6QP0 | pdb_00006qp0

Crystal structure of Chaetomium thermophilum Kti12 in complex with ADP-AlF3

• PDB DOI: https://doi.org/10.2210/pdb6QP0/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Thermochaetoides thermophila
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-02-13 Released: 2019-03-13 
• Deposition Author(s): Krutyholowa, R., Glatt, S.
• Funding Organization(s): Polish National Science Centre

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 
  0.275 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Literature

Kti12, a PSTK-like tRNA dependent ATPase essential for tRNA modification by Elongator.

Krutyholowa, R., Hammermeister, A., Zabel, R., Abdel-Fattah, W., Reinhardt-Tews, A., Helm, M., Stark, M.J.R., Breunig, K.D., Schaffrath, R., Glatt, S.

(2019) Nucleic Acids Res 47: 4814-4830

• PubMed: 30916349 
• DOI: https://doi.org/10.1093/nar/gkz190
• Primary Citation Related Structures: 
  6QP0


• PubMed Abstract: 
  

  Posttranscriptional RNA modifications occur in all domains of life. Modifications of anticodon bases are of particular importance for ribosomal decoding and proteome homeostasis. The Elongator complex modifies uridines in the wobble position and is highly conserved in eukaryotes. Despite recent insights into Elongator's architecture, the structure and function of its regulatory factor Kti12 have remained elusive. Here, we present the crystal structure of Kti12's nucleotide hydrolase domain trapped in a transition state of ATP hydrolysis. The structure reveals striking similarities to an O-phosphoseryl-tRNA kinase involved in the selenocysteine pathway. Both proteins employ similar mechanisms of tRNA binding and show tRNASec-dependent ATPase activity. In addition, we demonstrate that Kti12 binds directly to Elongator and that ATP hydrolysis is crucial for Elongator to maintain proper tRNA anticodon modification levels in vivo. In summary, our data reveal a hitherto uncharacterized link between two translational control pathways that regulate selenocysteine incorporation and affect ribosomal tRNA selection via specific tRNA modifications.

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Organizational Affiliation: 
• Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
Institut für Biologie, FG Mikrobiologie, Universität Kassel, Kassel, Germany.
Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany.
Institut für Pharmazie und Biochemie, Universität Mainz, Mainz, Germany.
Centre for Gene Regulation & Expression, University of Dundee, Dundee, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 30.8 kDa 
• Atom Count: 1,590 
• Modeled Residue Count: 188 
• Deposited Residue Count: 263 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative chromatin binding protein	A	263	Thermochaetoides thermophila	Mutation(s): 0  Gene Names: CTHT_0070100
UniProt
Find proteins for G0SHI1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0SHI1  Go to UniProtKB:  G0SHI1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MES	E [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
AF3 (Subject of Investigation/LOI)	C [auth A]	ALUMINUM FLUORIDE Al F3 KLZUFWVZNOTSEM-UHFFFAOYSA-K
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.275 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.02	α = 90
b = 71.02	β = 90
c = 88.57	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
SHELXS	phasing
RESOLVE	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-03-13 
Deposition Author(s): Krutyholowa, R., Glatt, S.

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Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	UMO-2015/19/B/NZ1/00343

Revision History  

• Version 1.0: 2019-03-13
  Type: Initial release
  
• Version 1.1: 2019-03-20
  Changes: Data collection, Refinement description
• Version 1.2: 2019-04-10
  Changes: Data collection, Database references
• Version 1.3: 2019-05-22
  Changes: Data collection, Database references
• Version 1.4: 2024-05-15
  Changes: Data collection, Database references