3DXB

Structure of the UHM domain of Puf60 fused to thioredoxin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

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
  • Primary Citation of Related Structures:  
    3DXB

  • 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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
thioredoxin N-terminally fused to Puf60(UHM)A, B, C, D, E, F, G, H222Escherichia coli O157:H7, Homo sapiens
This entity is chimeric		Mutation(s): 0 
Gene Names: trxA, Z5291, ECs4714
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
NIH Common Fund Data Resources
PHAROS  Q9UHX1
GTEx  ENSG00000179950
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
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E
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
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A, E, F, H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
HKL-2000data collection
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • 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