Structure of the UHM domain of Puf60 fused to thioredoxin

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

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Dimerization and Protein Binding Specificity of the U2AF Homology Motif of the Splicing Factor Puf60.

Corsini, L.Hothorn, M.Stier, G.Rybin, V.Scheffzek, K.Gibson, T.J.Sattler, M.

(2009) J Biol Chem 284: 630-639

  • DOI: https://doi.org/10.1074/jbc.M805395200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    PUF60 is an essential splicing factor functionally related and homologous to U2AF(65). Its C-terminal domain belongs to the family of U2AF (U2 auxiliary factor) homology motifs (UHM), a subgroup of RNA recognition motifs that bind to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Here, we show that the Puf60 UHM is mainly monomeric in physiological buffer, whereas its dimerization is induced upon the addition of SDS. The crystal structure of PUF60-UHM at 2.2 angstroms resolution, NMR data, and mutational analysis reveal that the dimer interface is mediated by electrostatic interactions involving a flexible loop. Using glutathione S-transferase pulldown experiments, isothermal titration calorimetry, and NMR titrations, we find that Puf60-UHM binds to ULM sequences in the splicing factors SF1, U2AF65, and SF3b155. Compared with U2AF65-UHM, Puf60-UHM has distinct binding preferences to ULMs in the N terminus of SF3b155. Our data suggest that the functional cooperativity between U2AF65 and Puf60 may involve simultaneous interactions of the two proteins with SF3b155.

  • Organizational Affiliation

    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, the Institute of Structural Biology, Helmholtz Zentrum Mu¨nchen, Ingolsta¨dter Landstrasse 1, 85764 Neuherberg, Germany, and the Munich Center for Integrated Protein Science and Chair Biomolecular NMR, Department Chemie, Technische Universita¨t Mu¨nchen, Lichtenbergstrasse 4, 85747 Garching, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
thioredoxin N-terminally fused to Puf60(UHM)
A, B, C, D, E
A, B, C, D, E, F, G, H
222Escherichia coli O157:H7Homo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: trxAZ5291ECs4714PUF60FIRROBPISIAHBP1
UniProt & NIH Common Fund Data Resources
Find proteins for P0AA27 (Escherichia coli O157:H7)
Explore P0AA27 
Go to UniProtKB:  P0AA27
Find proteins for Q9UHX1 (Homo sapiens)
Explore Q9UHX1 
Go to UniProtKB:  Q9UHX1
GTEx:  ENSG00000179950 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9UHX1P0AA27
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.12α = 90
b = 89.43β = 90
c = 299.39γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-01-09
    Changes: Database references
  • Version 1.3: 2017-08-02
    Changes: Source and taxonomy
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description