3EN9

Structure of the Methanococcus jannaschii KAE1-BUD32 fusion protein

• PDB DOI:  https://doi.org/10.2210/pdb3EN9/pdb

• Classification: HYDROLASE
• Organism(s): Methanocaldococcus jannaschii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-25 Released: 2008-11-04 
• Deposition Author(s): Neculai, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free: 0.264 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 

Literature

Atomic structure of the KEOPS complex: an ancient protein kinase-containing molecular machine.

Mao, D.Y., Neculai, D., Downey, M., Orlicky, S., Haffani, Y.Z., Ceccarelli, D.F., Ho, J.S., Szilard, R.K., Zhang, W., Ho, C.S., Wan, L., Fares, C., Rumpel, S., Kurinov, I., Arrowsmith, C.H., Durocher, D., Sicheri, F.

(2008) Mol Cell 32: 259-275

• PubMed: 18951093 
• DOI: https://doi.org/10.1016/j.molcel.2008.10.002
• Primary Citation of Related Structures:  
  2K8Y, 3EN9, 3ENC, 3ENH, 3ENO, 3ENP


• PubMed Abstract: 
  

Kae1 is a universally conserved ATPase and part of the essential gene set in bacteria. In archaea and eukaryotes, Kae1 is embedded within the protein kinase-containing KEOPS complex. Mutation of KEOPS subunits in yeast leads to striking telomere and transcription defects, but the exact biochemical function of KEOPS is not known. As a first step to elucidating its function, we solved the atomic structure of archaea-derived KEOPS complexes involving Kae1, Bud32, Pcc1, and Cgi121 subunits. Our studies suggest that Kae1 is regulated at two levels by the primordial protein kinase Bud32, which is itself regulated by Cgi121. Moreover, Pcc1 appears to function as a dimerization module, perhaps suggesting that KEOPS may be a processive molecular machine. Lastly, as Bud32 lacks the conventional substrate-recognition infrastructure of eukaryotic protein kinases including an activation segment, Bud32 may provide a glimpse of the evolutionary history of the protein kinase family.

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Organizational Affiliation: 

Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, M5G 1X5, Canada.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 126.39 kDa 
• Atom Count: 8,306 
• Modelled Residue Count: 1,030 
• Deposited Residue Count: 1,080 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-sialoglycoprotein endopeptidase/protein kinase	A, B	540	Methanocaldococcus jannaschii	Mutation(s): 0  Gene Names: gcp, MJ1130 EC: 3.4.24.57 (PDB Primary Data), 2.3.1.234 (UniProt), 2.7.11.1 (UniProt)
UniProt
Find proteins for Q58530 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58530  Go to UniProtKB:  Q58530

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TBR	D [auth A], F [auth B]	HEXATANTALUM DODECABROMIDE Br12 Ta6 YWYIQTPPCOBSGN-UHFFFAOYSA-M
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free: 0.264 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 
• Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.73	α = 90
b = 148.73	β = 90
c = 136.42	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-04 
Deposition Author(s): Neculai, D.

Revision History  

• Version 1.0: 2008-11-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance