Relaxed state of S65-phosphorylated ubiquitin

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 160 
  • Conformers Submitted: 30 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Ubiquitin S65 phosphorylation engenders a pH-sensitive conformational switch

Dong, X.Gong, Z.Lu, Y.B.Liu, K.Qin, L.Y.Ran, M.L.Zhang, C.L.Liu, Z.Zhang, W.P.Tang, C.

(2017) Proc Natl Acad Sci U S A 114: 6770-6775

  • DOI: https://doi.org/10.1073/pnas.1705718114
  • Primary Citation of Related Structures:  
    5XK4, 5XK5

  • PubMed Abstract: 

    Ubiquitin (Ub) is an important signaling protein. Recent studies have shown that Ub can be enzymatically phosphorylated at S65, and that the resulting pUb exhibits two conformational states-a relaxed state and a retracted state. However, crystallization efforts have yielded only the structure for the relaxed state, which was found similar to that of unmodified Ub. Here we present the solution structures of pUb in both states obtained through refinement against state-specific NMR restraints. We show that the retracted state differs from the relaxed state by the retraction of the last β-strand and by the extension of the second α-helix. Further, we show that at 7.2, the pK a value for the phosphoryl group in the relaxed state is higher by 1.4 units than that in the retracted state. Consequently, pUb exists in equilibrium between protonated and deprotonated forms and between retracted and relaxed states, with protonated/relaxed species enriched at slightly acidic pH and deprotonated/retracted species enriched at slightly basic pH. The heterogeneity of pUb explains the inability of phosphomimetic mutants to fully mimic pUb. The pH-sensitive conformational switch is likely preserved for polyubiquitin, as single-molecule FRET data indicate that pH change leads to quaternary rearrangement of a phosphorylated K63-linked diubiquitin. Because cellular pH varies among compartments and changes upon pathophysiological insults, our finding suggests that pH and Ub phosphorylation confer additional target specificities and enable an additional layer of modulation for Ub signals.

  • Organizational Affiliation

    Collaborative Innovation Center of Chemistry for Life Sciences, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polyubiquitin-B76Homo sapiensMutation(s): 0 
Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG47
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 0 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
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Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 160 
  • Conformers Submitted: 30 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
the Chinese Ministry of Science and TechnologyChina2013CB910200
the Chinese Ministry of Science and TechnologyChina2016YFA0501200
the National Natural Science Foundation of ChinaChina31225007
the National Natural Science Foundation of ChinaChina31500595
the National Natural Science Foundation of ChinaChina31400735
the National Natural Science Foundation of ChinaChina31400644

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-12
    Changes: Database references
  • Version 1.2: 2023-06-14
    Changes: Data collection, Database references, Other