The involvement of the aspartate triad of the active center in all catalytic activities of multisubunit RNA polymerase

Nucleic Acids Research

Volumn 33, Issue 13, 2005, Pages 4202-4211

  Sosunov, Vasily ^a   Zorov, Savva ^b,c   Sosunova, Ekaterina ^a,d   Nikolaev, Anatoly ^a   Zakeyeva, Irina ^b   Bass, Irina ^d   Goldfarb, Alex ^a   Nikiforov, Vadim ^a,d   Severinov, Konstantin ^b,d   Mustaev, Arkady ^a  

^a PUBLIC HEALTH RESEARCH INSTITUTE   (United States)

^b RUTGERS UNIVERSITY   (United States)

^c MOSCOW STATE UNIVERSITY   (Russian Federation)

^d INSTITUTE OF MOLECULAR GENETICS   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

ASPARTIC ACID; MAGNESIUM ION; RNA POLYMERASE; BETA' SUBUNIT OF RNA POLYMERASE; DNA DIRECTED RNA POLYMERASE; MAGNESIUM; PROTEIN SUBUNIT;

ARTICLE; BINDING AFFINITY; CATALYSIS; CRYSTALLOGRAPHY; ENZYME ACTIVITY; ESCHERICHIA COLI; METAL BINDING; MOLECULAR MODEL; MUTANT; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; PREDICTION; PRIORITY JOURNAL; PROTEIN MOTIF; RNA STRUCTURE; STEREOCHEMISTRY; STRUCTURE ANALYSIS; WILD TYPE; AMINO ACID SUBSTITUTION; CHEMICAL STRUCTURE; CHEMISTRY; ENZYME ACTIVE SITE; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

ESCHERICHIA COLI;

AMINO ACID SUBSTITUTION; ASPARTIC ACID; BASE SEQUENCE; CATALYSIS; CATALYTIC DOMAIN; DNA-DIRECTED RNA POLYMERASES; MAGNESIUM; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN SUBUNITS; TRANSCRIPTION, GENETIC;

EID: 22844436748     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki688     Document Type: Article

References (35)

1. Sosunov,V., Sosunova,E., Mustaev,A., Bass,I., Nikiforov,V. and Goldfarb,A. (2003) Unified two-metal mechanism of RNA synthesis and degradation by RNA polymerase. EMBO J., 22, 2234-2244.
2. Zaychikov,E., Martin,E., Denissova,L., Kozlov,M., Markovtsov,V., Kashlev,M., Heumann,H., Nikiforov,V., Goldfarb,A. and Mustaev,A. (1996) Mapping of catalytic residues in the RNA polymerase active center. Science, 273, 107-109.
3. Zhang,G., Campbell,E.A., Minakhin,L., Richter,C., Severinov,K. and Darst,S.A. (1999) Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution. Cell, 98, 811-824.
4. Gnatt,A.L., Cramer,P., Fu,J., Bushnell,D.A. and Kornberg,R.D. (2001) Structural basis of transcription: An RNA polymerase II elongation complex at 3.3 A resolution. Science, 292, 1876-1882.
5. Westover,K.D., Bushnell, D.A. and Kornberg,R.D. (2004) Structural basis of transcription: Nucleotide selection by rotation in the RNA polymerase II active center. Cell, 119, 481-489.
6. Borukhov,S., Laptenko,O. and Lee,J. (2001) Escherichia coli transcript cleavage factors GreA and GreB: Functions and mechanisms of action. Methods Enzymol., 342, 64-76.
7. Opalka,N., Chlenov,M., Chacon,P., Rice,W.J., Wriggers,W. and Darst,S.A. (2003) Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase. Cell, 114, 335-345.
8. Sosunova,E., Sosunov,V., Kozlov,M., Nikiforov,V., Goldfarb,A. and Mustaev,A. (2003) Donation of catalytic residues to RNA polymerase active center by transcription factor Gre. Proc. Natl Acad. Sci. USA, 100, 15469-15474.
9. Laptenko,O., Lee,J., Lomakin,I. and Borukhov,S. (2003) Transcript cleavage factors GreA and GreB act as transient catalytic components of RNA polymerase. EMBO J., 22, 6322-6334.
10. Kettenberger,H., Armache,K.J. and Cramer,P. (2004) Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol Cell, 16, 955-965.
11. Kettenberger,H., Armache,K.J. and Cramer,P. (2003) Architecture ofthe RNA polymerase II-TFIIS complex and implications for mRNA cleavage. Cell, 114, 347-357.
12. Borukhov,S. and Goldfarb,A. (1993) Recombinant Escherichia coli RNA polymerase: Purification of individually overexpressed subunits and in vitro assembly. Protein Expr. Purif., 4, 503-511.
13. Nedea,E.C., Markov,D., Naryshkina,T. and Severinov,K. (1999) Localization of Escherichia coli rpoC mutations that affect RNA polymerase assembly and activity at high temperature. J. Bacteriol., 181, 2663-2665.
14. Kashlev,M., Nudler,E., Severinov,K., Borukhov,S., Komissarova,N. and Goldfarb,A. (1996) Histidine-tagged RNA polymerase of Escherichia coli and transcription in solid phase. Methods Enzymol., 274, 326-334.
15. Sidorenkov,I., Komissarova,N. and Kashlev,M. (1998) Crucial role of the RNA:DNA hybrid in the processivity of transcription. Mol. Cell, 2, 55-64.
16. Korzheva,N., Mustaev,A., Nudler,E., Nikiforov,V. and Goldfarb,A. (1998) Mechanistic model of the elongation complex of Escherichia coli RNA polymerase. Cold Spring Harb. Symp. Quant. Biol., 63, 337-345.
17. Borukhov,S., Sagitov,V. and Goldfarb,A. (1993) Transcript cleavage factors from E.coli. Cell, 72, 459-466.
18. Copeland,W.C. and Wang,T.S. (1993) Mutational analysis of the human DNA polymerase alpha. The most conserved region in alpha-like DNA polymerases is involved in metal-specific catalysis. J. Biol. Chem., 268, 11028-11040.
19. Saturno,J., Lazaro,J.M., Blanco,L. and Salas,M. (1998) Role of the first aspartate residue of the 'YxDTDS' motif of phi29 DNA polymerase as a metal ligand during both TP-primed and DNA-primed DNA synthesis. J. Mol. Biol., 283, 633-642.
20. Pritchard,A.E. and McHenry,C.S. (1999) Identification of the acidic residues in the active site of DNA polymerase III. J. Mol. Biol., 285, 1067-1080.
21. Rhodes,G. and Chamberlin,M.J. (1974) Ribonucleic acid chain elongation by Escherichia coli ribonucleic acid polymerase. I. Isolation of ternary complexes and the kinetics of elongation. J. Biol. Chem., 249, 6675-6683.
22. Bonner,G., Patra,D., Lafer,E.M. and Sousa,R. (1992) Mutations in T7 RNA polymerase that support the proposal for a common polymerase active site structure. EMBO J., 11, 3767-3775.
23. Zakharova,E., Wang,J. and Konigsberg,W. (2004) The activity of selected RB69 DNA polymerase mutants can be restored by manganese ions: The existence of alternative metal ion ligands used during the polymerization cycle. Biochemistry, 43, 6587-6589.
24. Date,T., Yamamoto,S., Tanihara,K., Nishimoto,Y. and Matsukage,A. (1991) Aspartic acid residues at positions 190 and 192 of rat DNA polymerase beta are involved in primer binding. Biochemistry, 30, 5286-5292.
25. Menge,K.L., Hostomsky,Z., Nodes,B.R., Hudson,G.O., Rahmati,S., Moomaw,E.W., Almassy,R.J. and Hostomska,Z. (1995) Structure-function analysis of the mammalian DNA polymerase beta active site: Role of aspartic acid 256, arginine 254, and arginine 258 in nucleotidyl transfer. Biochemistry, 34, 15934-15942.
26. Kaushik,N., Rege,N., Yadav,P.N., Sarafianos,S.G., Modak,M.J. and Pandey,V.N. (1996) Biochemical analysis of catalytically crucial aspartate mutants of human immunodeficiency virus type 1 reverse transcriptase. Biochemistry, 35, 11536-11546.
27. Li,Y., Korolev,S. and Waksman,G. (1998) Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: Structural basis for nucleotide incorporation. EMBO J., 17, 7514-7525.
28. Lur'e,Yu. (1989) Handbook on Analytical Chemistry Khimia, Moscow.
29. Mustaev,A., Kozlov,M., Markovtsov,V., Zaychikov,E., Denissova,L. and Goldfarb,A. (1997) Modular organization of the catalytic center of RNA polymerase. Proc. Natl Acad. Sci. USA, 94, 6641-6645.
30. Steitz,T.A. (1999) DNA polymerases: Structural diversity and common mechanisms. J. Biol. Chem., 274, 17395-17398.
31. Svetlov,V., Vassylyev,D.G. and Artsimovitch,I. (2004) Discrimination against deoxyribonucleotide substrates by bacterial RNA polymerase. J. Biol. Chem., 279, 38087-38090.
32. Pelletier,H., Sawaya,M.R., Wolfle,W., Wilson,S.H. and Kraut,J. (1996) Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, processivity, and fidelity. Biochemistry, 35, 12742-12761.
33. Epshtein,V., Mustaev,A., Markovtsov,V., Bereshchenko,O., Nikiforov,V. and Goldfarb,A. (2002) Swing-gate model of nucleotide entry into the RNA polymerase active center. Mol. Cell, 10, 623-634.
34. Toulokhonov,I., Artsimovitch,I. and Landick,R. (2001) Allosteric control of RNA polymerase by a site that contacts nascent RNA hairpins. Science, 292, 730-733.
35. Polesky,A.H., Dahlberg,M.E., Benkovic,S.J., Grindley,N.D. and Joyce,C.M. (1992) Side chains involved in catalysis of the polymerase reaction of DNA polymerase I from Escherichia coli. J. Biol. Chem., 267, 8417-8428.