3DXB

Structure of the UHM domain of Puf60 fused to thioredoxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1074/jbc.M805395200

  • 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-conta ...

    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.


    Related Citations: 
    • Thioredoxin as a fusion tag for carrier-driven crystallization.
      Corsini, L.,Hothorn, M.,Scheffzek, K.,Sattler, M.,Stier, G.
      (2008) Protein Sci. 17: 2070


    Organizational Affiliation

    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
thioredoxin N-terminally fused to Puf60(UHM)
A, B, C, D, E, F, G, H
222Homo sapiensEscherichia coli O157:H7
This entity is chimeric
Mutation(s): 0 
Gene Names: PUF60 (FIR, ROBPI, SIAHBP1), trxA
Find proteins for Q9UHX1 (Homo sapiens)
Go to Gene View: PUF60
Go to UniProtKB:  Q9UHX1
Find proteins for P0AA27 (Escherichia coli O157:H7)
Go to UniProtKB:  P0AA27
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, E, F, H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
E
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 75.120α = 90.00
b = 89.430β = 90.00
c = 299.390γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-01-09
    Type: Database references
  • Version 1.3: 2017-08-02
    Type: Source and taxonomy