4DHZ

The structure of h/ceOTUB1-ubiquitin aldehyde-UBC13~Ub


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

The mechanism of OTUB1-mediated inhibition of ubiquitination.

Wiener, R.Zhang, X.Wang, T.Wolberger, C.

(2012) Nature 483: 618-622

  • DOI: 10.1038/nature10911
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Histones are ubiquitinated in response to DNA double-strand breaks (DSB), promoting recruitment of repair proteins to chromatin. UBC13 (also known as UBE2N) is a ubiquitin-conjugating enzyme (E2) that heterodimerizes with UEV1A (also known as UBE2V1) ...

    Histones are ubiquitinated in response to DNA double-strand breaks (DSB), promoting recruitment of repair proteins to chromatin. UBC13 (also known as UBE2N) is a ubiquitin-conjugating enzyme (E2) that heterodimerizes with UEV1A (also known as UBE2V1) and synthesizes K63-linked polyubiquitin (K63Ub) chains at DSB sites in concert with the ubiquitin ligase (E3), RNF168 (ref. 3). K63Ub synthesis is regulated in a non-canonical manner by the deubiquitinating enzyme, OTUB1 (OTU domain-containing ubiquitin aldehyde-binding protein 1), which binds preferentially to the UBC13∼Ub thiolester. Residues amino-terminal to the OTU domain, which had been implicated in ubiquitin binding, are required for binding to UBC13∼Ub and inhibition of K63Ub synthesis. Here we describe structural and biochemical studies elucidating how OTUB1 inhibits UBC13 and other E2 enzymes. We unexpectedly find that OTUB1 binding to UBC13∼Ub is allosterically regulated by free ubiquitin, which binds to a second site in OTUB1 and increases its affinity for UBC13∼Ub, while at the same time disrupting interactions with UEV1A in a manner that depends on the OTUB1 N terminus. Crystal structures of an OTUB1-UBC13 complex and of OTUB1 bound to ubiquitin aldehyde and a chemical UBC13∼Ub conjugate show that binding of free ubiquitin to OTUB1 triggers conformational changes in the OTU domain and formation of a ubiquitin-binding helix in the N terminus, thus promoting binding of the conjugated donor ubiquitin in UBC13∼Ub to OTUB1. The donor ubiquitin thus cannot interact with the E2 enzyme, which has been shown to be important for ubiquitin transfer. The N-terminal helix of OTUB1 is positioned to interfere with UEV1A binding to UBC13, as well as with attack on the thiolester by an acceptor ubiquitin, thereby inhibiting K63Ub synthesis. OTUB1 binding also occludes the RING E3 binding site on UBC13, thus providing a further component of inhibition. The general features of the inhibition mechanism explain how OTUB1 inhibits other E2 enzymes in a non-catalytic manner.


    Organizational Affiliation

    Department of Biophysics and Biophysical Chemistry and Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin thioesterase otubain-likeA288Homo sapiensCaenorhabditis elegans
This entity is chimeric
Mutation(s): 0 
Gene Names: OTUB1OTB1OTU1HSPC263C25D7.8otub-1
EC: 3.4.19.12
Find proteins for Q96FW1 (Homo sapiens)
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Go to UniProtKB:  Q96FW1
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PHAROS  Q96FW1
Find proteins for Q9XVR6 (Caenorhabditis elegans)
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Go to UniProtKB:  Q9XVR6
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin aldehydeB76Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
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Go to UniProtKB:  P0CG48
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PHAROS  P0CG48
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
UbiquitinE76Homo sapiensMutation(s): 1 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
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PHAROS  P0CG48
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 NF152Homo sapiensMutation(s): 0 
Gene Names: UBE2NBLU
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
Find proteins for P61088 (Homo sapiens)
Explore P61088 
Go to UniProtKB:  P61088
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PHAROS  P61088
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GLZ
Query on GLZ
BL-PEPTIDE LINKINGC2 H5 N OGLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.371α = 90
b = 123.371β = 90
c = 68.653γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CCP4model building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-22
    Type: Initial release
  • Version 1.1: 2012-02-29
    Changes: Database references
  • Version 1.2: 2012-03-14
    Changes: Database references
  • Version 1.3: 2012-04-04
    Changes: Database references
  • Version 1.4: 2017-07-26
    Changes: Source and taxonomy
  • Version 1.5: 2017-11-15
    Changes: Refinement description