6ZM3 | pdb_00006zm3

The structure of an E2 ubiquitin-conjugating complex (UBC2-UEV1) essential for Leishmania amastigote differentiation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.260 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.220 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Leishmania differentiation requires ubiquitin conjugation mediated by a UBC2-UEV1 E2 complex.

Burge, R.J.Damianou, A.Wilkinson, A.J.Rodenko, B.Mottram, J.C.

(2020) PLoS Pathog 16: e1008784-e1008784

  • DOI: https://doi.org/10.1371/journal.ppat.1008784
  • Primary Citation of Related Structures:  
    6ZM3

  • PubMed Abstract: 

    Post-translational modifications such as ubiquitination are important for orchestrating the cellular transformations that occur as the Leishmania parasite differentiates between its main morphological forms, the promastigote and amastigote. 2 E1 ubiquitin-activating (E1), 13 E2 ubiquitin-conjugating (E2), 79 E3 ubiquitin ligase (E3) and 20 deubiquitinating cysteine peptidase (DUB) genes can be identified in the Leishmania mexicana genome but, currently, little is known about the role of E1, E2 and E3 enzymes in this parasite. Bar-seq analysis of 23 E1, E2 and HECT/RBR E3 null mutants generated in promastigotes using CRISPR-Cas9 revealed numerous loss-of-fitness phenotypes in promastigote to amastigote differentiation and mammalian infection. The E2s UBC1/CDC34, UBC2 and UEV1 and the HECT E3 ligase HECT2 are required for the successful transformation from promastigote to amastigote and UBA1b, UBC9, UBC14, HECT7 and HECT11 are required for normal proliferation during mouse infection. Of all ubiquitination enzyme null mutants examined in the screen, Δubc2 and Δuev1 exhibited the most extreme loss-of-fitness during differentiation. Null mutants could not be generated for the E1 UBA1a or the E2s UBC3, UBC7, UBC12 and UBC13, suggesting these genes are essential in promastigotes. X-ray crystal structure analysis of UBC2 and UEV1, orthologues of human UBE2N and UBE2V1/UBE2V2 respectively, reveal a heterodimer with a highly conserved structure and interface. Furthermore, recombinant L. mexicana UBA1a can load ubiquitin onto UBC2, allowing UBC2-UEV1 to form K63-linked di-ubiquitin chains in vitro. Notably, UBC2 can cooperate in vitro with human E3s RNF8 and BIRC2 to form non-K63-linked polyubiquitin chains, showing that UBC2 can facilitate ubiquitination independent of UEV1, but association of UBC2 with UEV1 inhibits this ability. Our study demonstrates the dual essentiality of UBC2 and UEV1 in the differentiation and intracellular survival of L. mexicana and shows that the interaction between these two proteins is crucial for regulation of their ubiquitination activity and function.


  • Organizational Affiliation
    • York Biomedical Research Institute and Department of Biology, University of York, United Kingdom.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ubiquitin-conjugating enzyme e2A [auth AAA],
C [auth CCC]
151Leishmania mexicana MHOM/GT/2001/U1103Mutation(s): 0 
Gene Names: LMXM_04_0680
EC: 6.3.2.19
UniProt
Find proteins for E9AK51 (Leishmania mexicana (strain MHOM/GT/2001/U1103))
Explore E9AK51 
Go to UniProtKB:  E9AK51
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9AK51
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme-like proteinB [auth BBB],
D [auth DDD]
141Leishmania mexicana MHOM/GT/2001/U1103Mutation(s): 0 
Gene Names: LMXM_13_1580
EC: 6.3.2.19
UniProt
Find proteins for E9API2 (Leishmania mexicana (strain MHOM/GT/2001/U1103))
Explore E9API2 
Go to UniProtKB:  E9API2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9API2
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.260 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.220 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.523α = 90
b = 72.568β = 91.839
c = 120.094γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/N018230/1
Medical Research Council (MRC, United Kingdom)United KingdomMR/K019384/1
Wellcome TrustUnited Kingdom200807/Z/16/Z
Wellcome TrustUnited Kingdom101528/Z/13/Z

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-22
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description