Investigating protein structural plasticity by surveying the consequence of an amino acid deletion from TEM-1 β-lactamase

FEBS Letters

Volumn 581, Issue 21, 2007, Pages 3904-3908

  Simm, Alan M ^a   Baldwin, Amy J ^a   Busse, Kathy ^a   Jones, D Dafydd ^a  

^a CARDIFF UNIVERSITY   (United Kingdom)

Author keywords

Antibiotic resistance; Deletion mutations; Directed evolution; Indels; Protein plasticity

Indexed keywords

AMINO ACID; AMPICILLIN; BETA LACTAMASE TEM 1; CEFTAZIDIME;

ALPHA HELIX; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; BETA SHEET; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; ESCHERICHIA COLI; GENE DELETION; MINIMUM INHIBITORY CONCENTRATION; NONHUMAN; PRIORITY JOURNAL; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; AMPICILLIN; ANTI-BACTERIAL AGENTS; BETA-LACTAMASES; CEFTAZIDIME; EVOLUTION, MOLECULAR; PROTEIN STRUCTURE, SECONDARY; SEQUENCE DELETION; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY;

EID: 34547672953     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2007.07.018     Document Type: Article

References (22)

1. Chothia C., Gough J., Vogel C., and Teichmann S.A. Evolution of the protein repertoire. Science 300 (2003) 1701-1703
2. Grishin N.V. Fold change in evolution of protein structures. J. Struct. Biol. 134 (2001) 167-185
3. Pascarella S., and Argos P. Analysis of insertions/deletions in protein structures. J. Mol. Biol. 224 (1992) 461-471
4. Taylor M.S., Ponting C.P., and Copley R.R. Occurrence and consequences of coding sequence insertions and deletions in Mammalian genomes. Genome Res. 14 (2004) 555-566
5. de Wildt R.M., van Venrooij W.J., Winter G., Hoet R.M., and Tomlinson I.M. Somatic insertions and deletions shape the human antibody repertoire. J. Mol. Biol. 294 (1999) 701-710
6. Imamichi T., Murphy M.A., Imamichi H., and Lane H.C. Amino acid deletion at codon 67 and Thr-to-Gly change at codon 69 of human immunodeficiency virus type 1 reverse transcriptase confer novel drug resistance profiles. J. Virol. 75 (2001) 3988-3992
7. Kerem B., Rommens J.M., Buchanan J.A., Markiewicz D., Cox T.K., Chakravarti A., Buchwald M., and Tsui L.C. Identification of the cystic fibrosis gene: genetic analysis. Science 245 (1989) 1073-1080
8. Vetter I.R., Baase W.A., Heinz D.W., Xiong J.P., Snow S., and Matthews B.W. Protein structural plasticity exemplified by insertion and deletion mutants in T4 lysozyme. Protein Sci. 5 (1996) 2399-2415
9. O'Neil K.T., Bach II A.C., and DeGrado W.F. Structural consequences of an amino acid deletion in the B1 domain of protein G. Proteins 41 (2000) 323-333
10. Morris K.N., and Wool I.G. Determination by systematic deletion of the amino acids essential for catalysis by ricin A chain. Proc. Natl. Acad. Sci. USA 89 (1992) 4869-4873
11. Shortle D., and Sondek J. The emerging role of insertions and deletions in protein engineering. Curr. Opin. Biotechnol. 6 (1995) 387-393
12. Jones D.D. Triplet nucleotide removal at random positions in a target gene: the tolerance of TEM-1 beta-lactamase to an amino acid deletion. Nucleic Acids Res. 33 (2005) e80
13. Matagne A., Lamotte-Brasseur J., and Frere J.M. Catalytic properties of class A beta-lactamases: efficiency and diversity. Biochem. J. 330 Pt 2 (1998) 581-598
14. Bloom J.D., Meyer M.M., Meinhold P., Otey C.R., MacMillan D., and Arnold F.H. Evolving strategies for enzyme engineering. Curr. Opin. Struct. Biol. 15 (2005) 447-452
15. Lutz S., and Patrick W.M. Novel methods for directed evolution of enzymes: quality, not quantity. Curr. Opin. Biotechnol. 15 (2004) 291-297
16. Neylon C. Chemical and biochemical strategies for the randomization of protein encoding DNA sequences: library construction methods for directed evolution. Nucleic Acids Res. 32 (2004) 1448-1459
17. Garcia-Diaz M., and Kunkel T.A. Mechanism of a genetic glissando: structural biology of indel mutations. Trends Biochem. Sci. 31 (2006) 206-214
18. Huang W., Petrosino J., Hirsch M., Shenkin P.S., and Palzkill T. Amino acid sequence determinants of beta-lactamase structure and activity. J. Mol. Biol. 258 (1996) 688-703
19. Jelsch C., Mourey L., Masson J.M., and Samama J.P. Crystal structure of Escherichia coli TEM1 beta-lactamase at 1.8 A resolution. Proteins 16 (1993) 364-383
20. Fujii R., Kitaoka M., and Hayashi K. RAISE: a simple and novel method of generating random insertion and deletion mutations. Nucleic Acids Res. 34 (2006) e30
21. Murakami H., Hohsaka T., and Sisido M. Random insertion and deletion of arbitrary number of bases for codon-based random mutation of DNAs. Nat. Biotechnol. 20 (2002) 76-81
22. Ambler R.P., et al. A standard numbering scheme for the class A beta-lactamases. Biochem. J. 276 Pt 1 (1991) 269-270