8tg0

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Solution NMR structure of the cold shock domain of the Arabidopsis thaliana glycine-rich protein AtGRP2

Structural highlights

8tg0 is a 1 chain structure with sequence from Arabidopsis thaliana. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR, 20 models
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CSP2_ARATH Chaperone that binds to RNA, single- (ssDNA) and double-stranded (dsDNA) DNA, and unwinds nucleic acid duplex. Accelerates seed germination and seedling growth under cold stress, and contributes to enhancement of cold and freezing tolerance. Regulates flowering transition, and flower and seed development. Promotes seed germination under salt stress. May regulate respiratory oxygen uptake.[1] [2] [3] [4] [5] [6]

Publication Abstract from PubMed

AtGRP2 is a glycine-rich, RNA-binding protein that plays pivotal roles in abiotic stress response and flowering time regulation in Arabidopsis thaliana. AtGRP2 consists of an N-terminal cold shock domain (CSD) and two C-terminal CCHC-type zinc knuckles interspersed with glycine-rich regions. Here, we investigated the structure, dynamics, and nucleic acid binding properties of AtGRP2-CSD. The 2D [(1)H,(15)N] HSQC spectrum of AtGRP2-CSD(1-79) revealed the presence of a partially folded intermediate in equilibrium with the folded state. The addition of eleven residues at the C-terminus stabilized the folded conformation. The three-dimensional structure of AtGRP2-CSD(1-90) unveiled a beta-barrel composed of five antiparallel beta-strands and a 3(10) helical turn, along with an ordered C-terminal extension, a conserved feature in eukaryotic CSDs. Direct contacts between the C-terminal extension and the beta3-beta4 loop further stabilized the CSD fold. AtGRP2-CSD(1-90) exhibited nucleic acid binding via solvent-exposed residues on strands beta2 and beta3, as well as the beta3-beta4 loop, with higher affinity for DNA over RNA, particularly favoring pyrimidine-rich sequences. Furthermore, DNA binding induced rigidity in the beta3-beta4 loop, evidenced by (15)N-(1)H NOE values. Mutation of residues W17, F26, and F37, in the central beta-sheet, completely abolished DNA binding, highlighting the significance of pi-stacking interactions in the binding mechanism. These results shed light on the mechanism of nucleic acid recognition employed by AtGRP2, creating a framework for the development of biotechnological strategies aimed at enhancing plant resistance to abiotic stresses.

Structural basis of nucleic acid recognition by the N-terminal cold shock domain of the plant glycine-rich protein AtGRP2.,Pougy KC, Moraes BS, Malizia-Motta CLF, Lima LMTR, Sachetto-Martins G, Almeida FCL, Pinheiro AS J Biol Chem. 2024 Oct 17:107903. doi: 10.1016/j.jbc.2024.107903. PMID:39426727[7]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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References

  1. ↑ Fusaro AF, Bocca SN, Ramos RL, Barrôco RM, Magioli C, Jorge VC, Coutinho TC, Rangel-Lima CM, De Rycke R, Inzé D, Engler G, Sachetto-Martins G. AtGRP2, a cold-induced nucleo-cytoplasmic RNA-binding protein, has a role in flower and seed development. Planta. 2007 May;225(6):1339-51. PMID:17123099 doi:10.1007/s00425-006-0444-4
  2. ↑ Kim JS, Park SJ, Kwak KJ, Kim YO, Kim JY, Song J, Jang B, Jung CH, Kang H. Cold shock domain proteins and glycine-rich RNA-binding proteins from Arabidopsis thaliana can promote the cold adaptation process in Escherichia coli. Nucleic Acids Res. 2007;35(2):506-16. PMID:17169986 doi:10.1093/nar/gkl1076
  3. ↑ Kim JY, Park SJ, Jang B, Jung CH, Ahn SJ, Goh CH, Cho K, Han O, Kang H. Functional characterization of a glycine-rich RNA-binding protein 2 in Arabidopsis thaliana under abiotic stress conditions. Plant J. 2007 May;50(3):439-51. PMID:17376161 doi:10.1111/j.1365-313X.2007.03057.x
  4. ↑ Sasaki K, Kim MH, Imai R. Arabidopsis COLD SHOCK DOMAIN PROTEIN2 is a RNA chaperone that is regulated by cold and developmental signals. Biochem Biophys Res Commun. 2007 Dec 21;364(3):633-8. PMID:17963727 doi:10.1016/j.bbrc.2007.10.059
  5. ↑ Park SJ, Kwak KJ, Oh TR, Kim YO, Kang H. Cold shock domain proteins affect seed germination and growth of Arabidopsis thaliana under abiotic stress conditions. Plant Cell Physiol. 2009 Apr;50(4):869-78. PMID:19258348 doi:10.1093/pcp/pcp037
  6. ↑ Nakaminami K, Hill K, Perry SE, Sentoku N, Long JA, Karlson DT. Arabidopsis cold shock domain proteins: relationships to floral and silique development. J Exp Bot. 2009;60(3):1047-62. PMID:19269998 doi:10.1093/jxb/ern351
  7. ↑ Pougy KC, Moraes BS, Malizia-Motta CLF, Lima LMTR, Sachetto-Martins G, Almeida FCL, Pinheiro AS. Structural basis of nucleic acid recognition by the N-terminal cold shock domain of the plant glycine-rich protein AtGRP2. J Biol Chem. 2024 Oct 17:107903. PMID:39426727 doi:10.1016/j.jbc.2024.107903

Contents


PDB ID 8tg0

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