3RUQ

Crystal structure of Cpn-WT in complex with ADP from Methanococcus maripaludis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.798 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mechanism of nucleotide sensing in group II chaperonins.

Pereira, J.H.Ralston, C.Y.Douglas, N.R.Kumar, R.Lopez, T.McAndrew, R.P.Knee, K.M.King, J.A.Frydman, J.Adams, P.D.

(2012) Embo J. 31: 731-740

  • DOI: 10.1038/emboj.2011.468
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Group II chaperonins mediate protein folding in an ATP-dependent manner in eukaryotes and archaea. The binding of ATP and subsequent hydrolysis promotes the closure of the multi-subunit rings where protein folding occurs. The mechanism by which local ...

    Group II chaperonins mediate protein folding in an ATP-dependent manner in eukaryotes and archaea. The binding of ATP and subsequent hydrolysis promotes the closure of the multi-subunit rings where protein folding occurs. The mechanism by which local changes in the nucleotide-binding site are communicated between individual subunits is unknown. The crystal structure of the archaeal chaperonin from Methanococcus maripaludis in several nucleotides bound states reveals the local conformational changes associated with ATP hydrolysis. Residue Lys-161, which is extremely conserved among group II chaperonins, forms interactions with the γ-phosphate of ATP but shows a different orientation in the presence of ADP. The loss of the ATP γ-phosphate interaction with Lys-161 in the ADP state promotes a significant rearrangement of a loop consisting of residues 160-169. We propose that Lys-161 functions as an ATP sensor and that 160-169 constitutes a nucleotide-sensing loop (NSL) that monitors the presence of the γ-phosphate. Functional analysis using NSL mutants shows a significant decrease in ATPase activity, suggesting that the NSL is involved in timing of the protein folding cycle.


    Organizational Affiliation

    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chaperonin
A, B, C, D
543Methanococcus maripaludisMutation(s): 0 
Find proteins for Q877G8 (Methanococcus maripaludis)
Go to UniProtKB:  Q877G8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B, C, D
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.798 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.171 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 162.164α = 90.00
b = 185.002β = 90.00
c = 184.769γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-04
    Type: Initial release
  • Version 1.1: 2012-02-15
    Type: Database references