5XE9 | pdb_00005xe9

Crystal Structure of the Complex of the Peptidase Domain of Streptococcus mutans ComA with a Small Molecule Inhibitor.

• PDB DOI: https://doi.org/10.2210/pdb5XE9/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Streptococcus mutans UA159
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-04-03 Released: 2017-06-28 
• Deposition Author(s): Ishii, S., Fukui, K., Yokoshima, S., Kumagai, K., Beniyama, Y., Kodama, T., Fukuyama, T., Okabe, T., Nagano, T., Kojima, H., Yano, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.285 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.246 (Depositor), 0.247 (DCC) 
• R-Value Observed: 
  0.248 (Depositor) 

Starting Model: experimental

Literature

High-throughput Screening of Small Molecule Inhibitors of the Streptococcus Quorum-sensing Signal Pathway

Ishii, S., Fukui, K., Yokoshima, S., Kumagai, K., Beniyama, Y., Kodama, T., Fukuyama, T., Okabe, T., Nagano, T., Kojima, H., Yano, T.

(2017) Sci Rep 7: 4029-4029

• PubMed: 28642545 
• DOI: https://doi.org/10.1038/s41598-017-03567-2
• Primary Citation Related Structures: 
  5XE8, 5XE9


• PubMed Abstract: 
  

  The main components of the quorum-sensing system are expected to be favorable targets for drug development to combat various chronic infectious diseases. ComA of Streptococcus is an ATP-binding cassette transporter containing a peptidase domain (PEP), which is essential for the quorum-sensing signal production. Using high-throughput screening, we found a potent small molecule that suppressed the S. mutans quorum-sensing pathway through inhibition of PEP activity. The compound effectively attenuated the biofilm formation and competence development of S. mutans without inhibiting cell growth. The kinetic and structural studies with this molecule and a related compound unexpectedly revealed an allosteric site of PEP. This relatively hydrophobic site is thought to undergo large structural changes during the catalytic process. These compounds inhibit PEP activity by binding to and suppressing the structural changes of this site. These results showed that PEP is a good target for inhibitors of the Streptococcus quorum-sensing system.

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Organizational Affiliation: 
• Department of Biochemistry, Osaka Medical College, Takatsuki, Osaka, 569-8686, Japan. [e-mail].
Department of Biochemistry, Osaka Medical College, Takatsuki, Osaka, 569-8686, Japan.
Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.
Drug Discovery Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
Center for Membrane and Film Technology, Graduate School of Engineering, Kobe University, Kobe, Japan.
Department of Biochemistry, Osaka Medical College, Takatsuki, Osaka, 569-8686, Japan. [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)

Macromolecule Content 

• Total Structure Weight: 35.12 kDa 
• Atom Count: 2,080 
• Modeled Residue Count: 258 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative ABC transporter, ATP-binding protein ComA	A, B	152	Streptococcus mutans UA159	Mutation(s): 0  Gene Names: SMU_286
UniProt
Find proteins for Q8DW05 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DW05  Go to UniProtKB:  Q8DW05

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6CH	C [auth B]	[(1~{S},2~{R},4~{S},5~{R})-5-[5-(4-methoxyphenyl)-2-methyl-pyrazol-3-yl]-1-azabicyclo[2.2.2]octan-2-yl]methyl ~{N}-propylcarbamate C23 H32 N4 O3 WHTNZQHPDMCEMQ-NSHGMRRFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.285 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.246 (Depositor), 0.247 (DCC) 
• R-Value Observed: 0.248 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.785	α = 90
b = 59.764	β = 90
c = 122.589	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	model building
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-28 
Deposition Author(s): Ishii, S., Fukui, K., Yokoshima, S., Kumagai, K., Beniyama, Y., Kodama, T., Fukuyama, T., Okabe, T., Nagano, T., Kojima, H., Yano, T.

Revision History  

• Version 1.0: 2017-06-28
  Type: Initial release
  
• Version 1.1: 2017-08-16
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2023-11-22
  Changes: Refinement description