Solution structure of protein SRP19 of Archaeoglobus fulgidus signal recognition particle.
Protein SRP19 is an essential RNA-binding component of the signal recognition particle (SRP) in Archaea and Eucarya. A three-dimensional solution structure of the 104 residue SRP19 from the hyperthermophilic archaeon Archaeoglobus fulgidus, designated as Af19, was determined by NMR spectroscopy. Af19 contains three beta-strands, two alpha-helical regions, arranged in a betaalphabetabetaalpha topology, a 3(10) helix, and a disordered C-terminal tail. This fold is similar to the betaalphabetabetaalphabeta RNP motif present in numerous other RNA-binding proteins, which engage their cognate RNAs using conserved sequence motifs present within beta-strands 1 and 3. Mutagenesis studies of human SRP19, however, reveal the major contact sites with SRP RNA reside within loops 1, 3, and 4. These contacts were verified by the crystal structure of human SRP19 complexed to SRP RNA helix 6 reported subsequent to the submission of the manuscript. The crystal structure also reveals that, unlike canonical RNP motifs, SRP19 does not engage specific RNA bases through conserved sequence motifs present within beta-strands 1 and 3. Instead, SRP19 uses residues both within and flanking beta-strand 1 to stabilize the complex through direct and indirect contacts to the phosphate backbone of the tetraloop, leaving the bases of the tetraloop exposed. This, coupled with the fact that SRP19 appears relatively rigid and undergoes only minor changes in structure upon RNA binding, may underlie the molecular basis by which SRP19 functions to initiate SRP assembly.
Pakhomova
Olga N
ON
Department of Biochemistry, Center for Biomolecular Structure Analysis, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
Deep
Shashank
S
Huang
Qiaojia
Q
Zwieb
Christian
C
Hinck
Andrew P
AP
D000595:Amino Acid Sequence; D019843:Archaeal Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D019611:Archaeoglobus fulgidus / Q000737:chemistry* / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D018583:Pliability; D017433:Protein Structure, Secondary; D012313:RNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D018271:Signal Recognition Particle / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012996:Solutions; D013329:Structure-Activity Relationship; D013816:Thermodynamics
D019843:Archaeal Proteins; D016601:RNA-Binding Proteins; C117074:SRP19 protein, human; D018271:Signal Recognition Particle; D012996:Solutions; D012313:RNA