6KL4

Crystal structure of MavC-UBE2N-Ub


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Molecular Basis of Ubiquitination Catalyzed by the Bacterial Transglutaminase MavC.

Guan, H.Fu, J.Yu, T.Wang, Z.X.Gan, N.Huang, Y.Perculija, V.Li, Y.Luo, Z.Q.Ouyang, S.

(2020) Adv Sci (Weinh) 7: 2000871-2000871

  • DOI: 10.1002/advs.202000871
  • Primary Citation of Related Structures:  
    6KL4

  • PubMed Abstract: 
  • The Legionella pneumophila effector MavC is a transglutaminase that carries out atypical ubiquitination of the host ubiquitin (Ub)-conjugation enzyme UBE2N by catalyzing the formation of an isopeptide bond between Gln40 Ub and Lys92 ...

    The Legionella pneumophila effector MavC is a transglutaminase that carries out atypical ubiquitination of the host ubiquitin (Ub)-conjugation enzyme UBE2N by catalyzing the formation of an isopeptide bond between Gln40 Ub and Lys92 UBE2N , which leads to inhibition of signaling in the NF-κB pathway. In the absence of UBE2N, MavC deamidates Ub at Gln40 or catalyzes self-ubiquitination. However, the mechanisms underlying these enzymatic activities of MavC are poorly understood at the molecular level. This study reports the structure of the MavC-UBE2N-Ub ternary complex representing a snapshot of MavC-catalyzed crosslinking of UBE2N and Ub, which reveals the way by which UBE2N-Ub binds to the Insertion and Tail domains of MavC. Based on the structural and experimental data, the catalytic mechanism for the deamidase and transglutaminase activities of MavC is proposed. Finally, by comparing the structures of MavC and MvcA, the homologous protein that reverses MavC-induced UBE2N ubiquitination, several essential regions and two key residues (Trp255 MavC and Phe268 MvcA ) responsible for their respective enzymatic activities are identified. The results provide insights into the mechanisms for substrate recognition and ubiquitination mediated by MavC as well as explanations for the opposite activity of MavC and MvcA in terms of regulation of UBE2N ubiquitination.


    Organizational Affiliation

    Laboratory for Marine Biology and Biotechnology Pilot National Laboratory for Marine Science and Technology (Qingdao) Qingdao 266237 China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MavC A378Legionella pneumophilaMutation(s): 0 
Gene Names: C3927_10720
Find proteins for Q5ZTL4 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZTL4 
Go to UniProtKB:  Q5ZTL4
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 N B152Homo sapiensMutation(s): 1 
Gene Names: UBE2NBLU
EC: 2.3.2.23
Find proteins for P61088 (Homo sapiens)
Explore P61088 
Go to UniProtKB:  P61088
NIH Common Fund Data Resources
PHAROS:  P61088
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ub C76Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.561α = 90
b = 149.561β = 90
c = 58.774γ = 120
Software Package:
Software NamePurpose
xia2data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
Cootmodel building
HKL-3000phasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2019-07-29 
  • Released Date: 2020-04-15 
  • Deposition Author(s): Ouyang, S., Guan, H.

Revision History 

  • Version 1.0: 2020-04-15
    Type: Initial release
  • Version 1.1: 2020-05-20
    Changes: Database references
  • Version 1.2: 2020-07-01
    Changes: Database references, Source and taxonomy
  • Version 1.3: 2020-07-15
    Changes: Database references