X-ray structure of aminopeptidase A from Escherichia coli and a model for the nucleoprotein complex in Xer site-specific recombination

EMBO Journal

Volumn 18, Issue 16, 1999, Pages 4513-4522

  Sträter, Norbert ^a   Sherratt, David J ^b   Colloms, Sean D ^b  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

DNA looping; DNA binding proteins; Protein crystallography; Protein protein complexes; Site specific recombination

Indexed keywords

BACTERIAL ENZYME; CYTOSOL AMINOPEPTIDASE; DNA BINDING PROTEIN; GLUTAMYL AMINOPEPTIDASE; NUCLEOPROTEIN; REPRESSOR PROTEIN;

AMINO TERMINAL SEQUENCE; ARTICLE; BACTERIAL GENE; CONTROLLED STUDY; DNA BINDING; ENZYME STRUCTURE; GENETIC RECOMBINATION; MOLECULAR MODEL; NONHUMAN; OPERON; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; STEREOCHEMISTRY; TRANSCRIPTION REGULATION; X RAY CRYSTALLOGRAPHY;

AMINOPEPTIDASES; ANIMALS; BACTERIAL PROTEINS; BASE SEQUENCE; CATTLE; CRYSTALLOGRAPHY, X-RAY; DNA; DNA NUCLEOTIDYLTRANSFERASES; DNA, COMPLEMENTARY; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GLUTAMYL AMINOPEPTIDASE; INTEGRASES; LEUCYL AMINOPEPTIDASE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEOPROTEINS; PROTEIN BINDING; PROTEIN CONFORMATION; RECOMBINASES; RECOMBINATION, GENETIC; REPRESSOR PROTEINS;

EID: 0344931801     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/18.16.4513     Document Type: Article

References (37)

1. Alén, C., Sherratt, D.J. and Colloms, S.D. (1997) Direct interaction of aminopeptidase A with recombination site DNA in Xer site-specific recombination. EMBO J., 16, 5188-5197.
2. Blakely, G., May, G., McCulloch, R., Arciszewska, L., Burke, M., Lovett, S. and Sherratt, D.J. (1993) Two related recombinases are required for site-specific recombination at dif and cer in Escherichia coli K12. Cell, 75, 351-361.
3. Brünger, A.T. et al. (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr., D54, 905-921.
4. Burley, S.K., David, P.R., Taylor, A. and Lipscomb, W.N. (1990) Molecular structure of leucine aminopeptidase at 2.7 Å resolution. Proc. Natl Acad. Sci. USA, 87, 6878-6882.
5. (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr., D50, 760-763.
6. Charlier, D., Hassanzadeh, G., Kholti, A., Gigot, D., Piérard, A. and Glansdorff, N. (1995) carP, involved in pyrimidine regulation of the Escherichia coli carbamoylphosphate synthetase operon encodes a sequence-specific DNA-binding protein identical to XerB and PepA, also required for resolution of ColE1 multimers. J. Mol. Biol., 250, 392-406.
7. Colloms, S.D., Sykora, P., Szatmari, G. and Sherratt, D.J. (1990) Recombination at ColE1 cer requires the Escherichia coli xerC gene product, a member of the λ integrase family of site-specific recombinases. J. Bacteriol., 172, 6973-6980.
8. Colloms, S.D., McCulloch, R., Grant, K., Neilson, L. and Sherratt, D.J. (1996) Xer-mediated site-specific recombination in vitro. EMBO J., 15, 1172-1181.
9. Colloms, S.D., Bath, J. and Sherratt, D.J. (1997) Topological selectivity in Xer site-specific recombination. Cell, 88, 855-864.
10. Gilson, M.K., Sharp, K.A. and Honig, B.H. (1987) Calculating the electrostatic potential of molecules in solution: method and error assessment. J. Comp. Chem., 9, 327-335.
11. Gopaul, D.N., Guo, F. and van Duyne, G.D. (1998) Structure of the Holliday junction intermediate in Cre-lox P site-specific recombination. EMBO J., 17, 4175-4187.
12. Hayes, F., Hallet, B. and Cao, Y. (1997) Insertion mutagenesis as a tool in the modification of protein function. Extended substrate specificity conferred by pentapeptide insertions in the omega-loop of TEM-1 β-lactamase. J. Biol. Chem., 272, 28833-28836.
13. Hodgman, T.C., Griffiths, H. and Summers, D.K. (1998) Nucleoprotein architecture and ColE1 dimer resolution: a hypothesis. Mol. Microbiol., 29, 545-558.
14. Holm, L. and Sander, C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233, 123-138.
15. Jones, T.A., Zou, J.-Y., Cowan, S.W. and Kjeldgaard, M. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr., A47, 110-119.
16. Kholti, A., Charlier, D., Gigot, D., Huysveld, N., Roovers, M. and Glansdorff, N. (1998) pyrH-encoded UMP-kinase directly participates in pyrimidine-specific modulation of promoter activity in Escherichia coli. J. Mol. Biol. 280, 571-582.
17. Kim, H. and Lipscomb, W.N. (1994) Structure and mechanism of bovine lens leucine aminopeptidase. Adv. Enzymol., 68, 153-213.
18. Kraulis, P.J. (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr., 24, 946-950.
19. Luger, K., Mäder, A.W., Richmond, R.K., Sargent, D.F. and Richmond, T.J. (1997) Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature, 389, 251-260.
20. Macke, T. and Case, D.A. (1998) Modeling unusual nucleic acid structures. In Leontes, N.B. and SantaLucia, J. (eds), Molecular Modeling of Nucleic Acids. American Chemical Society, Washington, DC, pp.379-393.
21. McCulloch, R., Burke, M.E. and Sherratt, D.J. (1994) Peptidase activity of Escherichia coli aminopeptidase A is not required for its role in Xer site-specific recombination. Mol. Microbiol, 12, 241-251.
22. Merritt, E.A. and Bacon, D.J. (1997) Raster3D: photorealistic molecular graphics. Methods Enzymol., 277, 505-524.
23. Navaza, J. (1994) AMoRe: an automated package for molecular replacement. Acta Crystallogr., A50, 157-163.
24. Ni, J., Sakanyan, V., Charlier, D., Glansdorff, N. and van Duyne, G.D. (1999) Structure of the arginine represser from Bacillus stearothermophilus. Nature Struct. Biol., 6, 427-432.
25. Nicholls, A., Sharp, K. and Honig, B.H. (1991) Protein folding and association; insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins, 11, 281-296.
26. Otwinowski, Z. (1993) Data Collection and Processing. SERC Daresbury DL/SCI/R34, pp. 56-62.
27. Rice, P.A. and Steitz, T.A. (1994) Model for a DNA-mediated synaptic complex suggested by crystal packing of γδ resolvase subunits. EMBO J., 13, 1514-1524.
28. Stirling, C.J., Szatmari, G., Stewart, G., Smith, M.C.M. and Sherratt, D.J. (1988) The arginine represser is essential for plasmid-stabilising site-specific recombination at the ColE1 cer locus. EMBO J., 7, 4389-4395.
29. Stirling, C.J., Colloms, S.D., Collins, J.F., Szatmari, G. and Sherratt, D.J. (1989) xerB, an Escherichia coli gene required for plasmid ColE1 site-specific recombination, is identical to pepA, encoding aminopeptidase A, a protein with substantial similarity to bovine lens leucine aminopeptidase. EMBO J., 8, 1623-1627.
30. Sträter, N. and Lipscomb, W.N. (1995a) Two-metal ion mechanism of bovine lens leucine aminopeptidase: active site solvent structure and binding mode of L-leucinal, a gem-diolate transition state analogue, by X-ray crystallography. Biochemistry, 34, 14792-14800.
31. Sträter, N. and Lipscomb, W.N. (1995b) Transition state analogue L-leucinephosphonic acid bound to bovine lens leucine aminopeptidase: X-ray structure at 1.65 Å resolution in a new crystal form. Biochemistry, 34, 9200-9210.
32. Sträter, N. and Lipscomb, W.N. (1998) Leucyl aminopeptidase (animal and plant). In Barrett, A.J., Rawlings, N.D. and Woessner, J.F. (eds), Handbook of Proteolytic Enzymes. Academic Press, New York, NY, pp. 1384-1389.
33. Subramanya, H.S., Arciszewska, L.K., Baker, R.A., Bird, L.E., Sherratt, D.J. and Wigley, D.B. (1997) Crystal structure of the site-specific recombinase, XerD. EMBO J., 16, 5178-5187.
34. Summers, D.K. and Sherratt, D.J. (1984) Multimerisation of high copy number plasmids causes instability: ColE1 encodes a determinant for plasmid monomerisation and stability. Cell, 36, 1097-1103.
35. Sunnerhagen, M., Nilges, M., Otting, G. and Carey, J. (1997) Solution structure of the DNA-binding domain and model for the complex of multifunctional hexameric arginine repressor with DNA. Nature Struct. Biol., 4, 819-826.
36. van Duyne, G.D., Ghosh, G., Maas, W.K. and Sigler, P.B. (1996) Structure of the oligomerization and L-arginine binding domain of the arginine repressor of Escherichia coli. J. Mol. Biol., 256, 377-391.
37. Vogt, V.M. (1970) Purification and properties of an aminopeptidase from Escherichia coli. J. Biol. Chem., 245, 4760-4769.