4B52 | pdb_00004b52

Crystal structure of Gentlyase, the neutral metalloprotease of Paenibacillus polymyxa

• PDB DOI: https://doi.org/10.2210/pdb4B52/pdb

• Classification: HYDROLASE
• Organism(s): Paenibacillus polymyxa
• Expression System: Bacillus amyloliquefaciens
• Mutation(s): No 


• Deposited: 2012-08-02 Released: 2013-01-09 
• Deposition Author(s): Ruf, A., Stihle, M., Benz, J., Schmidt, M., Sobek, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.247 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa

Ruf, A., Stihle, M., Benz, J., Schmidt, M., Sobek, H.

(2013) Acta Crystallogr D Biol Crystallogr 69: 24

• PubMed: 23275160 
• DOI: https://doi.org/10.1107/S0907444912041169
• Primary Citation Related Structures: 
  4B52, 4GER


• PubMed Abstract: 
  

  Gentlyase is a bacterial extracellular metalloprotease that is widely applied in cell culture and for tissue dissociation and that belongs to the family of thermolysin-like proteases. The structure of thermolysin has been known since 1972 and that of Bacillus cereus neutral protease since 1992. However, the structure determination of other Bacillus neutral proteases has been hindered by their tendency to cannibalistic autolysis. High calcium conditions that allow the concentration and crystallization of the active Gentlyase metalloprotease without autoproteolysis were identified using thermal fluorescent shift assays. X-ray structures of the protease were solved in the absence and in the presence of the inhibitor phosphoramidon at 1.59 and 1.76 Å resolution, respectively. No domain movement was observed upon inhibitor binding, although such movement is thought to be a general feature of the thermolysin-like protease family. Further analysis of the structure shows that the observed calcium dependency of Gentlyase stability may arise from a partly degenerated calcium site Ca1-2 and a deletion near site Ca3.

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Organizational Affiliation: 
• pRED Pharma Research and Early Development, Small Molecule Research, Discovery Technologies, F. Hoffmann-La Roche Ltd, Basel, Switzerland. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 66.3 kDa 
• Atom Count: 5,295 
• Modeled Residue Count: 608 
• Deposited Residue Count: 608 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BACILLOLYSIN	A, B	304	Paenibacillus polymyxa	Mutation(s): 0  EC: 3.4.24.4 (PDB Primary Data), 3.4.24 (UniProt)
UniProt
Find proteins for E3E6L0 (Paenibacillus polymyxa (strain SC2)) Explore E3E6L0  Go to UniProtKB:  E3E6L0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RDF	G [auth A], M [auth B]	N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN C23 H34 N3 O10 P ZPHBZEQOLSRPAK-XLCYBJAPSA-N
ZN	C [auth A], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	D [auth A], E [auth A], F [auth A], J [auth B], K [auth B], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000638 (RDF)	G [auth A], M [auth B]	PHOSPHORAMIDON	Glycopeptide / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.247 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.121	α = 90
b = 77.021	β = 103.58
c = 64.443	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SADABS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-09 
Deposition Author(s): Ruf, A., Stihle, M., Benz, J., Schmidt, M., Sobek, H.

Revision History  

• Version 1.0: 2013-01-09
  Type: Initial release
  
• Version 1.1: 2013-01-23
  Changes: Database references
• Version 1.2: 2013-03-06
  Changes: Other
• Version 1.3: 2013-03-20
  Changes: Atomic model
• Version 1.4: 2013-07-24
  Changes: Other
• Version 1.5: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description