8I5K | pdb_00008i5k

Crystal structure of chitin oligosaccharide binding protein from Vibrio cholera in complex with chitotriose.

• PDB DOI: https://doi.org/10.2210/pdb8I5K/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-01-25 Released: 2024-01-03 
• Deposition Author(s): Ohnuma, T., Takeshita, D.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free: 
  0.187 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Periplasmic chitooligosaccharide-binding protein requires a three-domain organization for substrate translocation.

Ohnuma, T., Tsujii, J., Kataoka, C., Yoshimoto, T., Takeshita, D., Lampela, O., Juffer, A.H., Suginta, W., Fukamizo, T.

(2023) Sci Rep 13: 20558-20558

• PubMed: 37996461 
• DOI: https://doi.org/10.1038/s41598-023-47253-y
• Primary Citation Related Structures: 
  8I5J, 8I5K


• PubMed Abstract: 
  

  Periplasmic solute-binding proteins (SBPs) specific for chitooligosaccharides, (GlcNAc) _n (n = 2, 3, 4, 5 and 6), are involved in the uptake of chitinous nutrients and the negative control of chitin signal transduction in Vibrios. Most translocation processes by SBPs across the inner membrane have been explained thus far by two-domain open/closed mechanism. Here we propose three-domain mechanism of the (GlcNAc) _n translocation based on experiments using a recombinant VcCBP, SBP specific for (GlcNAc) _n from Vibrio cholerae. X-ray crystal structures of unliganded or (GlcNAc) ₃ -liganded VcCBP solved at 1.2-1.6 Å revealed three distinct domains, the Upper1, Upper2 and Lower domains for this protein. Molecular dynamics simulation indicated that the motions of the three domains are independent and that in the (GlcNAc) ₃ -liganded state the Upper2/Lower interface fluctuated more intensively, compared to the Upper1/Lower interface. The Upper1/Lower interface bound two GlcNAc residues tightly, while the Upper2/Lower interface appeared to loosen and release the bound sugar molecule. The three-domain mechanism proposed here was fully supported by binding data obtained by thermal unfolding experiments and ITC, and may be applicable to other translocation systems involving SBPs belonging to the same cluster.

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Organizational Affiliation: 
• Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara, 631-8505, Japan. [e-mail].
Agricultural Technology and Innovation Research Institute (ATIRI), Kindai University, 3327-204, Nakamachi, Nara, 631-8505, Japan. [e-mail].
Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara, 631-8505, Japan.
Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba-Shi, Ibaraki, 305-8566, Japan.
Biocenter Oulu, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland.
Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O.Box 5000, FI-90014, Oulu, Finland.
School of Biomolecular Science & Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley 555 Moo 1 Payupnai, Wangchan, Rayong, 21210, Thailand.
Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara, 631-8505, Japan. [e-mail].
School of Biomolecular Science & Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley 555 Moo 1 Payupnai, Wangchan, Rayong, 21210, Thailand. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 61.63 kDa 
• Atom Count: 4,851 
• Modeled Residue Count: 528 
• Deposited Residue Count: 536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter substrate-binding protein	A	536	Vibrio cholerae	Mutation(s): 0  Gene Names: appA_1, appA, D6U24_16190, ERS013201_01979, ERS013202_02445, EYB64_10090, F0H40_11710, F0M16_04225, FLM12_17525
UniProt
Find proteins for A0A085SLP2 (Vibrio cholerae) Explore A0A085SLP2  Go to UniProtKB:  A0A085SLP2

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan: G47362BJ GlyCosmos: G47362BJ GlyGen: G47362BJ

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900017	B	triacetyl-beta-chitotriose	Oligosaccharide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free:  0.187 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.087	α = 90
b = 51.683	β = 98.83
c = 70.328	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-01-03 
Deposition Author(s): Ohnuma, T., Takeshita, D.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-01-03
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary