Identification of an RNA-binding-loop in the N-terminal region of signal-recognition-particle protein SRP19

Shaun D. Black, Krishne Gowda, Kimberly Chittenden, Kerfoot P. Walker, Christian W Zwieb

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

Protein SRP19 is a 144-amino-acid polypeptide that associates intimately with the signal-recognition particle RNA (SRP RNA) and serves as an important structural and functional component of the SRP. We investigated the structure and RNA-binding activity of the human SRP19 protein by the use of comparative sequence analysis, high-stringency structure prediction, proteolytic susceptibility, and site-directed mutagenesis. SRP19 was found to consist of two distinct regions (called N-terminal and C-terminal regions) that are separated by a boundary of approximately 12-15 amino acid residues. Both regions contain an α-helix and several β-strands that are connected by loops or turns. In agreement with the hypothetical model, proteolytic susceptibility demonstrated the predominant accessibility of two sites: one in a surface loop of the N-terminal region (YLNNKKTIAEGR33), and another site in the C-terminal tail at residues L129 and E133. The RNA-binding activities of mutant polypeptides with changes of conserved lysines and arginines (mutants K27Q, R33Q and R34Q) demonstrated that the proteolytically accessible loop of the N-terminal region is in direct contact with the SRP RNA. In contrast, alteration of a certain basic amino acid residues in the C- terminal region (R83, K116 and R118), as well as a deletion of four amino acid residues located at the boundary between the two regions, had no effect on the RNA-binding ability. The structural model that emerges from our data is thematically similar to that of ribosomal protein S5, the N-domain of which contains a loop motif believed to interact with double-stranded RNA. The presence of a similar structural feature in protein SRP19 has significant implications for the structure and function of the SRP19-RNA complex.

Original languageEnglish (US)
Pages (from-to)564-572
Number of pages9
JournalEuropean Journal of Biochemistry
Volume245
Issue number3
StatePublished - 1997
Externally publishedYes

Fingerprint

Signal Recognition Particle
RNA
Proteins
Amino Acids
Basic Amino Acids
Mutagenesis
Peptides
Double-Stranded RNA
Structural Models
Site-Directed Mutagenesis
Lysine
Sequence Analysis
Arginine

Keywords

  • protein secondary structure
  • RNA-protein interaction
  • signal-recognition particle

ASJC Scopus subject areas

  • Biochemistry

Cite this

Black, S. D., Gowda, K., Chittenden, K., Walker, K. P., & Zwieb, C. W. (1997). Identification of an RNA-binding-loop in the N-terminal region of signal-recognition-particle protein SRP19. European Journal of Biochemistry, 245(3), 564-572.

Identification of an RNA-binding-loop in the N-terminal region of signal-recognition-particle protein SRP19. / Black, Shaun D.; Gowda, Krishne; Chittenden, Kimberly; Walker, Kerfoot P.; Zwieb, Christian W.

In: European Journal of Biochemistry, Vol. 245, No. 3, 1997, p. 564-572.

Research output: Contribution to journalArticle

Black, SD, Gowda, K, Chittenden, K, Walker, KP & Zwieb, CW 1997, 'Identification of an RNA-binding-loop in the N-terminal region of signal-recognition-particle protein SRP19', European Journal of Biochemistry, vol. 245, no. 3, pp. 564-572.
Black, Shaun D. ; Gowda, Krishne ; Chittenden, Kimberly ; Walker, Kerfoot P. ; Zwieb, Christian W. / Identification of an RNA-binding-loop in the N-terminal region of signal-recognition-particle protein SRP19. In: European Journal of Biochemistry. 1997 ; Vol. 245, No. 3. pp. 564-572.
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N2 - Protein SRP19 is a 144-amino-acid polypeptide that associates intimately with the signal-recognition particle RNA (SRP RNA) and serves as an important structural and functional component of the SRP. We investigated the structure and RNA-binding activity of the human SRP19 protein by the use of comparative sequence analysis, high-stringency structure prediction, proteolytic susceptibility, and site-directed mutagenesis. SRP19 was found to consist of two distinct regions (called N-terminal and C-terminal regions) that are separated by a boundary of approximately 12-15 amino acid residues. Both regions contain an α-helix and several β-strands that are connected by loops or turns. In agreement with the hypothetical model, proteolytic susceptibility demonstrated the predominant accessibility of two sites: one in a surface loop of the N-terminal region (YLNNKKTIAEGR33), and another site in the C-terminal tail at residues L129 and E133. The RNA-binding activities of mutant polypeptides with changes of conserved lysines and arginines (mutants K27Q, R33Q and R34Q) demonstrated that the proteolytically accessible loop of the N-terminal region is in direct contact with the SRP RNA. In contrast, alteration of a certain basic amino acid residues in the C- terminal region (R83, K116 and R118), as well as a deletion of four amino acid residues located at the boundary between the two regions, had no effect on the RNA-binding ability. The structural model that emerges from our data is thematically similar to that of ribosomal protein S5, the N-domain of which contains a loop motif believed to interact with double-stranded RNA. The presence of a similar structural feature in protein SRP19 has significant implications for the structure and function of the SRP19-RNA complex.

AB - Protein SRP19 is a 144-amino-acid polypeptide that associates intimately with the signal-recognition particle RNA (SRP RNA) and serves as an important structural and functional component of the SRP. We investigated the structure and RNA-binding activity of the human SRP19 protein by the use of comparative sequence analysis, high-stringency structure prediction, proteolytic susceptibility, and site-directed mutagenesis. SRP19 was found to consist of two distinct regions (called N-terminal and C-terminal regions) that are separated by a boundary of approximately 12-15 amino acid residues. Both regions contain an α-helix and several β-strands that are connected by loops or turns. In agreement with the hypothetical model, proteolytic susceptibility demonstrated the predominant accessibility of two sites: one in a surface loop of the N-terminal region (YLNNKKTIAEGR33), and another site in the C-terminal tail at residues L129 and E133. The RNA-binding activities of mutant polypeptides with changes of conserved lysines and arginines (mutants K27Q, R33Q and R34Q) demonstrated that the proteolytically accessible loop of the N-terminal region is in direct contact with the SRP RNA. In contrast, alteration of a certain basic amino acid residues in the C- terminal region (R83, K116 and R118), as well as a deletion of four amino acid residues located at the boundary between the two regions, had no effect on the RNA-binding ability. The structural model that emerges from our data is thematically similar to that of ribosomal protein S5, the N-domain of which contains a loop motif believed to interact with double-stranded RNA. The presence of a similar structural feature in protein SRP19 has significant implications for the structure and function of the SRP19-RNA complex.

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