9KHA | pdb_00009kha

Crystal structure of maltodextrin-binding protein SPs0871 from Streptococcus pyogenes at 2.20 A

• PDB DOI: https://doi.org/10.2210/pdb9KHA/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Streptococcus pyogenes M1 GAS
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-11-09 Released: 2025-06-25 
• Deposition Author(s): Caaveiro, J.M.M., Yamawaki, T., Tsumoto, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.224 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.193 (DCC) 

Starting Model: experimental

Literature

Development of a small compound that regulates the function of a maltodextrin-binding protein of Streptococcus pyogenes by multifaceted screenings.

Yamawaki, T., Nakakido, M., Nagatoishi, S., Caaveiro, J.M.M., Kuroda, D., Aikawa, C., Nakagawa, I., Tsumoto, K.

(2025) Sci Rep 15: 19341-19341

• PubMed: 40456803 
• DOI: https://doi.org/10.1038/s41598-025-02175-9
• Primary Citation of Related Structures:  
  9KHA


• PubMed Abstract: 
  

  Group A Streptococcus (GAS) are gram-positive bacteria that cause various symptoms. The treatment of GAS infections currently relies on antibiotics, but new treatment options are needed due to the spread of antibiotic resistance. To develop novel treatment methods that circumvent the generation of antibiotic resistance, we used virtual screening followed by several biophysical-based screening methods to identify antibacterial compounds that target SPs0871, which is a maltodextrin-binding protein that is involved in carbohydrate catabolism in GAS. We narrowed down the list of compounds in the library via multi-step screening and finally isolated a compound that bacteriostatically inhibited the growth of GAS. Together with our previous study showing that an anti-SPs0871 variable heavy domain of heavy chain antibody, which completely blocked ligand binding, did not suppress bacterial growth, our results provide guidelines for designing an antistreptococcal therapeutic.

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Organizational Affiliation: 
• Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8656, Japan.
Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8656, Japan. [e-mail].
Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8656, Japan. [e-mail].
Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8656, Japan.
Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8656, Japan.
Department of Protein Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan.
Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-Ku, Tokyo, 162-8640, Japan.
Section of Applied Veterinary Sciences, Division of Veterinary Sciences, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, Hokkaido, 080-8555, Japan.
Department of Microbiology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-Cho, Sakyo-Ku, Kyoto, 606-8501, Japan.
Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8656, Japan. [e-mail].
Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8656, Japan. [e-mail].
Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8656, Japan. [e-mail].
Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, Minato-Ku, Tokyo, 108-8639, Japan. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 84 kDa 
• Atom Count: 5,954 
• Modeled Residue Count: 738 
• Deposited Residue Count: 778 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular solute-binding protein	A, B	389	Streptococcus pyogenes M1 GAS	Mutation(s): 0  Gene Names: E0F66_03780
UniProt
Find proteins for A0A0H2UUQ6 (Streptococcus pyogenes serotype M3 (strain ATCC BAA-595 / MGAS315)) Explore A0A0H2UUQ6  Go to UniProtKB:  A0A0H2UUQ6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.224 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.193 (DCC) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.189	α = 90
b = 118.189	β = 90
c = 353.944	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-25 
Deposition Author(s): Caaveiro, J.M.M., Yamawaki, T., Tsumoto, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2025-06-25
  Type: Initial release