6Z6S

Crystal structure of Uba4-Urm1 from Chaetomium thermophilum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular basis for the bifunctional Uba4-Urm1 sulfur-relay system in tRNA thiolation and ubiquitin-like conjugation.

Pabis, M.Termathe, M.Ravichandran, K.E.Kienast, S.D.Krutyholowa, R.Sokolowski, M.Jankowska, U.Grudnik, P.Leidel, S.A.Glatt, S.

(2020) EMBO J 39: e105087-e105087

  • DOI: 10.15252/embj.2020105087
  • Primary Citation of Related Structures:  
    6YUB, 6YUC, 6Z6S

  • PubMed Abstract: 
  • The chemical modification of tRNA bases by sulfur is crucial to tune translation and to optimize protein synthesis. In eukaryotes, the ubiquitin-related modifier 1 (Urm1) pathway is responsible for the synthesis of 2-thiolated wobble uridine (U 34 ) ...

    The chemical modification of tRNA bases by sulfur is crucial to tune translation and to optimize protein synthesis. In eukaryotes, the ubiquitin-related modifier 1 (Urm1) pathway is responsible for the synthesis of 2-thiolated wobble uridine (U 34 ). During the key step of the modification cascade, the E1-like activating enzyme ubiquitin-like protein activator 4 (Uba4) first adenylates and thiocarboxylates the C-terminus of its substrate Urm1. Subsequently, activated thiocarboxylated Urm1 (Urm1-COSH) can serve as a sulfur donor for specific tRNA thiolases or participate in ubiquitin-like conjugation reactions. Structural and mechanistic details of Uba4 and Urm1 have remained elusive but are key to understand the evolutionary branch point between ubiquitin-like proteins (UBL) and sulfur-relay systems. Here, we report the crystal structures of full-length Uba4 and its heterodimeric complex with its substrate Urm1. We show how the two domains of Uba4 orchestrate recognition, binding, and thiocarboxylation of the C-terminus of Urm1. Finally, we uncover how the catalytic domains of Uba4 communicate efficiently during the reaction cycle and identify a mechanism that enables Uba4 to protect itself against self-conjugation with its own product, namely activated Urm1-COSH.


    Organizational Affiliation

    Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Adenylyltransferase and sulfurtransferase uba4A [auth DDD]301Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 1 
Gene Names: uba4cnxFCTHT_0055980
EC: 2.7.7.80 (PDB Primary Data), 2.8.1.11 (PDB Primary Data)
UniProt
Find proteins for G0SC54 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SC54 
Go to UniProtKB:  G0SC54
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-related modifier 1B [auth GGG]101Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: URM1CTHT_0062030
UniProt
Find proteins for G0SE11 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SE11 
Go to UniProtKB:  G0SE11
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth DDD]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.210 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 197.735α = 90
b = 197.735β = 90
c = 99.566γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePoland2018/31/B/NZ1/03559
Foundation for Polish SciencePolandFirstTEAM/2016-1/2
Foundation for Polish SciencePolandTEAM TECH CORE FACILITY/2017-4/6

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-22
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references
  • Version 1.2: 2020-10-14
    Changes: Database references