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Human UP1 as a model for understanding purine recognition in the family of proteins containing the RNA recognition motif (RRM).

Myers JC, Shamoo Y
J Mol Biol 342 743-56 (2004)
Related entries: 1u1k, 1u1l, 1u1m, 1u1n, 1u1o, 1u1p, 1u1q

Cited: 35 times
EuropePMC logo PMID: 15342234

Abstract

Heterogeneous ribonucleoprotein A1 (hnRNP A1) is a prototype for the family of eukaryotic RNA processing proteins containing the common RNA recognition motif (RRM). The region consisting of residues 1-195 of hnRNP A1 is referred to as UP1. This region has two RRMs and has a high affinity for both single-stranded RNA and the human telomeric repeat sequence d(TTAGGG)(n). We have used UP1's novel DNA binding to investigate how RRMs bind nucleic acid bases through their highly conserved RNP consensus sequences. Nine complexes of UP1 bound to modified telomeric repeats were investigated using equilibrium fluorescence binding and X-ray crystallography. In two of the complexes, alteration of a guanine to either 2-aminopurine or nebularine resulted in an increase in K(d) from 88nM to 209nM and 316nM, respectively. The loss of these orienting interactions between UP1 and the substituted base allows it to flip between syn and anti conformations. Substitution of the same base with 7-deaza-guanine preserves the O6/N1 contacts but still increases the K(d) to 296nM and suggests that it is not simply the loss of affinity that gives rise to the base mobility, but also the stereochemistry of the specific contact to O6. Although these studies provide details of UP1 interactions to nucleic acids, three general observations about RRMs are also evident: (1) as suggested by informatic studies, main-chain to base hydrogen bonding makes up an important aspect of ligand recognition (2) steric clashes generated by modification of a hydrogen bond donor-acceptor pair to a donor-donor pair are poorly tolerated and (3) a conserved lysine position proximal to RNP-2 (K(106)-IFVGGI) orients the purine to allow stereochemical discrimination between adenine and guanine based on the 6-position. This single interaction is well-conserved in known RRM structures and appears to be a broad indicator for purine preference in the larger family of RRM proteins.

Reviews - 1u1r mentioned but not cited (3)

  1. Psychrophilic enzymes: from folding to function and biotechnology. Feller G. Scientifica (Cairo) 2013 512840 (2013)
  2. Idiosyncrasies of hnRNP A1-RNA recognition: Can binding mode influence function. Levengood JD, Tolbert BS. Semin Cell Dev Biol 86 150-161 (2019)
  3. hnRNP A/B Proteins: An Encyclopedic Assessment of Their Roles in Homeostasis and Disease. Thibault PA, Ganesan A, Kalyaanamoorthy S, Clarke JWE, Salapa HE, Levin MC. Biology (Basel) 10 712 (2021)

Articles - 1u1r mentioned but not cited (4)

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  2. Structural basis for terminal loop recognition and stimulation of pri-miRNA-18a processing by hnRNP A1. Kooshapur H, Choudhury NR, Simon B, Mühlbauer M, Jussupow A, Fernandez N, Jones AN, Dallmann A, Gabel F, Camilloni C, Michlewski G, Caceres JF, Sattler M. Nat Commun 9 2479 (2018)
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  4. The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins. Chakraborty S, Rendón-Ramírez A, Ásgeirsson B, Dutta M, Ghosh AS, Oda M, Venkatramani R, Rao BJ, Dandekar AM, Goñi FM. F1000Res 2 286 (2013)


Reviews citing this publication (5)

  1. Sequence-specific binding of single-stranded RNA: is there a code for recognition? Auweter SD, Oberstrass FC, Allain FH. Nucleic Acids Res 34 4943-4959 (2006)
  2. hnRNP A1: the Swiss army knife of gene expression. Jean-Philippe J, Paz S, Caputi M. Int J Mol Sci 14 18999-19024 (2013)
  3. Single-stranded DNA-binding proteins: multiple domains for multiple functions. Dickey TH, Altschuler SE, Wuttke DS. Structure 21 1074-1084 (2013)
  4. Heterogeneous nuclear ribonucleoprotein A1 in health and neurodegenerative disease: from structural insights to post-transcriptional regulatory roles. Bekenstein U, Soreq H. Mol Cell Neurosci 56 436-446 (2013)
  5. Single-Stranded DNA Binding Proteins and Their Identification Using Machine Learning-Based Approaches. Guo JT, Malik F. Biomolecules 12 1187 (2022)

Articles citing this publication (23)

  1. DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces. Tjong H, Zhou HX. Nucleic Acids Res 35 1465-1477 (2007)
  2. Protein-RNA interactions: exploring binding patterns with a three-dimensional superposition analysis of high resolution structures. Morozova N, Allers J, Myers J, Shamoo Y. Bioinformatics 22 2746-2752 (2006)
  3. Structural lability in stem-loop 1 drives a 5' UTR-3' UTR interaction in coronavirus replication. Li L, Kang H, Liu P, Makkinje N, Williamson ST, Leibowitz JL, Giedroc DP. J Mol Biol 377 790-803 (2008)
  4. Structure of Musashi1 in a complex with target RNA: the role of aromatic stacking interactions. Ohyama T, Nagata T, Tsuda K, Kobayashi N, Imai T, Okano H, Yamazaki T, Katahira M. Nucleic Acids Res 40 3218-3231 (2012)
  5. hnRNP A2, a potential ssDNA/RNA molecular adapter at the telomere. Moran-Jones K, Wayman L, Kennedy DD, Reddel RR, Sara S, Snee MJ, Smith R. Nucleic Acids Res 33 486-496 (2005)
  6. Structural basis for the dual RNA-recognition modes of human Tra2-β RRM. Tsuda K, Someya T, Kuwasako K, Takahashi M, He F, Unzai S, Inoue M, Harada T, Watanabe S, Terada T, Kobayashi N, Shirouzu M, Kigawa T, Tanaka A, Sugano S, Güntert P, Yokoyama S, Muto Y. Nucleic Acids Res 39 1538-1553 (2011)
  7. Tandem hnRNP A1 RNA recognition motifs act in concert to repress the splicing of survival motor neuron exon 7. Beusch I, Barraud P, Moursy A, Cléry A, Allain FH. Elife 6 e25736 (2017)
  8. Exposure of male rats to cyclophosphamide alters the chromatin structure and basic proteome in spermatozoa. Codrington AM, Hales BF, Robaire B. Hum Reprod 22 1431-1442 (2007)
  9. High-affinity interaction of hnRNP A1 with conserved RNA structural elements is required for translation and replication of enterovirus 71. Levengood JD, Tolbert M, Li ML, Tolbert BS. RNA Biol 10 1136-1145 (2013)
  10. Solution structure of the two RNA recognition motifs of hnRNP A1 using segmental isotope labeling: how the relative orientation between RRMs influences the nucleic acid binding topology. Barraud P, Allain FH. J Biomol NMR 55 119-138 (2013)
  11. Site-specific variations in RNA folding thermodynamics visualized by 2-aminopurine fluorescence. Ballin JD, Bharill S, Fialcowitz-White EJ, Gryczynski I, Gryczynski Z, Wilson GM. Biochemistry 46 13948-13960 (2007)
  12. Structure, stability and specificity of the binding of ssDNA and ssRNA with proteins. Pal A, Levy Y. PLoS Comput Biol 15 e1006768 (2019)
  13. Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe C. Edwards TE, Cekan P, Reginsson GW, Shelke SA, Ferré-D'Amaré AR, Schiemann O, Sigurdsson ST. Nucleic Acids Res 39 4419-4426 (2011)
  14. Unique proteomic features induced by a potential antiglioma agent, Nordy (dl-nordihydroguaiaretic acid), in glioma cells. Bian XW, Xu JP, Ping YF, Wang Y, Chen JH, Xu CP, Wu YZ, Wu J, Zhou XD, Chen YS, Shi JQ, Wang JM. Proteomics 8 484-494 (2008)
  15. RRM proteins interacting with the cap region of topoisomerase I. Trzcińska-Daneluti AM, Górecki A, Czubaty A, Kowalska-Loth B, Girstun A, Murawska M, Lesyng B, Staroń K. J Mol Biol 369 1098-1112 (2007)
  16. The Thermus thermophilus DEAD box helicase Hera contains a modified RNA recognition motif domain loosely connected to the helicase core. Rudolph MG, Klostermeier D. RNA 15 1993-2001 (2009)
  17. ATP regulates RNA-driven cold inducible RNA binding protein phase separation. Zhou Q, Usluer S, Zhang F, Lenard AJ, Bourgeois BMR, Madl T. Protein Sci 30 1438-1453 (2021)
  18. Immunogenicity of mammary tumor cells can be induced by shikonin via direct binding-interference with hnRNPA1. Yin SY, Efferth T, Efferth T, Jian FY, Chen YH, Liu CI, Wang AH, Chen YR, Hsiao PW, Yang NS. Oncotarget 7 43629-43653 (2016)
  19. Crystal structure of the human heterogeneous ribonucleoprotein A18 RNA-recognition motif. Coburn K, Melville Z, Aligholizadeh E, Roth BM, Varney KM, Carrier F, Pozharski E, Weber DJ. Acta Crystallogr F Struct Biol Commun 73 209-214 (2017)
  20. Recognition of essential purines by the U1A protein. Benitex Y, Baranger AM. BMC Biochem 8 22 (2007)
  21. hnRNPA1/UP1 Unfolds KRAS G-Quadruplexes and Feeds a Regulatory Axis Controlling Gene Expression. Ferino A, Marquevielle J, Choudhary H, Cinque G, Robert C, Bourdoncle A, Picco R, Mergny JL, Salgado GF, Xodo LE. ACS Omega 6 34092-34106 (2021)
  22. Phase Separation of Heterogeneous Nuclear Ribonucleoprotein A1 upon Specific RNA-Binding Observed by Magnetic Resonance. Ritsch I, Lehmann E, Emmanouilidis L, Yulikov M, Allain F, Jeschke G. Angew Chem Int Ed Engl 61 e202204311 (2022)
  23. Sequence- and structure-specific RNA oligonucleotide binding attenuates heterogeneous nuclear ribonucleoprotein A1 dysfunction. Clarke JP, Thibault PA, Fatima S, Salapa HE, Kalyaanamoorthy S, Ganesan A, Levin MC. Front Mol Biosci 10 1178439 (2023)


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