5G1S

Open conformation of Francisella tularensis ClpP at 1.7 A

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Open and compressed conformations of Francisella tularensis ClpP.

Diaz-Saez, L., Pankov, G., Hunter, W.N.

(2017) Proteins 85: 188-194

  • DOI: https://doi.org/10.1002/prot.25197
  • Primary Citation of Related Structures:  
    5G1Q, 5G1R, 5G1S

  • PubMed Abstract: 

    Caseinolytic proteases are large oligomeric assemblies responsible for maintaining protein homeostasis in bacteria and in so doing influence a wide range of biological processes. The functional assembly involves three chaperones together with the oligomeric caseinolytic protease catalytic subunit P (ClpP). This protease represents a potential target for therapeutic intervention in pathogenic bacteria. Here, we detail an efficient protocol for production of recombinant ClpP from Francisella tularensis, and the structural characterization of three crystal forms which grow under similar conditions. One crystal form reveals a compressed state of the ClpP tetradecamer and two forms an open state. A comparison of the two types of structure infers that differences at the enzyme active site result from a conformational change involving a highly localized disorder-order transition of a β-strand α-helix combination. This transition occurs at a subunit-subunit interface. Our study may now underpin future efforts in a structure-based approach to target ClpP for inhibitor or activator development. Proteins 2016; 85:188-194. © 2016 Wiley Periodicals, Inc.

    • Organizational Affiliation: 

    Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease proteolytic subunit
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U
201Francisella tularensisMutation(s): 0 
Gene Names: clpP, DR86_1343
EC: 3.4.21.92
UniProt
Find proteins for Q5NH47 (Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4))
Explore Q5NH47 
Go to UniProtKB:  Q5NH47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5NH47
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD
Download Ideal Coordinates CCD File 
AB [auth M]
CB [auth N]
FA [auth E]
HA [auth F]
IA [auth F]
AB [auth M],
CB [auth N],
FA [auth E],
HA [auth F],
IA [auth F],
LA [auth G],
MB [auth S],
OA [auth I],
PB [auth T],
RA [auth J],
UB [auth U],
X [auth B],
YA [auth L],
Z [auth C]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
MRD
Query on MRD
Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
DB [auth N]
EA [auth D]
FB [auth O]
AA [auth C],
BA [auth C],
DB [auth N],
EA [auth D],
FB [auth O],
HB [auth P],
JB [auth Q],
KA [auth G],
NB [auth S],
PA [auth I],
QB [auth T],
RB [auth T],
TA [auth K],
TB [auth U],
UA [auth K],
V [auth A],
VA [auth K],
XA [auth L]
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
ACT
Query on ACT
Download Ideal Coordinates CCD File 
BB [auth M]
CA [auth C]
DA [auth D]
EB [auth N]
GA [auth E]
BB [auth M],
CA [auth C],
DA [auth D],
EB [auth N],
GA [auth E],
GB [auth O],
IB [auth P],
JA [auth F],
KB [auth Q],
LB [auth R],
MA [auth G],
NA [auth H],
OB [auth S],
QA [auth I],
SA [auth J],
SB [auth T],
VB [auth U],
W [auth A],
WA [auth K],
Y [auth B],
ZA [auth L]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.226α = 90
b = 127.924β = 90
c = 353.843γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2017-03-15
    Changes: Database references
  • Version 1.2: 2019-03-06
    Changes: Advisory, Data collection, Experimental preparation
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation