Englund, and S.L.Hajduk (2002).
A trypanosome mitochondrial RNA polymerase is required for transcription and replication.
  J Biol Chem, 277, 16952-16959.  
12411499 K.M.Kazmierczak, E.K.Davydova, A.A.Mustaev, and L.B.Rothman-Denes (2002).
The phage N4 virion RNA polymerase catalytic domain is related to single-subunit RNA polymerases.
  EMBO J, 21, 5815-5823.  
12186873 K.Ma, D.Temiakov, M.Jiang, M.Anikin, and W.T.McAllister (2002).
Major conformational changes occur during the transition from an initiation complex to an elongation complex by T7 RNA polymerase.
  J Biol Chem, 277, 43206-43215.  
11863453 M.Boudvillain, A.Schwartz, and A.R.Rahmouni (2002).
Limited topological alteration of the T7 RNA polymerase active center at intrinsic termination sites.
  Biochemistry, 41, 3137-3146.  
11877396 M.R.Laurila, E.V.Makeyev, and D.H.Bamford (2002).
Bacteriophage phi 6 RNA-dependent RNA polymerase: molecular details of initiating nucleic acid synthesis without primer.
  J Biol Chem, 277, 17117-17124.  
12193610 S.H.Willis, K.M.Kazmierczak, R.H.Carter, and L.B.Rothman-Denes (2002).
N4 RNA polymerase II, a heterodimeric RNA polymerase with homology to the single-subunit family of RNA polymerases.
  J Bacteriol, 184, 4952-4961.  
12422209 T.H.Tahirov, D.Temiakov, M.Anikin, V.Patlan, W.T.McAllister, D.G.Vassylyev, and S.Yokoyama (2002).
Structure of a T7 RNA polymerase elongation complex at 2.9 A resolution.
  Nature, 420, 43-50.
PDB code: 1h38
12134065 T.Lisowsky, D.Wilkens, T.Stein, B.Hedtke, T.Börner, and A.Weihe (2002).
The C-terminal region of mitochondrial single-subunit RNA polymerases contains species-specific determinants for maintenance of intact mitochondrial genomes.
  Mol Biol Cell, 13, 2245-2255.  
11522820 A.Grigoriev (2001).
A relationship between gene expression and protein interactions on the proteome scale: analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae.
  Nucleic Acids Res, 29, 3513-3519.  
11551915 D.Ahuja, D.S.Karow, J.E.Kilpatrick, and M.J.Imperiale (2001).
RNA polymerase II-dependent positional effects on mRNA 3' end processing in the adenovirus major late transcription unit.
  J Biol Chem, 276, 41825-41831.  
11567089 F.D.Schubot, C.J.Chen, J.P.Rose, T.A.Dailey, H.A.Dailey, and B.C.Wang (2001).
Crystal structure of the transcription factor sc-mtTFB offers insights into mitochondrial transcription.
  Protein Sci, 10, 1980-1988.
PDB code: 1i4w
11318872 H.Song, and C.Kang (2001).
Sequence-specific termination by T7 RNA polymerase requires formation of paused conformation prior to the point of RNA release.
  Genes Cells, 6, 291-301.  
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.  
11828447 S.Brakmann, and S.Grzeszik (2001).
An error-prone T7 RNA polymerase mutant generated by directed evolution.
  Chembiochem, 2, 212-219.  
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.  
11514661 W.A.Breyer, and B.W.Matthews (2001).
A structural basis for processivity.
  Protein Sci, 10, 1699-1711.  
11274475 Y.Griko, N.Sreerama, P.Osumi-Davis, R.W.Woody, and A.Y.Woody (2001).
Thermal and urea-induced unfolding in T7 RNA polymerase: calorimetry, circular dichroism and fluorescence study.
  Protein Sci, 10, 845-853.  
11095736 D.Temiakov, P.E.Mentesana, K.Ma, A.Mustaev, S.Borukhov, and W.T.McAllister (2000).
The specificity loop of T7 RNA polymerase interacts first with the promoter and then with the elongating transcript, suggesting a mechanism for promoter clearance.
  Proc Natl Acad Sci U S A, 97, 14109-14114.  
10679468 G.M.Cheetham, and T.A.Steitz (2000).
Insights into transcription: structure and function of single-subunit DNA-dependent RNA polymerases.
  Curr Opin Struct Biol, 10, 117-123.  
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.  
10995224 J.Huang, L.G.Brieba, and R.Sousa (2000).
Misincorporation by wild-type and mutant T7 RNA polymerases: identification of interactions that reduce misincorporation rates by stabilizing the catalytically incompetent open conformation.
  Biochemistry, 39, 11571-11580.  
10681506 J.J.Arnold, and C.E.Cameron (2000).
Poliovirus RNA-dependent RNA polymerase (3D(pol)). Assembly of stable, elongation-competent complexes by using a symmetrical primer-template substrate (sym/sub).
  J Biol Chem, 275, 5329-5336.  
10585459 B.Canard, K.Chowdhury, R.Sarfati, S.Doublié, and C.C.Richardson (1999).
The motif D loop of human immunodeficiency virus type 1 reverse transcriptase is critical for nucleoside 5'-triphosphate selectivity.
  J Biol Chem, 274, 35768-35776.  
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.  
10329782 C.J.Chen, Z.J.Liu, J.P.Rose, and B.C.Wang (1999).
Low-salt crystallization of T7 RNA polymerase: a first step towards the transcription bubble complex.
  Acta Crystallogr D Biol Crystallogr, 55, 1188-1192.  
10213596 C.Place, J.Oddos, H.Buc, W.T.McAllister, and M.Buckle (1999).
Studies of contacts between T7 RNA polymerase and its promoter reveal features in common with multisubunit RNA polymerases.
  Biochemistry, 38, 4948-4957.  
10047577 J.Jäger, and J.D.Pata (1999).
Getting a grip: polymerases and their substrate complexes.
  Curr Opin Struct Biol, 9, 21-28.  
10364165 T.A.Steitz (1999).
DNA polymerases: structural diversity and common mechanisms.
  J Biol Chem, 274, 17395-17398.  
9843402 A.Y.Woody, P.A.Osumi-Davis, M.M.Hiremath, and R.W.Woody (1998).
Pre-steady-state and steady-state kinetic studies on transcription initiation catalyzed by T7 RNA polymerase and its active-site mutants K631R and Y639F.
  Biochemistry, 37, 15958-15964.  
9670025 D.Jeruzalmi, and T.A.Steitz (1998).
Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme.
  EMBO J, 17, 4101-4113.
PDB code: 1aro
9792681 D.Yue, A.M.Weiner, and N.Maizels (1998).
The CCA-adding enzyme has a single active site.
  J Biol Chem, 273, 29693-29700.  
9545247 G.J.Jensen, G.Meredith, D.A.Bushnell, and R.D.Kornberg (1998).
Structure of wild-type yeast RNA polymerase II and location of Rpb4 and Rpb7.
  EMBO J, 17, 2353-2358.  
9649630 G.P.Harrison, M.S.Mayo, E.Hunter, and A.M.Lever (1998).
Pausing of reverse transcriptase on retroviral RNA templates is influenced by secondary structures both 5' and 3' of the catalytic site.
  Nucleic Acids Res, 26, 3433-3442.  
9826686 I.K.Cann, K.Komori, H.Toh, S.Kanai, and Y.Ishino (1998).
A heterodimeric DNA polymerase: evidence that members of Euryarchaeota possess a distinct DNA polymerase.
  Proc Natl Acad Sci U S A, 95, 14250-14255.  
9642244 J.Mote, and D.Reines (1998).
Recognition of a human arrest site is conserved between RNA polymerase II and prokaryotic RNA polymerases.
  J Biol Chem, 273, 16843-16852.  
9603929 M.Izawa, N.Sasaki, M.Watahiki, E.Ohara, Y.Yoneda, M.Muramatsu, Y.Okazaki, and Y.Hayashizaki (1998).
Recognition sites of 3'-OH group by T7 RNA polymerase and its application to transcriptional sequencing.
  J Biol Chem, 273, 14242-14246.  
9435223 M.Rong, B.He, W.T.McAllister, and R.K.Durbin (1998).
Promoter specificity determinants of T7 RNA polymerase.
  Proc Natl Acad Sci U S A, 95, 515-519.  
9553077 M.Rong, R.K.Durbin, and W.T.McAllister (1998).
Template strand switching by T7 RNA polymerase.
  J Biol Chem, 273, 10253-10260.  
9671817 N.Arnaud-Barbe, V.Cheynet-Sauvion, G.Oriol, B.Mandrand, and F.Mallet (1998).
Transcription of RNA templates by T7 RNA polymerase.
  Nucleic Acids Res, 26, 3550-3554.  
9520387 N.Sasaki, M.Izawa, M.Watahiki, K.Ozawa, T.Tanaka, Y.Yoneda, S.Matsuura, P.Carninci, M.Muramatsu, Y.Okazaki, and Y.Hayashizaki (1998).
Transcriptional sequencing: A method for DNA sequencing using RNA polymerase.
  Proc Natl Acad Sci U S A, 95, 3455-3460.  
9689042 S.Sastry, and B.M.Ross (1998).
RNA-binding site in T7 RNA polymerase.
  Proc Natl Acad Sci U S A, 95, 9111-9116.  
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.  
10333564 Y.Ishino, and I.K.Cann (1998).
The euryarchaeotes, a subdomain of Archaea, survive on a single DNA polymerase: fact or farce?
  Genes Genet Syst, 73, 323-336.  
9374875 A.Kumar, and S.S.Patel (1997).
Inhibition of T7 RNA polymerase: transcription initiation and transition from initiation to elongation are inhibited by T7 lysozyme via a ternary complex with RNA polymerase and promoter DNA.
  Biochemistry, 36, 13954-13962.  
9171081 A.Weihe, B.Hedtke, and T.Börner (1997).
Cloning and characterization of a cDNA encoding a bacteriophage-type RNA polymerase from the higher plant Chenopodium album.
  Nucleic Acids Res, 25, 2319-2325.  
9242608 B.Hedtke, T.Börner, and A.Weihe (1997).
Mitochondrial and chloroplast phage-type RNA polymerases in Arabidopsis.
  Science, 277, 809-811.  
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.  
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
9016716 J.R.Kiefer, C.Mao, C.J.Hansen, S.L.Basehore, H.H.Hogrefe, J.C.Braman, and L.S.Beese (1997).
Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 A resolution.
  Structure, 5, 95.
PDB codes: 1bdp 1xwl
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
9164459 K.Bebenek, W.A.Beard, T.A.Darden, L.Li, R.Prasad, B.A.Luton, D.G.Gorenstein, S.H.Wilson, and T.A.Kunkel (1997).
A minor groove binding track in reverse transcriptase.
  Nat Struct Biol, 4, 194-197.  
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.  
9388236 M.Oliveros, R.J.Yáñez, M.L.Salas, J.Salas, E.Viñuela, and L.Blanco (1997).
Characterization of an African swine fever virus 20-kDa DNA polymerase involved in DNA repair.
  J Biol Chem, 272, 30899-30910.  
9287335 O.C.Richards, and E.Ehrenfeld (1997).
One of two NTP binding sites in poliovirus RNA polymerase required for RNA replication.
  J Biol Chem, 272, 23261-23264.  
  9353258 P.F.Cliften, J.Y.Park, B.P.Davis, S.H.Jang, and J.A.Jaehning (1997).
Identification of three regions essential for interaction between a sigma-like factor and core RNA polymerase.
  Genes Dev, 11, 2897-2909.  
9062929 S.L.Daubendiek, and E.T.Kool (1997).
Generation of catalytic RNAs by rolling transcription of synthetic DNA nanocircles.
  Nat Biotechnol, 15, 273-277.  
9204868 Y.Huang, F.Eckstein, R.Padilla, and R.Sousa (1997).
Mechanism of ribose 2'-group discrimination by an RNA polymerase.
  Biochemistry, 36, 8231-8242.  
9374495 Y.Jia, and S.S.Patel (1997).
Kinetic mechanism of GTP binding and RNA synthesis during transcription initiation by bacteriophage T7 RNA polymerase.
  J Biol Chem, 272, 30147-30153.  
8798669 A.Monaghan, and R.T.Hay (1996).
Pyridoxal 5'-phosphate inhibition of adenovirus DNA polymerase.
  J Biol Chem, 271, 24242-24248.  
8931555 A.Ujvári, and C.T.Martin (1996).
Thermodynamic and kinetic measurements of promoter binding by T7 RNA polymerase.
  Biochemistry, 35, 14574-14582.  
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.  
  8887555 C.Klinger, J.Huet, D.Song, G.Petersen, M.Riva, E.K.Bautz, A.Sentenac, P.Oudet, and P.Schultz (1996).
Localization of yeast RNA polymerase I core subunits by immunoelectron microscopy.
  EMBO J, 15, 4643-4653.  
  8524330 D.Gilley, and E.H.Blackburn (1996).
Specific RNA residue interactions required for enzymatic functions of Tetrahymena telomerase.
  Mol Cell Biol, 16, 66-75.  
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.  
  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.  
9016657 J.Portugal, and A.Rodríguez-Campos (1996).
T7 RNA polymerase cannot transcribe through a highly knotted DNA template.
  Nucleic Acids Res, 24, 4890-4894.  
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.  
  8887568 L.Hartvig, and J.Christiansen (1996).
Intrinsic termination of T7 RNA polymerase mediated by either RNA or DNA.
  EMBO J, 15, 4767-4774.  
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.  
8604305 N.Cermakian, T.M.Ikeda, R.Cedergren, and M.W.Gray (1996).
Sequences homologous to yeast mitochondrial and bacteriophage T3 and T7 RNA polymerases are widespread throughout the eukaryotic lineage.
  Nucleic Acids Res, 24, 648-654.  
8528255 P.L.Bartel, J.A.Roecklein, D.SenGupta, and S.Fields (1996).
A protein linkage map of Escherichia coli bacteriophage T7.
  Nat Genet, 12, 72-77.  
8871404 R.Sousa (1996).
Structural and mechanistic relationships between nucleic acid polymerases.
  Trends Biochem Sci, 21, 186-190.  
8918794 S.Prasartkaew, N.M.Zijlstra, P.Wilairat, J.P.Overdulve, and E.de Vries (1996).
Molecular cloning of a Plasmodium falciparum gene interrupted by 15 introns encoding a functional primase 53 kDa subunit as demonstrated by expression in a baculovirus system.
  Nucleic Acids Res, 24, 3934-3941.  
8954159 T.Hermann, and H.Heumann (1996).
Strained template under the thumbs. How reverse transcriptase of human immunodeficiency virus type 1 moves along its template.
  Eur J Biochem, 242, 98.  
8619992 T.Li, H.H.Ho, M.Maslak, C.Schick, and C.T.Martin (1996).
Major groove recognition elements in the middle of the T7 RNA polymerase promoter.
  Biochemistry, 35, 3722-3727.  
  8868064 Y.M.Henskens, E.C.Veerman, and A.V.Nieuw Amerongen (1996).
Cystatins in health and disease.
  Biol Chem Hoppe Seyler, 377, 71-86.  
8521466 A.Polyakov, E.Severinova, and S.A.Darst (1995).
Three-dimensional structure of E. coli core RNA polymerase: promoter binding and elongation conformations of the enzyme.
  Cell, 83, 365-373.  
7479898 B.Canard, B.Cardona, and R.S.Sarfati (1995).
Catalytic editing properties of DNA polymerases.
  Proc Natl Acad Sci U S A, 92, 10859-10863.  
  7592405 C.M.Joyce, and T.A.Steitz (1995).
Polymerase structures and function: variations on a theme?
  J Bacteriol, 177, 6321-6329.  
8846216 C.M.Nunn, and S.Neidle (1995).
The structure of chain-linked DNA as a possible model for the transcription bubble.
  Nat Struct Biol, 2, 1060-1061.  
7673156 D.C.Thomas, X.Veaute, R.P.Fuchs, and T.A.Kunkel (1995).
Frequency and fidelity of translesion synthesis of site-specific N-2-acetylaminofluorene adducts during DNA replication in a human cell extract.
  J Biol Chem, 270, 21226-21233.  
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.  
8901507 G.Krupp (1995).
Enzymatic RNA synthesis and RNase P. Evolutionary aspects.
  Mol Biol Rep, 22, 177-180.  
7503687 H.W.Ackermann, A.Elzanowski, G.Fobo, and G.Stewart (1995).
Relationships of tailed phages: a survey of protein sequence identity.
  Arch Virol, 140, 1871-1884.  
7829532 M.Astatke, N.D.Grindley, and C.M.Joyce (1995).
Deoxynucleoside triphosphate and pyrophosphate binding sites in the catalytically competent ternary complex for the polymerase reaction catalyzed by DNA polymerase I (Klenow fragment).
  J Biol Chem, 270, 1945-1954.  
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
8618879 O.V.Makarova, E.M.Makarov, R.Sousa, and M.Dreyfus (1995).
Transcribing of Escherichia coli genes with mutant T7 RNA polymerases: stability of lacZ mRNA inversely correlates with polymerase speed.
  Proc Natl Acad Sci U S A, 92, 12250-12254.  
  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.  
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
8539242 U.K.Urs, D.J.Sharkey, T.S.Peat, W.A.Hendrickson, and K.Murthy (1995).
Characterization of crystals of the thermostable DNA polymerase I from Thermus aquaticus.
  Proteins, 23, 111-114.  
7553869 V.M.Studitsky, D.J.Clark, and G.Felsenfeld (1995).
Overcoming a nucleosomal barrier to transcription.
  Cell, 83, 19-27.  
7876136 W.C.Copeland, and X.Tan (1995).
Active site mapping of the catalytic mouse primase subunit by alanine scanning mutagenesis.
  J Biol Chem, 270, 3905-3913.  
7885829 W.Cannon, S.Austin, M.Moore, and M.Buck (1995).
Identification of close contacts between the sigma N (sigma 54) protein and promoter DNA in closed promoter complexes.
  Nucleic Acids Res, 23, 351-356.  
7664337 W.Zhou, D.Reines, and P.W.Doetsch (1995).
T7 RNA polymerase bypass of large gaps on the template strand reveals a critical role of the nontemplate strand in elongation.
  Cell, 82, 577-585.  
7940759 D.Eick, A.Wedel, and H.Heumann (1994).
From initiation to elongation: comparison of transcription by prokaryotic and eukaryotic RNA polymerases.
  Trends Genet, 10, 292-296.  
7530020 J.Ding, A.Jacobo-Molina, C.Tantillo, X.Lu, R.G.Nanni, and E.Arnold (1994).
Buried surface analysis of HIV-1 reverse transcriptase p66/p51 heterodimer and its interaction with dsDNA template/primer.
  J Mol Recognit, 7, 157-161.  
8137427 J.F.Davies, R.J.Almassy, Z.Hostomska, R.A.Ferre, and Z.Hostomsky (1994).
2.3 A crystal structure of the catalytic domain of DNA polymerase beta.
  Cell, 76, 1123-1133.
PDB code: 1rpl
7529124 J.Jäger, S.J.Smerdon, J.Wang, D.C.Boisvert, and T.A.Steitz (1994).
Comparison of three different crystal forms shows HIV-1 reverse transcriptase displays an internal swivel motion.
  Structure, 2, 869-876.  
8052534 M.Frugier, C.Florentz, M.W.Hosseini, J.M.Lehn, and R.Giegé (1994).
Synthetic polyamines stimulate in vitro transcription by T7 RNA polymerase.
  Nucleic Acids Res, 22, 2784-2790.  
  8137808 M.Lindahl, L.A.Svensson, A.Liljas, S.E.Sedelnikova, I.A.Eliseikina, N.P.Fomenkova, N.Nevskaya, S.V.Nikonov, M.B.Garber, and T.A.Muranova (1994).
Crystal structure of the ribosomal protein S6 from Thermus thermophilus.
  EMBO J, 13, 1249-1254.
PDB code: 1ris
8168131 R.L.Tinker, K.P.Williams, G.A.Kassavetis, and E.P.Geiduschek (1994).
Transcriptional activation by a DNA-tracking protein: structural consequences of enhancement at the T4 late promoter.
  Cell, 77, 225-237.  
7527138 T.Hermann, T.Meier, M.Götte, and H.Heumann (1994).
The 'helix clamp' in HIV-1 reverse transcriptase: a new nucleic acid binding motif common in nucleic acid polymerases.
  Nucleic Acids Res, 22, 4625-4633.  
8171031 X.Cheng, X.Zhang, J.W.Pflugrath, and F.W.Studier (1994).
The structure of bacteriophage T7 lysozyme, a zinc amidase and an inhibitor of T7 RNA polymerase.
  Proc Natl Acad Sci U S A, 91, 4034-4038.
PDB code: 1lba
7509668 S.Wain-Hobson (1993).
The fastest genome evolution ever described: HIV variation in situ.
  Curr Opin Genet Dev, 3, 878-883.  
7526118 W.T.McAllister, and C.A.Raskin (1993).
The phage RNA polymerases are related to DNA polymerases and reverse transcriptases.
  Mol Microbiol, 10, 1-6.  
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.