4CI7 | pdb_00004ci7

The crystal structure of the cysteine protease and lectin-like domains of Cwp84, a surface layer associated protein of Clostridium difficile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.169 (Depositor), 0.193 (DCC) 
  • R-Value Work: 
    0.138 (Depositor) 
  • R-Value Observed: 
    0.140 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

The Structure of the Cysteine Protease and Lectin-Like Domains of Cwp84, a Surface Layer-Associated Protein from Clostridium Difficile

Bradshaw, W.J.Kirby, J.M.Thiyagarajan, N.Chambers, C.J.Davies, A.H.Roberts, A.K.Shone, C.C.Acharya, K.R.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1983

  • DOI: https://doi.org/10.1107/S1399004714009997
  • Primary Citation Related Structures: 
    4CI7

  • PubMed Abstract: 

    Clostridium difficile is a major problem as an aetiological agent for antibiotic-associated diarrhoea. The mechanism by which the bacterium colonizes the gut during infection is poorly understood, but undoubtedly involves a myriad of components present on the bacterial surface. The mechanism of C. difficile surface-layer (S-layer) biogenesis is also largely unknown but involves the post-translational cleavage of a single polypeptide (surface-layer protein A; SlpA) into low- and high-molecular-weight subunits by Cwp84, a surface-located cysteine protease. Here, the first crystal structure of the surface protein Cwp84 is described at 1.4 Å resolution and the key structural components are identified. The truncated Cwp84 active-site mutant (amino-acid residues 33-497; C116A) exhibits three regions: a cleavable propeptide and a cysteine protease domain which exhibits a cathepsin L-like fold followed by a newly identified putative carbohydrate-binding domain with a bound calcium ion, which is referred to here as a lectin-like domain. This study thus provides the first structural insights into Cwp84 and a strong base to elucidate its role in the C. difficile S-layer maturation mechanism.


  • Organizational Affiliation
    • Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, England.

Macromolecule Content 

  • Total Structure Weight: 106.3 kDa 
  • Atom Count: 8,436 
  • Modeled Residue Count: 910 
  • Deposited Residue Count: 940 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CELL SURFACE PROTEIN (PUTATIVE CELL SURFACE-ASSOCIATED CYSTEINE PROTEASE)
A, B
470Clostridioides difficile QCD-32g58Mutation(s): 1 
EC: 3.4.22.15

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE

Query on PGE



Download:Ideal Coordinates CCD File
K [auth A]
L [auth A]
M [auth A]
N [auth A]
Q [auth B]
K [auth A],
L [auth A],
M [auth A],
N [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A],
O [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
J [auth A],
P [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.169 (Depositor), 0.193 (DCC) 
  • R-Value Work:  0.138 (Depositor) 
  • R-Value Observed: 0.140 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.91α = 90
b = 73.49β = 93.57
c = 125.63γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
CRANKphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2014-07-09
    Changes: Database references
  • Version 1.2: 2014-07-23
    Changes: Database references
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other