4MKS

Crystal structure of enolase from Lactobacillus gasseri

• PDB DOI: https://doi.org/10.2210/pdb4MKS/pdb

• Classification: LYASE
• Organism(s): Lactobacillus gasseri ATCC 33323 = JCM 1131
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-09-05 Released: 2014-05-21 
• Deposition Author(s): Raghunathan, K., Harris, P.T., Spurbeck, R.R., Arvidson, C.G., Arvidson, D.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.234 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Starting Model: experimental

Literature

Crystal structure of an efficacious gonococcal adherence inhibitor: An enolase from Lactobacillus gasseri.

Raghunathan, K., Harris, P.T., Spurbeck, R.R., Arvidson, C.G., Arvidson, D.N.

(2014) FEBS Lett 588: 2212-2216

• PubMed: 24859038 
• DOI: https://doi.org/10.1016/j.febslet.2014.05.020
• Primary Citation of Related Structures:  
  4MKS


• PubMed Abstract: 
  

  Enolases are highly conserved metalloenzymes ubiquitous to cellular metabolism. While these enzymes share a large degree of sequence and structural similarity, they have been shown to possess a wide range of moonlighting functions. Recent studies showed that an enolase from Lactobacillus gasseri impedes the ability of Neisseria gonorrhoeae to adhere to epithelial cells. We present the crystal structure of this enolase, the first from Lactobacillus, with one of its Mg(2+) cofactors. Determined using molecular replacement to 2.08Å, the structure has a flexible and surface exposed catalytic loop containing lysines, and may play a role in the inhibitory function.

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Organizational Affiliation: 

Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA. Electronic address: [e-mail].

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)

Biological Assembly 2  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 96.09 kDa 
• Atom Count: 6,614 
• Modelled Residue Count: 797 
• Deposited Residue Count: 880 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enolase 2	A, B	440	Lactobacillus gasseri ATCC 33323 = JCM 1131	Mutation(s): 0  Gene Names: eno2, LGAS_1305 EC: 4.2.1.11
UniProt
Find proteins for Q042F4 (Lactobacillus gasseri (strain ATCC 33323 / DSM 20243 / BCRC 14619 / CIP 102991 / JCM 1131 / KCTC 3163 / NCIMB 11718 / NCTC 13722 / AM63)) Explore Q042F4  Go to UniProtKB:  Q042F4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	D [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.234 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.24	α = 90
b = 145.24	β = 90
c = 99.86	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
ARP/wARP	model building
PHENIX	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-21 
Deposition Author(s): Raghunathan, K., Harris, P.T., Spurbeck, R.R., Arvidson, C.G., Arvidson, D.N.

Revision History  

• Version 1.0: 2014-05-21
  Type: Initial release
  
• Version 1.1: 2014-06-18
  Changes: Database references
• Version 1.2: 2014-07-02
  Changes: Database references
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description