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
1FHT 1996-07-11 RNA-BINDING DOMAIN OF THE U1A SPLICEOSOMAL PROTEIN U1A117, NMR, 43 STRUCTURES
2U1A 1997-09-26 RNA BINDING DOMAIN 2 OF HUMAN U1A PROTEIN, NMR, 20 STRUCTURES
1AUD 1998-02-25 U1A-UTRRNA, NMR, 31 STRUCTURES
1DZ5 2000-03-29 The NMR structure of the 38KDa U1A protein-PIE RNA complex reveals the basis of cooperativity in regulation of polyadenylation by human U1A protein
2A3J 2006-06-06 Structure of URNdesign, a complete computational redesign of human U1A protein
1NU4 2003-02-14 1.8 U1A RNA binding domain at 1.8 angstrom resolution reveals a pre-organized C-terminal helix
1URN 1996-03-08 1.92 U1A MUTANT/RNA COMPLEX + GLYCEROL
4YB1 2015-04-15 2.08 20A Mutant c-di-GMP Vc2 Riboswitch bound with 3',3'-cGAMP
1SJ3 2004-05-18 2.2 Hepatitis Delta Virus Gemonic Ribozyme Precursor, with Mg2+ Bound
1M5O 2002-10-12 2.2 Transition State Stabilization by a Catalytic RNA
3EGZ 2008-10-28 2.2 Crystal structure of an in vitro evolved tetracycline aptamer and artificial riboswitch
5DDP 2015-12-23 2.3 L-glutamine riboswitch bound with L-glutamine
3MXH 2010-08-25 2.3 Native structure of a c-di-GMP riboswitch from V. cholerae
1DRZ 1999-02-16 2.3 U1A SPLICEOSOMAL PROTEIN/HEPATITIS DELTA VIRUS GENOMIC RIBOZYME COMPLEX
4PR6 2014-10-29 2.3 A Second Look at the HDV Ribozyme Structure and Dynamics.
4PRF 2014-10-29 2.39 A Second Look at the HDV Ribozyme Structure and Dynamics.
2OIH 2007-03-27 2.4 Hepatitis Delta Virus gemonic ribozyme precursor with C75U mutation and bound to monovalent cation Tl+
1M5K 2002-08-02 2.4 Crystal structure of a hairpin ribozyme in the catalytically-active conformation
1OIA 2003-06-26 2.4 U1A rnp domain 1-95
5DDQ 2015-12-23 2.4 L-glutamine riboswitch bound with L-glutamine soaked with Mn2+
1M5V 2002-10-12 2.4 Transition State Stabilization by a Catalytic RNA
1VC0 2004-05-18 2.5 Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U mutaion, in Imidazole and Sr2+ solution
2NZ4 2007-01-16 2.5 Structural investigation of the GlmS ribozyme bound to its catalytic cofactor
4PKD 2014-12-31 2.5 U1-70k in complex with U1 snRNA stem-loops 1 and U1-A RRM in complex with stem-loop 2
1M5P 2002-10-12 2.6 Transition State Stabilization by a Catalytic RNA
5DDR 2015-12-23 2.61 L-glutamine riboswitch bound with L-glutamine soaked with Cs+
1SJ4 2004-05-18 2.7 Crystal structure of a C75U mutant Hepatitis Delta Virus ribozyme precursor, in Cu2+ solution
3IRW 2009-11-10 2.7 Structure of a c-di-GMP riboswitch from V. cholerae
3UD4 2012-01-04 2.7 The C92U mutant c-di-GMP-I riboswitch bound to GpA
1VBX 2004-05-18 2.7 Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U mutaion, in EDTA solution
1SJF 2004-05-18 2.75 Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U mutaion, in Cobalt Hexammine solution
3UCU 2012-01-04 2.8 The c-di-GMP-I riboswitch bound to pGpG
3CUL 2008-06-24 2.8 Aminoacyl-tRNA synthetase ribozyme
3UCZ 2012-01-04 2.8 The c-di-GMP-I riboswitch bound to GpG
1VBZ 2004-05-18 2.8 Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U mutaion, in Ba2+ solution
1VC6 2004-05-18 2.8 Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Product with C75U Mutaion, cleaved in Imidazole and Mg2+ solutions
3L3C 2009-12-29 2.85 Crystal structure of the Bacillus anthracis glmS ribozyme bound to Glc6P
3MUM 2010-08-25 2.9 Crystal Structure of the G20A mutant c-di-GMP riboswith bound to c-di-GMP
2OJ3 2007-03-27 2.9 Hepatitis Delta Virus ribozyme precursor structure, with C75U mutation, bound to Tl+ and cobalt hexammine (Co(NH3)63+)
1VBY 2004-05-18 2.9 Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U mutaion, and Mn2+ bound
3G9C 2009-11-03 2.9 Crystal structure of the product Bacillus anthracis glmS ribozyme
4C4W 2014-02-12 2.95 Structure of a rare, non-standard sequence k-turn bound by L7Ae protein
5FJ4 2016-05-25 2.95 Structure of the standard kink turn HmKt-7 as stem loop bound with U1A and L7Ae proteins
3HHN 2009-11-24 2.99 Crystal structure of class I ligase ribozyme self-ligation product, in complex with U1A RBD
3MUT 2010-08-25 3.0 Crystal Structure of the G20A/C92U mutant c-di-GMP riboswith bound to c-di-GMP
3G8T 2009-11-03 3.0 Crystal structure of the G33A mutant Bacillus anthracis glmS ribozyme bound to GlcN6P
3CUN 2008-06-24 3.0 Aminoacyl-tRNA synthetase ribozyme
3MUR 2010-08-25 3.0 Crystal Structure of the C92U mutant c-di-GMP riboswith bound to c-di-GMP
3G96 2009-11-03 3.01 Crystal structure of the Bacillus anthracis glmS ribozyme bound to MaN6P
1U6B 2004-08-10 3.1 CRYSTAL STRUCTURE OF A SELF-SPLICING GROUP I INTRON WITH BOTH EXONS
5DDO 2015-12-23 3.1 Structural and Dynamic Basis for Low Affinity-High Selectivity Binding of L-glutamine by the Gln-riboswitch
3K0J 2009-12-22 3.1 Crystal structure of the E. coli ThiM riboswitch in complex with thiamine pyrophosphate and the U1A crystallization module
3G8S 2009-11-03 3.1 Crystal structure of the pre-cleaved Bacillus anthracis glmS ribozyme
3UD3 2012-01-04 3.1 The C92U mutant c-di-GMP-I riboswitch bound to pGpA
4W90 2014-10-15 3.12 Crystal structure of Bacillus subtilis cyclic-di-AMP riboswitch ydaO
3R1L 2011-08-31 3.12 Crystal structure of the Class I ligase ribozyme-substrate preligation complex, C47U mutant, Mg2+ bound
3R1H 2011-08-31 3.15 Crystal structure of the Class I ligase ribozyme-substrate preligation complex, C47U mutant, Ca2+ bound
3IWN 2009-11-10 3.2 Co-crystal structure of a bacterial c-di-GMP riboswitch
3MUV 2010-08-25 3.2 Crystal Structure of the G20A/C92U mutant c-di-GMP riboswith bound to c-di-AMP
4W92 2014-10-22 3.21 Crystal structure of Bacillus subtilis cyclic-di-AMP riboswitch ydaO
6QX9 2019-04-17 3.28 Structure of a human fully-assembled precatalytic spliceosome (pre-B complex).
3BO2 2008-04-01 3.31 A relaxed active site following exon ligation by a group I intron
3BO4 2008-04-01 3.33 A relaxed active site following exon ligation by a group I intron
1ZZN 2005-08-30 3.37 Crystal structure of a group I intron/two exon complex that includes all catalytic metal ion ligands.
1VC5 2004-05-18 3.4 Crystal Structure of the Wild Type Hepatitis Delta Virus Gemonic Ribozyme Precursor, in EDTA solution
3BO3 2008-04-01 3.4 A relaxed active site following exon ligation by a group I intron
3P49 2011-04-06 3.55 Crystal Structure of a Glycine Riboswitch from Fusobacterium nucleatum
3IIN 2010-03-09 4.18 Plasticity of the kink turn structural motif
3PGW 2010-12-29 4.4 Crystal structure of human U1 snRNP

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