2Y6I | pdb_00002y6i

Crystal Structure of Collagenase G from Clostridium histolyticum in complex with Isoamylphosphonyl-Gly-Pro-Ala at 3.25 Angstrom Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 
    0.266 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2Y6I

This is version 1.4 of the entry. See complete history

Literature

Structure of Collagenase G Reveals a Chew-and -Digest Mechanism of Bacterial Collagenolysis

Eckhard, U.Schoenauer, E.Nuess, D.Brandstetter, H.

(2011) Nat Struct Mol Biol 18: 1109

  • DOI: https://doi.org/10.1038/nsmb.2127
  • Primary Citation Related Structures: 
    2Y3U, 2Y50, 2Y6I, 2Y72

  • PubMed Abstract: 

    Collagen constitutes one-third of body protein in humans, reflecting its extensive role in health and disease. Of similar importance, therefore, are the idiosyncratic proteases that have evolved for collagen remodeling. The most efficient collagenases are those that enable clostridial bacteria to colonize their host tissues; but despite intense study, the structural and mechanistic basis of these enzymes has remained elusive. Here we present the crystal structure of collagenase G from Clostridium histolyticum at 2.55-Å resolution. By combining the structural data with enzymatic and mutagenesis studies, we derive a conformational two-state model of bacterial collagenolysis, in which recognition and unraveling of collagen microfibrils into triple helices, as well as unwinding of the triple helices, are driven by collagenase opening and closing.


  • Organizational Affiliation
    • Division of Structural Biology, Department of Molecular Biology, University of Salzburg, Salzburg, Austria.

Macromolecule Content 

  • Total Structure Weight: 90.48 kDa 
  • Atom Count: 5,378 
  • Modeled Residue Count: 675 
  • Deposited Residue Count: 789 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
COLLAGENASE785Hathewaya histolyticaMutation(s): 0 
EC: 3.4.24.3
UniProt
Find proteins for Q9X721 (Hathewaya histolytica)
Explore Q9X721 
Go to UniProtKB:  Q9X721
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X721
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ISOAMYLPHOSPHONYL-GLY-PRO-ALA4synthetic constructMutation(s): 0 

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE

Query on 1PE



Download:Ideal Coordinates CCD File
J [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
FLC

Query on FLC



Download:Ideal Coordinates CCD File
D [auth A]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
TRS

Query on TRS



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG

Query on PEG



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free:  0.266 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.12α = 90
b = 108.84β = 90
c = 181.03γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-28
    Type: Initial release
  • Version 1.1: 2011-10-19
    Changes: Database references
  • Version 1.2: 2012-11-30
    Changes: Other
  • Version 1.3: 2015-09-16
    Changes: Source and taxonomy
  • Version 1.4: 2024-10-09
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary