User:Dzmitry Mukha/sandbox1

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Nucleic acid binding mechanism of hnRNP A1

hnRNP A1 (alternative gene names: ALS19, ALS20, HNRPA1, IBMPFD3, HNRPA1L3) is a member of A/B subfamily of heterogeneous nuclear ribonucleoproteins (hnRNPs). The hnRNPs are RNA binding proteins and they complex with heterogeneous nuclear RNA (hnRNA). hnRNP A1 is involved in the packaging of premature mRNA into hnRNP particles and transport of poly(A) mRNA from the nucleus to the cytoplasm. hnRNP A1 has been characterized as a component of protein complexes bound to premature mRNA (hnRNP complexes). hnRNP A1 is one of the most abundant and best-characterized components of hnRNP complexes. Human hnRNP functions also in telomere length regulation and miRNA biogenesis. It may play a role in the replication of RNA viruses.

Contents 1 Nucleic acid binding mechanism of hnRNP A1 2 Structure overview 3 Binding mechanism 4 Conservative residues 5 Interaction between RRM domains 6 Protein-protein interactions 7 Medical implications 8 Structures 8.1 X-ray 8.2 Solution NMR 9 References

Structure overview

spinqualitylabelsall models Human hnRNP A1 structure overview Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image Human hnRNP A1 consists of 320 amino acids. N-terminal region is composed of two RNA recognition motifs (RRM) followed by highly flexible C-terminal glycine-rich region. The structure of disordered C-terminal region which contains 45 % of glycine in its sequence has not been resolved till now. However, a short peptide from C-terminal region (residues 315 – 341) is available in the structure of (2H4M). and (together span residues 1 to 196) form . The secondary structure of the RRM is characterized by a βαβαββαβ-fold in which the four β-strands make an anti-parallel β-sheet that forms most of the nucleic acid binding surface. To date, several crystal structures of UP1 have been solved both in their free form and bound to repeats of telomeric DNA fragments [1][2][3][4][5]. NMR structure of hnRNP A1 RRM domains was determined using a segmental labeling strategy [6]. Post-translational modifications

Binding mechanism

Conservative residues

Interaction between RRM domains

Two RRMs are interaction with one another via two Arg-Asp salt bridges. The interactions between domains of UP1 is quite weak, since the orientation of the two RRMs can be influenced by nucleic acid binding or by contacts with neighboring molecules in the crystal lattice.

In the solution structure of free UP1, the two Arg-Asp salt bridges are conserved at the interface between RRM1 and RRM2.

Protein-protein interactions

Medical implications

Structures

X-ray

• 1ha1
• 1l3k
• 1pgz
• 1po6
• 1u1k
• 1u1l
• 1u1m
• 1u1n
• 1u1o
• 1u1p
• 1u1q
• 1u1r
• 1up1
• 2h4m
• 2up1

Solution NMR

• 2lyv

References

1. ↑ Xu RM, Jokhan L, Cheng X, Mayeda A, Krainer AR. Crystal structure of human UP1, the domain of hnRNP A1 that contains two RNA-recognition motifs. Structure. 1997 Apr 15;5(4):559-70. PMID:9115444
2. ↑ Vitali J, Ding J, Jiang J, Zhang Y, Krainer AR, Xu RM. Correlated alternative side chain conformations in the RNA-recognition motif of heterogeneous nuclear ribonucleoprotein A1. Nucleic Acids Res. 2002 Apr 1;30(7):1531-8. PMID:11917013
3. ↑ Ding J, Hayashi MK, Zhang Y, Manche L, Krainer AR, Xu RM. Crystal structure of the two-RRM domain of hnRNP A1 (UP1) complexed with single-stranded telomeric DNA. Genes Dev. 1999 May 1;13(9):1102-15. PMID:10323862
4. ↑ Myers JC, Moore SA, Shamoo Y. Structure-based incorporation of 6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine into the human telomeric repeat DNA as a probe for UP1 binding and destabilization of G-tetrad structures. J Biol Chem. 2003 Oct 24;278(43):42300-6. Epub 2003 Aug 6. PMID:12904298 doi:http://dx.doi.org/10.1074/jbc.M306147200
5. ↑ Myers JC, Shamoo Y. Human UP1 as a model for understanding purine recognition in the family of proteins containing the RNA recognition motif (RRM). J Mol Biol. 2004 Sep 17;342(3):743-56. PMID:15342234 doi:10.1016/j.jmb.2004.07.029
6. ↑ Barraud P, Allain FH. 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. J Biomol NMR. 2012 Dec 18. PMID:23247503 doi:http://dx.doi.org/10.1007/s10858-012-9696-4