2Y3U | pdb_00002y3u

Crystal structure of apo collagenase G from Clostridium histolyticum at 2.55 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb2Y3U/pdb

• Classification: HYDROLASE
• Organism(s): Hathewaya histolytica
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2010-12-26 Released: 2011-09-28 
• Deposition Author(s): Eckhard, U., Brandstetter, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.256 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

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

• PubMed: 21947205 
• 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 90.17 kDa 
• Atom Count: 5,615 
• Modeled Residue Count: 679 
• Deposited Residue Count: 785 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COLLAGENASE	A	785	Hathewaya histolytica	Mutation(s): 0  EC: 3.4.24.3 Membrane Entity: Yes
UniProt
Find proteins for Q9X721 (Hathewaya histolytica) Explore Q9X721  Go to UniProtKB:  Q9X721

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	B [auth A]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
FLC	C [auth A]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
PEG	D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

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: 2.55 Å
• R-Value Free:  0.256 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.96	α = 90
b = 109.05	β = 90
c = 182.46	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-28 
Deposition Author(s): Eckhard, U., Brandstetter, H.

Revision History  

• Version 1.0: 2011-09-28
  Type: Initial release
  
• Version 1.1: 2011-10-19
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary