3PTF

X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Modulation of K11-Linkage Formation by Variable Loop Residues within UbcH5A.

Bosanac, I., Phu, L., Pan, B., Zilberleyb, I., Maurer, B., Dixit, V.M., Hymowitz, S.G., Kirkpatrick, D.S.

(2011) J Mol Biol 408: 420-431

  • DOI: 10.1016/j.jmb.2011.03.011
  • Primary Citation of Related Structures:  
    3PTF

  • PubMed Abstract: 

    • Ubiquitination refers to the covalent addition of ubiquitin (Ub) to substrate proteins or other Ub molecules via the sequential action of three enzymes (E1, E2, and E3). Recent advances in mass spectrometry proteomics have made it possible to identify and quantify Ub linkages in biochemical and cellular systems ...

    Ubiquitination refers to the covalent addition of ubiquitin (Ub) to substrate proteins or other Ub molecules via the sequential action of three enzymes (E1, E2, and E3). Recent advances in mass spectrometry proteomics have made it possible to identify and quantify Ub linkages in biochemical and cellular systems. We used these tools to probe the mechanisms controlling linkage specificity for UbcH5A. UbcH5A is a promiscuous E2 enzyme with an innate preference for forming polyubiquitin chains through lysine 11 (K11), lysine 48 (K48), and lysine 63 (K63) of Ub. We present the crystal structure of a noncovalent complex between Ub and UbcH5A. This structure reveals an interaction between the Ub surface flanking K11 and residues adjacent to the E2 catalytic cysteine and suggests a possible role for this surface in formation of K11 linkages. Structure-guided mutagenesis, in vitro ubiquitination and quantitative mass spectrometry have been used to characterize the ability of residues in the vicinity of the E2 active site to direct synthesis of K11- and K63-linked polyubiquitin. Mutation of critical residues in the interface modulated the linkage specificity of UbcH5A, resulting in generation of more K63-linked chains at the expense of K11-linkage synthesis. This study provides direct evidence that the linkage specificity of E2 enzymes may be altered through active-site mutagenesis.

    Organizational Affiliation: 

    Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 D1A, B153Homo sapiensMutation(s): 0 
Gene Names: SFT, UBC5A, UBCH5, UBCH5A, UBE2D1
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt), 2.3.2.24 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P51668 (Homo sapiens)
Explore P51668 
Go to UniProtKB:  P51668
PHAROS:  P51668
GTEx:  ENSG00000072401 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51668
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-BC, D79Homo sapiensMutation(s): 0 
Gene Names: Ubiquitin, UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
PHAROS:  P0CG48
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG48
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.462α = 90
b = 102.903β = 90
c = 159.806γ = 90
Software Package:
Software NamePurpose
BOSdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance