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PDBsum entry 2bl5

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protein links
RNA binding PDB id
2bl5
Jmol
Contents
Protein chain
135 a.a. *
* Residue conservation analysis
PDB id:
2bl5
Name: RNA binding
Title: Solution structure of the kh-qua2 region of the xenopus star-gsg quaking protein.
Structure: Mgc83862 protein. Chain: a. Fragment: kh-qua2 region, residues 82-215. Synonym: quaking protein. Engineered: yes
Source: Xenopus laevis. African clawed frog. Organism_taxid: 8355. Expressed in: escherichia coli. Expression_system_taxid: 469008. Other_details: gene expression was induced by the addition of iptg to a final concentration of 0.5 mm and the cells were incubated for 3 h at 37 degrees c. The cells were harvested by centrifugation at 6000 rpm for 20 min and
NMR struc: 17 models
Authors: M.L.Maguire,G.Guler-Gane,D.Nietlispach,A.R.C.Raine,A.M.Zorn, N.Standart,R.W.Broadhurst
Key ref:
M.L.Maguire et al. (2005). Solution structure and backbone dynamics of the KH-QUA2 region of the Xenopus STAR/GSG quaking protein. J Mol Biol, 348, 265-279. PubMed id: 15811367 DOI: 10.1016/j.jmb.2005.02.058
Date:
01-Mar-05     Release date:   14-Apr-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q32NN2  (QKIA_XENLA) -  Protein quaking-A
Seq:
Struc:
341 a.a.
135 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     RNA binding     1 term  

 

 
DOI no: 10.1016/j.jmb.2005.02.058 J Mol Biol 348:265-279 (2005)
PubMed id: 15811367  
 
 
Solution structure and backbone dynamics of the KH-QUA2 region of the Xenopus STAR/GSG quaking protein.
M.L.Maguire, G.Guler-Gane, D.Nietlispach, A.R.Raine, A.M.Zorn, N.Standart, R.W.Broadhurst.
 
  ABSTRACT  
 
The Quaking protein belongs to the family of STAR/GSG domain RNA-binding proteins and is involved in multiple cell signalling and developmental processes in vertebrates, including the formation of myelin. Heteronuclear NMR methods were used to determine the solution structure of a 134 residue fragment spanning the KH and QUA2 homology regions of the Quaking protein from Xenopus laevis (pXqua) in the absence of RNA. The protein is shown to adopt an extended type I KH domain fold that is connected to a structured alpha-helix in the C-terminal QUA2 region by means of a highly flexible linker. A comparison with the solution structure of the related protein splicing factor 1 (SF1) indicates that most aspects of the RNA-binding interface are conserved in pXqua, although the "variable loop" region that follows the second beta-strand possesses two additional alpha-helices. The structure of pXqua provides an appropriate template for building models of important homologues, such as GLD-1 and Sam68. Measurements of the (15)N relaxation parameters of pXqua confirm that the polypeptide backbone of the QUA2 region is more dynamic than that of the KH portion, and that the C-terminal helix is partially structured in the absence of RNA. By comparison with a random coil reference state, the nascent structure in the QUA2 region is estimated to contribute 15.5kJmol(-1) to the change in conformational free energy that occurs on forming a complex with RNA. Since STAR/GSG proteins may regulate alternative splicing by competing with SF1 in the nucleus for specific branch-point sequences that signal intronic RNA, the formation of secondary structure in the QUA2 region in the unbound state of pXqua has important functional consequences.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. (a) Superposition of backbone traces from the final ensemble of 16 solution structures of pXqua, coloured from blue at the N terminus to red at the C terminus. (b) A representation of the fold of one member of the final ensemble with elements of secondary structure indicated, using the same colour scheme as in (a).
Figure 3.
Figure 3. Histograms describing the experimental 15N relaxation parameters of pXqua as a function of residue number: (a) the longitudinal relaxation rate, R[1]; (b) the transverse relaxation rate R[2]; and (c) the heteronuclear NOE, y.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 348, 265-279) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20573244 A.B.Carmel, J.Wu, K.A.Lehmann-Blount, and J.R.Williamson (2010).
High-affinity consensus binding of target RNAs by the STAR/GSG proteins GLD-1, STAR-2 and Quaking.
  BMC Mol Biol, 11, 48.  
20223220 C.Beuck, B.R.Szymczyna, D.E.Kerkow, A.B.Carmel, L.Columbus, R.L.Stanfield, and J.R.Williamson (2010).
Structure of the GLD-1 homodimerization domain: insights into STAR protein-mediated translational regulation.
  Structure, 18, 377-389.
PDB codes: 3k6t 3kbl
19956763 J.Liu, and J.Song (2009).
Insights into protein aggregation by NMR characterization of insoluble SH3 mutants solubilized in salt-free water.
  PLoS One, 4, e7805.  
17787018 C.A.Chénard, and S.Richard (2008).
New implications for the QUAKING RNA binding protein in human disease.
  J Neurosci Res, 86, 233-242.  
18411422 J.Liu, J.Zhang, Y.Yang, H.Huang, W.Shen, Q.Hu, X.Wang, J.Wu, and Y.Shi (2008).
Conformational change upon ligand binding and dynamics of the PDZ domain from leukemia-associated Rho guanine nucleotide exchange factor.
  Protein Sci, 17, 1003-1014.  
18701464 Z.Du, S.Fenn, R.Tjhen, and T.L.James (2008).
Structure of a Construct of a Human Poly(C)-binding Protein Containing the First and Second KH Domains Reveals Insights into Its Regulatory Mechanisms.
  J Biol Chem, 283, 28757-28766.  
17159918 A.Oddone, E.Lorentzen, J.Basquin, A.Gasch, V.Rybin, E.Conti, and M.Sattler (2007).
Structural and biochemical characterization of the yeast exosome component Rrp40.
  EMBO Rep, 8, 63-69.
PDB code: 2ja9
16424921 C.W.Sugnet, K.Srinivasan, T.A.Clark, G.O'Brien, M.S.Cline, H.Wang, A.Williams, D.Kulp, J.E.Blume, D.Haussler, and M.Ares (2006).
Unusual intron conservation near tissue-regulated exons found by splicing microarrays.
  PLoS Comput Biol, 2, e4.  
16861232 S.M.Garrey, R.Voelker, and J.A.Berglund (2006).
An extended RNA binding site for the yeast branch point-binding protein and the role of its zinc knuckle domains in RNA binding.
  J Biol Chem, 281, 27443-27453.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.