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PDBsum entry 1s29

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protein links
RNA binding protein PDB id
1s29
Jmol
Contents
Protein chain
92 a.a. *
Waters ×100
* Residue conservation analysis
PDB id:
1s29
Name: RNA binding protein
Title: La autoantigen n-terminal domain
Structure: La protein. Chain: a. Fragment: n-terminal fragment. Engineered: yes
Source: Trypanosoma brucei. Organism_taxid: 5691. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.60Å     R-factor:   0.232     R-free:   0.250
Authors: G.Dong,G.Chakshusmathi,S.L.Wolin,K.M.Reinisch
Key ref:
G.Dong et al. (2004). Structure of the La motif: a winged helix domain mediates RNA binding via a conserved aromatic patch. EMBO J, 23, 1000-1007. PubMed id: 14976553 DOI: 10.1038/sj.emboj.7600115
Date:
08-Jan-04     Release date:   23-Mar-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9NIH4  (Q9NIH4_9TRYP) -  RNA binding protein La-like protein
Seq:
Struc:
335 a.a.
92 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     ribonucleoprotein complex   2 terms 
  Biological process     RNA processing   1 term 
  Biochemical function     RNA binding     1 term  

 

 
DOI no: 10.1038/sj.emboj.7600115 EMBO J 23:1000-1007 (2004)
PubMed id: 14976553  
 
 
Structure of the La motif: a winged helix domain mediates RNA binding via a conserved aromatic patch.
G.Dong, G.Chakshusmathi, S.L.Wolin, K.M.Reinisch.
 
  ABSTRACT  
 
The La protein is a ubiquitous nuclear phosphoprotein that recognizes the 3' uridylates found in all newly synthesized RNA polymerase III transcripts. La binding stabilizes these transcripts from exonucleases and may also assist their folding. Here we present the first structural insights into how the La protein specifically interacts with its RNA substrates. The most conserved region of the La protein is the La motif, a domain also found in several other RNA-binding proteins. We have determined the structure of the La motif from the Trypanosoma brucei La protein to 1.6 A resolution (PDB code 1S29). The La motif adopts a winged helix-turn-helix architecture that has a highly conserved patch of mainly aromatic surface residues. Mutagenesis experiments support a critical role for this patch in RNA binding and show that it partly determines binding specificity for RNAs ending in 3' hydroxyl, a defining characteristic of the La protein. These findings reveal that the La motif is essential for high-affinity binding and also contributes to specificity.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 (A) Ribbon views of the LM of T. brucei La. (B) Ribbon view of a wHTH motif as observed in the Z-DNA-binding domain of the adenosine deaminase ADAR1 (PDB accession number 1QBJ). The topology of the LM is similar to that of the wHTH motif of some transcription factors. MOLSCRIPT (Kraulis, 1991) was used to prepare this figure.
Figure 3.
Figure 3 Binding of wild-type and mutant La proteins to RNA. (A) 32P-labeled yeast pre-tRNA[CCG]Arg (left panel) or pre-tRNA[CCG]Arg lacking the 9 nt 3' trailer (right panel) was incubated without protein (lane 1) or with the truncated T. brucei La protein (LM+RRM; amino acids 1 -192) at the indicated protein concentrations. The pre-tRNA concentration in the reaction was 0.15 nM. Naked RNAs and RNPs were separated in native gels. (B) 32P-labeled yeast pre-tRNA[CCG]Arg (final concentration 0.15 nM) was incubated with either no protein (lane 1) or the indicated concentrations of full-length La (lanes 2 -4), La 1 -192 (lanes 5 -8), the isolated LM (amino acids 1 -89; lanes 9 -11), the RRM (residues 94 -192; lanes 12 -14), or a 1:1 mixture of the LM and RRM (lanes 15 -17). Naked RNAs and RNPs were separated by native gel electrophoresis. (C) Binding of La 1 -192 (left panel) and the D27A mutant (right panel) to pre-tRNA[CCG]Arg was performed as described in (A). Protein concentrations in the reactions are indicated above the lanes. In lanes 1 and 10, no protein was added. We quantitated the difference in binding affinity of La 1 -192 and the D27A mutant by performing multiple experiments. These revealed that La 1 -192 bound the RNA with a K[d] of 4.1 0.7 nM, while the D27A mutant bound the RNA with a K[d] of 14.6 2.9 nM, an approximately 3.6-fold decrease in affinity. (D) pre-tRNA[CCG]Arg was subjected to gel shift analysis using either the wild-type La 1 -192 (lanes 2 -4) or the mutants Q14A/E16A (lanes 5 -7), F29A (lanes 8 -10), F50A (lanes 11 -13), F17A (lanes 14 -16), and Y18A (lanes 17 -19). Protein concentrations in each lane are given in nM. Lanes 1 and 20, no protein.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2004, 23, 1000-1007) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21255607 M.Chourasia, G.M.Sastry, and G.N.Sastry (2011).
Aromatic-Aromatic Interactions Database, A(2)ID: An analysis of aromatic π-networks in proteins.
  Int J Biol Macromol, 48, 540-552.  
21212361 N.J.Kucera, M.E.Hodsdon, and S.L.Wolin (2011).
An intrinsically disordered C terminus allows the La protein to assist the biogenesis of diverse noncoding RNA precursors.
  Proc Natl Acad Sci U S A, 108, 1308-1313.  
20573744 K.Schäffler, K.Schulz, A.Hirmer, J.Wiesner, M.Grimm, A.Sickmann, and U.Fischer (2010).
A stimulatory role for the La-related protein 4B in translation.
  RNA, 16, 1488-1499.  
20138158 M.A.Bayfield, R.Yang, and R.J.Maraia (2010).
Conserved and divergent features of the structure and function of La and La-related proteins (LARPs).
  Biochim Biophys Acta, 1799, 365-378.  
19299548 C.Bousquet-Antonelli, and J.M.Deragon (2009).
A comprehensive analysis of the La-motif protein superfamily.
  RNA, 15, 750-764.  
18836485 F.Brenet, N.D.Socci, N.Sonenberg, and E.C.Holland (2009).
Akt phosphorylation of La regulates specific mRNA translation in glial progenitors.
  Oncogene, 28, 128-139.  
19287396 M.A.Bayfield, and R.J.Maraia (2009).
Precursor-product discrimination by La protein during tRNA metabolism.
  Nat Struct Mol Biol, 16, 430-437.  
19416841 M.Barboric, T.Lenasi, H.Chen, E.B.Johansen, S.Guo, and B.M.Peterlin (2009).
7SK snRNP/P-TEFb couples transcription elongation with alternative splicing and is essential for vertebrate development.
  Proc Natl Acad Sci U S A, 106, 7798-7803.  
18515547 K.Nykamp, M.H.Lee, and J.Kimble (2008).
C. elegans La-related protein, LARP-1, localizes to germline P bodies and attenuates Ras-MAPK signaling during oogenesis.
  RNA, 14, 1378-1389.  
18547518 O.Kotik-Kogan, E.R.Valentine, D.Sanfelice, M.R.Conte, and S.Curry (2008).
Structural analysis reveals conformational plasticity in the recognition of RNA 3' ends by the human La protein.
  Structure, 16, 852-862.
PDB codes: 2vod 2von 2voo 2vop
18854356 S.B.Patel, and M.Bellini (2008).
The assembly of a spliceosomal small nuclear ribonucleoprotein particle.
  Nucleic Acids Res, 36, 6482-6493.  
18820297 S.W.Park, A.M.Parrott, D.T.Fritz, Y.Park, M.B.Mathews, and C.G.Lee (2008).
Regulation of the catalytic function of topoisomerase II alpha through association with RNA.
  Nucleic Acids Res, 36, 6080-6090.  
17459889 S.Fleurdépine, J.M.Deragon, M.Devic, J.Guilleminot, and C.Bousquet-Antonelli (2007).
A bona fide La protein is required for embryogenesis in Arabidopsis thaliana.
  Nucleic Acids Res, 35, 3306-3321.  
17041599 G.Fuchs, A.J.Stein, C.Fu, K.M.Reinisch, and S.L.Wolin (2006).
Structural and biochemical basis for misfolded RNA recognition by the Ro autoantigen.
  Nat Struct Mol Biol, 13, 1002-1009.
PDB code: 2i91
16449655 J.M.Park, M.J.Kohn, M.W.Bruinsma, C.Vech, R.V.Intine, S.Fuhrmann, A.Grinberg, I.Mukherjee, P.E.Love, M.S.Ko, M.L.DePamphilis, and R.J.Maraia (2006).
The multifunctional RNA-binding protein La is required for mouse development and for the establishment of embryonic stem cells.
  Mol Cell Biol, 26, 1445-1451.  
16387655 M.Teplova, Y.R.Yuan, A.T.Phan, L.Malinina, S.Ilin, A.Teplov, and D.J.Patel (2006).
Structural basis for recognition and sequestration of UUU(OH) 3' temini of nascent RNA polymerase III transcripts by La, a rheumatic disease autoantigen.
  Mol Cell, 21, 75-85.
PDB codes: 1yty 1zh5
16427005 R.J.Maraia, and M.A.Bayfield (2006).
The La protein-RNA complex surfaces.
  Mol Cell, 21, 149-152.  
16648637 S.Caputo, J.Couprie, I.Duband-Goulet, E.Kondé, F.Lin, S.Braud, M.Gondry, B.Gilquin, H.J.Worman, and S.Zinn-Justin (2006).
The carboxyl-terminal nucleoplasmic region of MAN1 exhibits a DNA binding winged helix domain.
  J Biol Chem, 281, 18208-18215.
PDB code: 2ch0
16679019 S.Curry, and M.R.Conte (2006).
A terminal affair: 3'-end recognition by the human La protein.
  Trends Biochem Sci, 31, 303-305.  
17381333 S.L.Wolin, and E.J.Wurtmann (2006).
Molecular chaperones and quality control in noncoding RNA biogenesis.
  Cold Spring Harb Symp Quant Biol, 71, 505-511.  
16799560 Y.Huang, M.A.Bayfield, R.V.Intine, and R.J.Maraia (2006).
Separate RNA-binding surfaces on the multifunctional La protein mediate distinguishable activities in tRNA maturation.
  Nat Struct Mol Biol, 13, 611-618.  
16107699 F.Brenet, N.Dussault, J.Borch, G.Ferracci, C.Delfino, P.Roepstorff, R.Miquelis, and L.Ouafik (2005).
Mammalian peptidylglycine alpha-amidating monooxygenase mRNA expression can be modulated by the La autoantigen.
  Mol Cell Biol, 25, 7505-7521.  
15808743 L.Aravind, V.Anantharaman, S.Balaji, M.M.Babu, and L.M.Iyer (2005).
The many faces of the helix-turn-helix domain: transcription regulation and beyond.
  FEMS Microbiol Rev, 29, 231-262.  
15665870 S.Yoshizawa, L.Rasubala, T.Ose, D.Kohda, D.Fourmy, and K.Maenaka (2005).
Structural basis for mRNA recognition by elongation factor SelB.
  Nat Struct Mol Biol, 12, 198-203.
PDB code: 1wsu
15048103 D.J.Kenan, and J.D.Keene (2004).
La gets its wings.
  Nat Struct Mol Biol, 11, 303-305.  
15485924 E.I.Schwartz, R.V.Intine, and R.J.Maraia (2004).
CK2 is responsible for phosphorylation of human La protein serine-366 and can modulate rpL37 5'-terminal oligopyrimidine mRNA metabolism.
  Mol Cell Biol, 24, 9580-9591.  
15341724 N.LaRonde-LeBlanc, and A.Wlodawer (2004).
Crystal structure of A. fulgidus Rio2 defines a new family of serine protein kinases.
  Structure, 12, 1585-1594.
PDB codes: 1tqi 1tqm 1tqp
15572691 R.V.Intine, M.Dundr, A.Vassilev, E.Schwartz, Y.Zhao, Y.Zhao, M.L.Depamphilis, and R.J.Maraia (2004).
Nonphosphorylated human La antigen interacts with nucleolin at nucleolar sites involved in rRNA biogenesis.
  Mol Cell Biol, 24, 10894-10904.  
15371415 S.Horke, K.Reumann, C.Schulze, F.Grosse, and T.Heise (2004).
The La motif and the RNA recognition motifs of human La autoantigen contribute individually to RNA recognition and subcellular localization.
  J Biol Chem, 279, 50302-50309.  
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.