8WL9

X-ray structure of Enterobacter cloacae allose-binding protein in complex with D-ribose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 

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Literature

X-ray structures of Enterobacter cloacae allose-binding protein in complexes with monosaccharides demonstrate its unique recognition mechanism for high affinity to allose.

Kamitori, S.

(2023) Biochem Biophys Res Commun 682: 187-192

  • DOI: https://doi.org/10.1016/j.bbrc.2023.10.016
  • Primary Citation of Related Structures:  
    8WL5, 8WL7, 8WL9, 8WLB

  • PubMed Abstract: 

    d-Allose is an aldohexose of the C3-epimer of d-glucose, existing in very small amounts in nature, called a rare sugar. The operon responsible for d-allose metabolism, the allose operon, was found in several bacteria, which consists of seven genes: alsR, alsB, alsA, alsC, alsE, alsK, and rpiB. To understand the biological implication of the allose operon utilizing a rare sugar of d-allose as a carbon source, it is important to clarify whether the allose operon functions specifically for d-allose or also functions for other ligands. It was proposed that the allose operon can function for d-ribose, which is essential as a component of nucleotides and abundant in nature. Allose-binding protein, AlsB, coded in the allose operon, is thought to capture a ligand outside the cell, and is expected to show high affinity for the specific ligand. X-ray structure determinations of Enterobacter cloacae AlsB (EtcAlsB) in ligand-free form, and in complexes with d-allose, d-ribose, and d-allulose, and measurements of the thermal parameters of the complex formation using an isothermal titration calorimeter were performed. The results demonstrated that EtcAlsB has a unique recognition mechanism for high affinity to d-allose by changing its conformation from an open to a closed form depending on d-allose-binding, and that the binding of d-ribose to EtcAlsB could not induce a completely closed form but an intermediate form, explaining the low affinity for d-ribose.


  • Organizational Affiliation

    Research Facility Center for Science & Technology and Faculty of Medicine, International Institute of Rare Sugar Research and Education, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan. Electronic address: kamitori.shigehiro@kagawa-u.ac.jp.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Allose ABC transporter309Enterobacter cloacaeMutation(s): 0 
Gene Names: AI2656V1_0345AI2799V1_0351CGS27_05760
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RIP (Subject of Investigation/LOI)
Query on RIP

Download Ideal Coordinates CCD File 
B [auth A]beta-D-ribopyranose
C5 H10 O5
SRBFZHDQGSBBOR-TXICZTDVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.85α = 90
b = 110.68β = 90
c = 37.26γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2023-10-25 
  • Deposition Author(s): Kamitori, S.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-25
    Type: Initial release