Contribution of the tyrosines to the structure and function of the human U1A N-terminal RNA binding domain.


Abstract

RNA binding domains (RBDs) are members of a large family of proteins that share minimal sequence conservation but adopt an alpha beta sandwich global fold. Defining the contributions of specific amino acids to RBD structure and RNA binding is critical to understanding the functions of these proteins. In these experiments with the human U1A N-terminal RNA binding domain (RBD1), the contributions from each of its four tyrosines to protein structure, stability, and RNA binding were measured. Each tyrosine was substituted with phenylalanine and one other selected residue, and the resulting proteins were characterized by chemical denaturation to measure their unfolding free energy, by binding free energies to the wild-type RNA hairpin, and by 19F NMR to probe for structural changes. Features of the protein identified in these experiments include a possible tyrosine/lysine contact in an alpha-helix, which may be an example of an energetically favorable aromatic/amino side chain interaction. One long loop of the protein, which shows unusual 15N backbone and tyrosine side-chain dynamics, is implicated in protein:protein association. The diverse interactions of the four tyrosine residues in the organization of RBD1 illustrate how each member of this family of proteins will have unique molecular details that contribute to function. Study holds ProTherm entries: 8731, 8732, 8733, 8734, 8735, 8736, 8737, 8738, 8739 Extra Details: N-terminal RNA binding domain NMR; protein sturucture and energetics; RNA binding domain

Submission Details

ID: JihoeLER4

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:36 p.m.

Version: 1

Publication Details
Kranz JK;Lu J;Hall KB,Protein Sci. (1996) Contribution of the tyrosines to the structure and function of the human U1A N-terminal RNA binding domain. PMID:8844847
Additional Information

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
4PKD 2014-05-14T00:00:00+0000 2.5 U1-70k in complex with U1 snRNA stem-loops 1 and U1-A RRM in complex with stem-loop 2
1AUD 1997-08-22T00:00:00+0000 0 U1A-UTRRNA, NMR, 31 STRUCTURES
1DRZ 1998-09-01T00:00:00+0000 2.3 U1A SPLICEOSOMAL PROTEIN/HEPATITIS DELTA VIRUS GENOMIC RIBOZYME COMPLEX
1DZ5 2000-02-16T00:00:00+0000 0 The NMR structure of the 38KDa U1A protein-PIE RNA complex reveals the basis of cooperativity in regulation of polyadenylation by human U1A protein
1FHT 1996-02-21T00:00:00+0000 0 RNA-BINDING DOMAIN OF THE U1A SPLICEOSOMAL PROTEIN U1A117, NMR, 43 STRUCTURES
1M5K 2002-07-09T00:00:00+0000 2.4 Crystal structure of a hairpin ribozyme in the catalytically-active conformation
1M5O 2002-07-09T00:00:00+0000 2.2 Transition State Stabilization by a Catalytic RNA
1M5P 2002-07-09T00:00:00+0000 2.6 Transition State Stabilization by a Catalytic RNA
1M5V 2002-07-09T00:00:00+0000 2.4 Transition State Stabilization by a Catalytic RNA
1NU4 2003-01-30T00:00:00+0000 1.8 U1A RNA binding domain at 1.8 angstrom resolution reveals a pre-organized C-terminal helix

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
91.6 U1 small nuclear ribonucleoprotein A P45429 SNRPA_XENLA
94.7 U1 small nuclear ribonucleoprotein A Q62189 SNRPA_MOUSE
100.0 U1 small nuclear ribonucleoprotein A Q06AA4 SNRPA_PIG
100.0 U1 small nuclear ribonucleoprotein A P09012 SNRPA_HUMAN
100.0 U1 small nuclear ribonucleoprotein A Q2KIR1 SNRPA_BOVIN