6RFU

In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of ATP and GMP as genuine co-factors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors.

Nass, K.Redecke, L.Perbandt, M.Yefanov, O.Klinge, M.Koopmann, R.Stellato, F.Gabdulkhakov, A.Schonherr, R.Rehders, D.Lahey-Rudolph, J.M.Aquila, A.Barty, A.Basu, S.Doak, R.B.Duden, R.Frank, M.Fromme, R.Kassemeyer, S.Katona, G.Kirian, R.Liu, H.Majoul, I.Martin-Garcia, J.M.Messerschmidt, M.Shoeman, R.L.Weierstall, U.Westenhoff, S.White, T.A.Williams, G.J.Yoon, C.H.Zatsepin, N.Fromme, P.Duszenko, M.Chapman, H.N.Betzel, C.

(2020) Nat Commun 11: 620-620

  • DOI: https://doi.org/10.1038/s41467-020-14484-w
  • Primary Citation of Related Structures:  
    6RFU

  • PubMed Abstract: 

    Sleeping sickness is a fatal disease caused by the protozoan parasite Trypanosoma brucei (Tb). Inosine-5'-monophosphate dehydrogenase (IMPDH) has been proposed as a potential drug target, since it maintains the balance between guanylate deoxynucleotide and ribonucleotide levels that is pivotal for the parasite. Here we report the structure of TbIMPDH at room temperature utilizing free-electron laser radiation on crystals grown in living insect cells. The 2.80 Å resolution structure reveals the presence of ATP and GMP at the canonical sites of the Bateman domains, the latter in a so far unknown coordination mode. Consistent with previously reported IMPDH complexes harboring guanosine nucleotides at the second canonical site, TbIMPDH forms a compact oligomer structure, supporting a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity. The oligomeric TbIMPDH structure we present here reveals the potential of in cellulo crystallization to identify genuine allosteric co-factors from a natural reservoir of specific compounds.


  • Organizational Affiliation

    Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inosine-5'-monophosphate dehydrogenase
A, B
512Trypanosoma brucei bruceiMutation(s): 0 
EC: 1.1.1.205
UniProt
Find proteins for P50098 (Trypanosoma brucei brucei)
Explore P50098 
Go to UniProtKB:  P50098
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50098
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209α = 90
b = 209β = 90
c = 92γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyEXC 1074 - project ID 194651731.
German Federal Ministry for Education and ResearchGermany05K2018-2017-06734

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Advisory, Data collection, Database references, Refinement description