2DHR | pdb_00002dhr

Whole cytosolic region of ATP-dependent metalloprotease FtsH (G399L)

• PDB DOI: https://doi.org/10.2210/pdb2DHR/pdb

• Classification: HYDROLASE
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-03-24 Released: 2006-06-27 
• Deposition Author(s): Suno, R., Niwa, H., Tsuchiya, D., Zhang, X., Yoshida, M., Morikawa, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.90 Å
• R-Value Free: 
  0.342 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.299 (Depositor) 
• R-Value Observed: 
  0.301 (Depositor) 

Literature

Structure of the Whole Cytosolic Region of ATP-Dependent Protease FtsH

Suno, R., Niwa, H., Tsuchiya, D., Zhang, X., Yoshida, M., Morikawa, K.

(2006) Mol Cell 22: 575-585

• PubMed: 16762831 
• DOI: https://doi.org/10.1016/j.molcel.2006.04.020
• Primary Citation Related Structures: 
  2DHR, 2DI4, 4EIW


• PubMed Abstract: 
  

  An ATP-dependent protease, FtsH, digests misassembled membrane proteins in order to maintain membrane integrity and digests short-lived soluble proteins in order to control their cellular regulation. This enzyme has an N-terminal transmembrane segment and a C-terminal cytosolic region consisting of an AAA+ ATPase domain and a protease domain. Here we present two crystal structures: the protease domain and the whole cytosolic region. The cytosolic region fully retains an ATP-dependent protease activity and adopts a three-fold-symmetric hexameric structure. The protease domains displayed a six-fold symmetry, while the AAA+ domains, each containing ADP, alternate two orientations relative to the protease domain, making "open" and "closed" interdomain contacts. Apparently, ATPase is active only in the closed form, and protease operates in the open form. The protease catalytic sites are accessible only through a tunnel following from the AAA+ domain of the adjacent subunit, raising a possibility of translocation of polypeptide substrate to the protease sites through this tunnel.

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Organizational Affiliation: 
• Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8503, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 334.78 kDa 
• Atom Count: 21,460 
• Modeled Residue Count: 2,715 
• Deposited Residue Count: 2,994 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FtsH	A, B, C, D, E, F	499	Thermus thermophilus	Mutation(s): 1  EC: 3.4.24
UniProt
Find proteins for Q5SI82 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SI82  Go to UniProtKB:  Q5SI82

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.90 Å
• R-Value Free:  0.342 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.299 (Depositor) 
• R-Value Observed: 0.301 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.153	α = 90
b = 146.153	β = 90
c = 349.064	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-27 
Deposition Author(s): Suno, R., Niwa, H., Tsuchiya, D., Zhang, X., Yoshida, M., Morikawa, K.

Revision History  

• Version 1.0: 2006-06-27
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.4: 2024-05-29
  Changes: Data collection