4FWG | pdb_00004fwg

Crystal structure of the Lon-like protease MtaLonC in complex with lactacystin

• PDB DOI: https://doi.org/10.2210/pdb4FWG/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Meiothermus taiwanensis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-07-01 Released: 2013-06-26 
• Deposition Author(s): Chang, C.I., Kuo, C.I., Huang, K.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.259 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Structures of an ATP-independent Lon-like protease and its complexes with covalent inhibitors

Liao, J.H., Ihara, K., Kuo, C.I., Huang, K.F., Wakatsuki, S., Wu, S.H., Chang, C.I.

(2013) Acta Crystallogr D Biol Crystallogr 69: 1395-1402

• PubMed: 23897463 
• DOI: https://doi.org/10.1107/S0907444913008214
• Primary Citation Related Structures: 
  4FW9, 4FWD, 4FWG, 4FWH


• PubMed Abstract: 
  

  The Lon proteases are a unique family of chambered proteases with a built-in AAA+ (ATPases associated with diverse cellular activities) module. Here, crystal structures of a unique member of the Lon family with no intrinsic ATPase activity in the proteolytically active form are reported both alone and in complexes with three covalent inhibitors: two peptidomimetics and one derived from a natural product. This work reveals the unique architectural features of an ATP-independent Lon that selectively degrades unfolded protein substrates. Importantly, these results provide mechanistic insights into the recognition of inhibitors and polypeptide substrates within the conserved proteolytic chamber, which may aid the development of specific Lon-protease inhibitors.

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Organizational Affiliation: 
• Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (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: 81.38 kDa 
• Atom Count: 5,178 
• Modeled Residue Count: 594 
• Deposited Residue Count: 732 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TTC1975 peptidase	A	732	Meiothermus taiwanensis	Mutation(s): 5  EC: 3.4.21.53
UniProt
Find proteins for C9DRU9 (Meiothermus taiwanensis) Explore C9DRU9  Go to UniProtKB:  C9DRU9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SLA	B [auth A]	Omuralide, open form C10 H17 N O4 NREVXJAQSWMFJZ-CHIQAWFVSA-N
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.259 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.987	α = 90
b = 115.987	β = 90
c = 135.054	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-26 
Deposition Author(s): Chang, C.I., Kuo, C.I., Huang, K.F.

Revision History  

• Version 1.0: 2013-06-26
  Type: Initial release
  
• Version 1.1: 2013-09-11
  Changes: Database references
• Version 1.2: 2014-08-13
  Changes: Non-polymer description
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-12-06
  Changes: Data collection
• Version 1.5: 2024-10-16
  Changes: Structure summary