6RFU | pdb_00006rfu

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

• PDB DOI: https://doi.org/10.2210/pdb6RFU/pdb

• Classification: IMMUNOSUPPRESSANT
• Organism(s): Trypanosoma brucei brucei
• Expression System: Insect cell expression vector pTIE1
• Mutation(s): No 


• Deposited: 2019-04-16 Released: 2020-02-19 
• Deposition Author(s): Nass, K., Redecke, L., Perbandt, M., Yefanov, O., Gabdulkhakov, A., Duszenko, M., Chapman, H.N., Betzel, C.
• Funding Organization(s): German Research Foundation, German Federal Ministry for Education and Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.232 (DCC) 
• R-Value Work: 
  0.209 (DCC) 

Starting Model: experimental

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

• PubMed: 32001697 
• DOI: https://doi.org/10.1038/s41467-020-14484-w
• Primary Citation 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.

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Organizational Affiliation: 
• Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.
Paul Scherrer Institute (PSI), Forschungstrasse 111, 5232, Villigen, PSI, Switzerland.
Joint Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg, and Institute of Biochemistry, University of Lübeck, at Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, 22607, Hamburg, Germany.
German Centre for Infection Research, University of Lübeck, 23562, Lübeck, Germany.
Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.
Deutsches Elektronen Synchrotron (DESY), Photon Science, Notkestr. 85, 22607, Hamburg, Germany.
Institute of Biochemistry and Molecular Biology, University of Hamburg, at Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, 22607, Hamburg, Germany.
The Hamburg Centre for Ultrafast Imaging (CUI), Luruper Chaussee 149, 22761, Hamburg, Germany.
BioAgilytix Europe GmbH, Lademannbogen 10, 22339, Hamburg, Germany.
Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str.4, 72076, Tübingen, Germany.
Dipartimento di Fisica, Università di Roma Tor Vergata and INFN, Via della Ricerca Scientifica 1, 00133, Rome, Italy.
Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya Str., Pushchino, Moscow Region, Russia, 142290.
BODE Chemie GmbH, Melanchthonstraße 27, 22525, Hamburg, Germany.
LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA.
Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ, 85287-160, USA.
European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, Grenoble, France.
Department of Physics, Arizona State University, Tempe, AZ, 85411, USA.
Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany.
Institute of Biology, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.
Biology and Biotechnology Division, Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA.
Max-Planck-Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany.
Department of Chemistry and Molecular Biology, University of Gothenburg, 40530, Gothenburg, Sweden.
Complex Systems Division, Beijing Computational Science Research Center, 100193, Beijing, China.
Center for Applied Structural Discovery (CASD), Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ, 85287, USA.
Brookhaven National Laboratory (BNL), PO Box 5000, Upton, NY, 11973-5000, USA.
ARC Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria, 3086, Australia.
Institute of Neurophysiology, University of Tübingen, Keplerstr. 15, 72074, Tübingen, Germany.
Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
Institute of Biochemistry and Molecular Biology, University of Hamburg, at Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, 22607, Hamburg, Germany. [e-mail].
The Hamburg Centre for Ultrafast Imaging (CUI), Luruper Chaussee 149, 22761, Hamburg, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 113.3 kDa 
• Atom Count: 6,909 
• Modeled Residue Count: 893 
• Deposited Residue Count: 1,024 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-5'-monophosphate dehydrogenase	A, B	512	Trypanosoma brucei brucei	Mutation(s): 0  EC: 1.1.1.205
UniProt
Find proteins for P50098 (Trypanosoma brucei brucei) Explore P50098  Go to UniProtKB:  P50098

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	C [auth A], E [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
5GP	D [auth A], F [auth B]	GUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O8 P RQFCJASXJCIDSX-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.232 (DCC) 
• R-Value Work:  0.209 (DCC) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 209	α = 90
b = 209	β = 90
c = 92	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-02-19 
Deposition Author(s): Nass, K., Redecke, L., Perbandt, M., Yefanov, O., Gabdulkhakov, A., Duszenko, M., Chapman, H.N., Betzel, C.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	EXC 1074 - project ID 194651731.
German Federal Ministry for Education and Research	Germany	05K2018-2017-06734

Revision History  

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