The DOI matches its Crossref record; 93 of the 93 references it cites were found in a registry or an index.
Similarities and differences among 105 members of the Int family of site-specific recombinases
Open accessAbstract
Alignments of 105 site-specific recombinases belonging to the Int family of proteins identified extended areas of similarity and three types of structural differences. In addition to the previously recognized conservation of the tetrad R-H-R-Y, located in boxes I and II, several newly identified sequence patches include charged amino acids that are highly conserved and a specific pattern of buried residues contributing to the overall protein fold. With some notable exceptions, unconserved regions correspond to loops in the crystal structures of the catalytic domains of lambda Int (Int c170) and HP1 Int (HPC) and of the recombinases XerD and Cre. Two structured regions also harbor some pronounced differences. The first comprises beta-sheets 4 and 5, alpha-helix D and the adjacent loop connecting it to alpha-helix E: two Ints of phages infecting thermophilic bacteria are missing this region altogether; the crystal structures of HPC, XerD and Cre reveal a lack of beta-sheets 4 and 5; Cre displays two additional beta-sheets following alpha-helix D; five recombinases carry large insertions. The second involves the catalytic tyrosine and is seen in a comparison of the four crystal structures. The yeast recombinases can theoretically be fitted to the Int fold, but the overall differences, involving changes in spacing as well as in motif structure, are more substantial than seen in most other proteins. The phenotypes of mutations compiled from several proteins are correlated with the available structural information and structure-function relationships are discussed. In addition, a few prokaryotic and eukaryotic enzymes with partial homology with the Int family of recombinases may be distantly related, either through divergent or convergent evolution. These include a restriction enzyme and a subgroup of eukaryotic RNA helicases (D-E-A-D proteins).
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The Complete Genome Sequence of Escherichia coli K-12
Blattner, F. R., Plunkett, G., Bloch, C. A., Perna, N. T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C. K., Mayhew, G. F., et al. (1997) · Science · doi:10.1126/science.277.5331.1453 · Cited by 7,452
Whole-Genome Random Sequencing and Assembly of Haemophilus influenzae Rd
Fleischmann, R. D., Adams, M. D., White, O., Clayton, R. A., Kirkness, E. F., Kerlavage, A. R., Bult, C. J., Tomb, J.-F., Dougherty, B. A., Merrick, J. M., et al. (1995) · Science · doi:10.1126/science.7542800 · Cited by 5,654
Atlas of protein sequence and structure
Chang, M.-Y., Dayhoff, M. O., Eck, R. V., & Sochard, M. R. (1965) · NASA Technical Reports Server (NASA) · Cited by 4,383
The complete genome sequence of the gastric pathogen Helicobacter pylori
Tomb, J.-F., White, O., Kerlavage, A. R., Clayton, R. A., Sutton, G. G., Fleischmann, R. D., Ketchum, K. A., Klenk, H. P., Gill, S., Dougherty, B. A., et al. (1997) · Nature · doi:10.1038/41483 · Cited by 3,529
Kaneko, T., Sato, S., Kotani, H., Tanaka, A., Asamizu, E., Nakamura, Y., Miyajima, N., Hirosawa, M., Sugiura, M., Sasamoto, S., et al. (1996) · DNA Research · doi:10.1093/dnares/3.3.185 · Cited by 2,432
Kaneko, T., Sato, S., Kotani, H., Tanaka, A., Asamizu, E., Nakamura, Y., Miyajima, N., Hirosawa, M., Sugiura, M., Sasamoto, S., et al. (1996) · DNA Research · doi:10.1093/dnares/3.3.109 · Cited by 2,132
Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii
Bult, C. J., White, O., Olsen, G. J., Zhou, L., Fleischmann, R. D., Sutton, G. G., Blake, J. A., FitzGerald, L. M., Clayton, R. A., Gocayne, J. D., et al. (1996) · Science · doi:10.1126/science.273.5278.1058 · Cited by 2,082
The V(D)J recombination activating gene, RAG-1
Schatz, D. G., Oettinger, M. A., & Baltimore, D. (1989) · Cell · doi:10.1016/0092-8674(89)90760-5 · Cited by 1,164
Molecular basis of symbiosis between Rhizobium and legumes
Freiberg, C., Fellay, R., Bairoch, A., Broughton, W. J., Rosenthal, A., & Perret, X. (1997) · Nature · doi:10.1038/387394a0 · Cited by 765
Gene cassettes: a new class of mobile element
Recchia, G. D., & Hall, R. M. (1995) · Microbiology · doi:10.1099/13500872-141-12-3015 · Cited by 657
Cited by
Integrons: agents of bacterial evolution
Mazel, D. (2006) · Nature Reviews Microbiology · doi:10.1038/nrmicro1462 · Cited by 1,107
Three Prochlorococcus Cyanophage Genomes: Signature Features and Ecological Interpretations
Sullivan, M. B., Coleman, M. L., Weigele, P., Rohwer, F., & Chisholm, S. W. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030144 · Cited by 554
Resistance integrons and super-integrons
Fluit, A. C., & Schmitz, F.-J. (2004) · Clinical Microbiology and Infection · doi:10.1111/j.1198-743x.2004.00858.x · Cited by 419
Improved properties of FLP recombinase evolved by cycling mutagenesis
Buchholz, F., Angrand, P.-O., & Stewart, A. F. (1998) · Nature Biotechnology · doi:10.1038/nbt0798-657 · Cited by 403
Identification and analysis of integrons and cassette arrays in bacterial genomes
Cury, J., Jové, T., Touchon, M., Néron, B., & Rocha, E. P. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw319 · Cited by 317
Metadata
- Authors
- Nunes-Duby, S. E., Kwon, H. J., Tirumalai, R. S., Ellenberger, T., & Landy, A.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 1998-01-01
- Volume
- 26
- Issue
- 2
- Pages
- 391-406
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2161620968
- Cited by
- 450
- References
- 93
- FWCI
- 17.07
- Type
- journal article
- Language
- en
- Open access
- bronze
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