Escherichia coli signal peptide peptidase A is a serine-lysine protease with a lysine recruited to the nonconserved amino-terminal domain in the S49 protease family

Biochemistry

Volumn 47, Issue 24, 2008, Pages 6361-6369

  Wang, Peng ^a   Shim, Eunjung ^a   Cravatt, Benjamin ^c   Jacobsen, Richard ^d   Schoeniger, Joe ^d   Kim, Apollos C ^b   Paetzel, Mark ^b   Dalbey, Ross E ^a  

^a OHIO STATE UNIVERSITY   (United States)

^b SIMON FRASER UNIVERSITY   (Canada)

^c SCRIPPS RESEARCH INSTITUTE   (United States)

^d SANDIA NATIONAL LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINATION; AMINES; BIOMOLECULES; COENZYMES; ESCHERICHIA COLI; GENE ENCODING; MUTAGENESIS; PORT TERMINALS; PROTEINS; TISSUE; WATER POLLUTION;

ALKALINE PHOSPHATASE (ALPASE); AMERICAN CHEMICAL SOCIETY (ACS); AMINO-TERMINAL DOMAIN (ATD); C-TERMINAL DOMAIN (CTD); CARBOXYL TERMINAL; CARBOXYL TERMINAL DOMAIN (CTD); E. COLI; ENZYMATIC ACTIVITIES; FUSION EXPERIMENTS; GENERAL (CO); HISTIDINE RESIDUES; HYDROLASE; N TERMINAL DOMAIN (NTD); PERIPLASMIC SPACE; REACTIVITY (CHEMICAL); SERINE PROTEASES; SIGNAL PEPTIDASE; SIGNAL PEPTIDE (SP); SITE DIRECTED MUTAGENESIS; TRANSMEMBRANE SEGMENTS;

AMINO ACIDS;

ALKALINE PHOSPHATASE; AMINOPEPTIDASE; BIOTIN; HYBRID PROTEIN; LYSINE; MEMBRANE PROTEIN; SERINE; SERINE 409; SIGNAL PEPTIDE;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; ENZYME ACTIVITY; ESCHERICHIA COLI; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DEGRADATION;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; BINDING SITES; CATALYSIS; CONSERVED SEQUENCE; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; LYSINE; MEMBRANE PROTEINS; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; PROTEIN STRUCTURE, TERTIARY; SEQUENCE HOMOLOGY, AMINO ACID; SERINE; SERINE ENDOPEPTIDASES;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 45749095796     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi800657p     Document Type: Article

References (29)

1. Paetzel, M., Karla, A., Strynadka, N. C., and Dalbey, R. E. (2002) Signal peptidases. Chem. Rev. 102, 4549-4580.
2. Zwizinski, C., and Wickner, W. (1980) Purification and characterization of leader (signal) peptidase from Escherichia coli. J. Biol. Chem. 255, 7973-7977.
3. Hussain, M., Ozawa, Y., Ichihara, S., and Mizushima, S. (1982) Signal peptide digestion in Escherichia coli. Effect of protease inhibitors on hydrolysis of the cleaved signal peptide of the major outer-membrane lipoprotein. Eur. J. Biochem. 129, 233-239.
4. Ichihara, S., Beppu, N., and Mizushima, S. (1984) Protease IV, a cytoplasmic membrane protein of Escherichia coli, has signal peptide peptidase activity. J. Biol. Chem. 259, 9853-9857.
5. Pacaud, M. (1982) Purification and characterization of two novel proteolytic enzymes in membranes of Escherichia coli. Protease IV and protease V. J. Biol. Chem. 257, 4333-4339.
6. Ichihara, S., Suzuki, T., Suzuki, M., and Mizushima, S. (1986) Molecular cloning and sequencing of the sppA gene and characterization of the encoded protease IV, a signal peptide peptidase, of Escherichia coli. J. Biol. Chem. 261, 9405-9411.
7. Rawlings, N. D., and Barrett, A. J. (1999) MEROPS: The peptidase database. Nucleic Acids Res. 27, 325-331.
8. Baird, L., Lipinska, B., Raina, S., and Georgopoulos, C. (1991) Identification of the Escherichia coli sohB gene, a multicopy suppressor of the HtrA (DegP) null phenotype. J. Bacteriol. 173, 5763-5770.
9. Liu, J., and Mushegian, A. (2004) Displacements of prohead protease genes in the late operons of double-stranded-DNA bacteriophages. J. Bacteriol. 186, 4369-4375.
10. Yokoyama, H., and Matsui, I. (2005) A novel thermostable membrane protease forming an operon with a stomatin homolog from the hyperthermophilic archaebacterium Pyrococcus horikoshii. J Biol. Chem. 280, 6588-6594.
11. Matsumi, R., Atomi, H., and Imanaka, T. (2005) Biochemical properties of a putative signal peptide peptidase from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J. Bacteriol. 187, 7072-7080.
12. Matsumi, R., Atomi, H., and Imanaka, T. (2006) Identification of the amino acid residues essential for proteolytic activity in an archaeal signal peptide peptidase. J. Biol. Chem. 281, 10533-10539.
13. Paetzel, M., Dalbey, R. E., and Strynadka, N. C. (1998) Crystal structure of a bacterial signal peptidase in complex with a β-lactam inhibitor. Nature 396, 186-190. (Erratum: (1998) Nature 396, 707).
14. Slilaty, S. N., and Little, J. W. (1987) Lysine-156 and serine-119 are required for LexA repressor cleavage: A possible mechanism. Proc. Natl. Acad. Sci. U.S.A. 84, 3987-3991.
15. Peat, T. S., Frank, E. G., McDonald, J. P., Levine, A. S., Woodgate, R., and Hendrickson, W. A. (1996) Structure of the UmuD′ protein and its regulation in response to DNA damage. Nature 380, 727-730.
16. Silber, K. R., Keiler, K. C., and Sauer, R. T. (1992) Tsp: A tail-specific protease that selectively degrades proteins with nonpolar C termini. Proc. Natl. Acad. Sci. U.S.A. 89, 295-299.
17. Rotanova, T. V., Mel'nikov, E. E., and Tsirul'nikov, K. B. (2003) [Catalytic dyad Ser-Lys at the active site of Escherichia coli ATP-dependent Lon-proteinase]. Bioorg. Khim. 29, 97-99.
18. Feldman, A. R., Lee, J., Delmas, B., and Paetzel, M. (2006) Crystal structure of a novel viral protease with a serine/lysine catalytic dyad mechanism. J. Mol. Biol. 358, 1378-1389.
19. Johnston, S., Lee, J. H., and Ray, D. S. (1985) High-level expression of M13 gene II protein from an inducible polycistronic messenger RNA. Gene 34, 137-145.
20. Liu, Y., Patricelli, M. P., and Cravatt, B. F. (1999) Activity-based protein profiling: The serine hydrolases. Proc. Natl. Acad. Sci. U.S.A. 96, 14694-14699.
21. San Millan, J. L., Boyd, D., Dalbey, R., Wickner, W., and Beckwith, J. (1989) Use of phoA fusions to study the topology of the Escherichia coli inner membrane protein leader peptidase. J. Bacteriol. 171, 5536-5541.
22. Michaelis, S., Inouye, H., Oliver, D., and Beckwith, J. (1983) Mutations that alter the signal sequence of alkaline phosphatase in Escherichia coli. J. Bacteriol. 154, 366-374.
23. Krogh, A., Larsson, B., von Heijne, G., and Sonnhammer, E. L. (2001) Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J. Mol. Biol. 305, 567-580.
24. von Heijne, G. (1992) Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. J. Mol. Biol. 225, 487-494.
25. Manoil, C., and Beckwith, J. (1986) A genetic approach to analyzing membrane protein topology. Science 233, 1403-1408.
26. Kim, A. C., Oliver, D. C., and Paetzel, M. (2008) Crystal structure of a bacterial signal peptide peptidase. J. Mol. Biol. 376, 352-366.
27. VanValkenburgh, C., Chen, X., Mullins, C., Fang, H., and Green, N. (1999) The catalytic mechanism of endoplasmic reticulum signal peptidase appears to be distinct from most eubacterial signal peptidases. J. Biol. Chem. 274, 11519-11525.
28. Weihofen, A., Binns, K., Lemberg, M. K., Ashman, K., and Martoglio, B. (2002) Identification of signal peptide peptidase, a presenilin-type aspartic protease. Science 296, 2215-2218.
29. Yokoyama, H., Matsui, E., Akiba, T., Harata, K., and Matsui, I. (2006) Molecular structure of a novel membrane protease specific for a stomatin homolog from the hyperthermophilic archaeon Pyrococcus horikoshii. J. Mol. Biol. 358, 1152-1164.