3S2Z

Crystal structure of the Lactobacillus johnsonii cinnamoyl esterase LJ0536 S106A mutant in complex with caffeic acid

• PDB DOI: https://doi.org/10.2210/pdb3S2Z/pdb

• Classification: HYDROLASE
• Organism(s): Lactobacillus johnsonii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-05-17 Released: 2011-08-31 
• Deposition Author(s): Stogios, P.J., Lai, K.K., Vu, C., Xu, X., Cui, H., Molloy, S., Gonzalez, C.F., Yakunin, A., Savchenko, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.209 
• R-Value Work: 0.143 
• R-Value Observed: 0.146 

Literature

An inserted alpha/beta subdomain shapes the catalytic pocket of Lactobacillus johnsonii cinnamoyl esterase.

Lai, K.K., Stogios, P.J., Vu, C., Xu, X., Cui, H., Molloy, S., Savchenko, A., Yakunin, A., Gonzalez, C.F.

(2011) PLoS One 6: e23269-e23269

• PubMed: 21876742 
• DOI: https://doi.org/10.1371/journal.pone.0023269
• Primary Citation of Related Structures:  
  3PF8, 3PF9, 3PFB, 3PFC, 3QM1, 3S2Z


• PubMed Abstract: 
  

  Microbial enzymes produced in the gastrointestinal tract are primarily responsible for the release and biochemical transformation of absorbable bioactive monophenols. In the present work we described the crystal structure of LJ0536, a serine cinnamoyl esterase produced by the probiotic bacterium Lactobacillus johnsonii N6.2.

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Organizational Affiliation: 

Department of Microbiology and Cell Science, Genetics Institute, University of Florida, Gainesville, Florida, United States of America.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 60.95 kDa 
• Atom Count: 4,409 
• Modelled Residue Count: 501 
• Deposited Residue Count: 540 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cinnamoyl esterase	A, B	270	Lactobacillus johnsonii	Mutation(s): 1  Gene Names: LJ0536 EC: 3.1.1
UniProt
Find proteins for D3YEX6 (Lactobacillus johnsonii) Explore D3YEX6  Go to UniProtKB:  D3YEX6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DHC	L [auth A], T [auth B]	CAFFEIC ACID C9 H8 O4 QAIPRVGONGVQAS-DUXPYHPUSA-N
CL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.209 
• R-Value Work: 0.143 
• R-Value Observed: 0.146 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.318	α = 90
b = 84.168	β = 97.56
c = 87.604	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-31 
Deposition Author(s): Stogios, P.J., Lai, K.K., Vu, C., Xu, X., Cui, H., Molloy, S., Gonzalez, C.F., Yakunin, A., Savchenko, A.

Revision History  

• Version 1.0: 2011-08-31
  Type: Initial release
  
• Version 1.1: 2012-10-24
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description