4Q0U

Crystal structure of Acinetobacter sp. DL28 L-ribose isomerase mutant E204Q in complex with L-ribose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 3.2 of the entry. See complete history


Literature

X-ray structure of a novel L-ribose isomerase acting on a non-natural sugar L-ribose as its ideal substrate.

Yoshida, H.Yoshihara, A.Teraoka, M.Terami, Y.Takata, G.Izumori, K.Kamitori, S.

(2014) FEBS J 281: 3150-3164

  • DOI: https://doi.org/10.1111/febs.12850
  • Primary Citation of Related Structures:  
    4Q0P, 4Q0Q, 4Q0S, 4Q0U, 4Q0V

  • PubMed Abstract: 

    l-Ribose, a pentose, is not known to exist in nature. Although organisms typically do not have a metabolic pathway that uses l-ribose as a carbon source, prokaryotes use various sugars as carbon sources for survival. Acinetobacter sp. DL-28 has been shown to express the novel enzyme, l-ribose isomerase (AcL-RbI), which catalyzes reversible isomerization between l-ribose and l-ribulose. AcL-RbI showed the highest activity to l-ribose, followed by d-lyxose with 47% activity, and had no significant amino acid sequence similarity to structure-known proteins, except for weak homology with the d-lyxose isomerases from Escherichia coli O157 : H7 (18%) and Bacillus subtilis strain (19%). Thus, AcL-RbI is expected to have the unique three-dimensional structure to recognize l-ribose as its ideal substrate. The X-ray structures of AcL-RbI in complexes with substrates were determined. AcL-RbI had a cupin-type β-barrel structure, and the catalytic site was found between two large β-sheets with a bound metal ion. The catalytic site structures clearly showed that AcL-RbI adopted a cis-enediol intermediate mechanism for the isomerization reaction using two glutamate residues (Glu113 and Glu204) as acid/base catalysts. In its crystal form, AcL-RbI formed a unique homotetramer with many substrate sub-binding sites, which likely facilitated capture of the substrate. The atomic coordinates and structure factors of AcL-RbI/l-ribose, AcL-RbI/l-ribulose, AcL-RbI/ribitol, E204Q/l-ribose and E204Q/l-ribulose have been deposited in the Protein Data Bank under accession codes, 4Q0P, 4Q0Q, 4Q0S, 4Q0U and 4Q0V.


  • Organizational Affiliation

    Life Science Research Center and Faculty of Medicine, Kagawa University, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-Ribose isomerase260Acinetobacter sp. DL-28Mutation(s): 1 
Gene Names: L-RI
EC: 5.3.1
UniProt
Find proteins for Q93UQ5 (Acinetobacter sp. DL-28)
Explore Q93UQ5 
Go to UniProtKB:  Q93UQ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93UQ5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NCO
Query on NCO

Download Ideal Coordinates CCD File 
H [auth A]COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-UHFFFAOYSA-N
0MK
Query on 0MK

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F [auth A]beta-L-ribopyranose
C5 H10 O5
SRBFZHDQGSBBOR-FCAWWPLPSA-N
Z6J
Query on Z6J

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
G [auth A]
alpha-L-ribofuranose
C5 H10 O5
HMFHBZSHGGEWLO-NEEWWZBLSA-N
ROR
Query on ROR

Download Ideal Coordinates CCD File 
C [auth A]L-ribose
C5 H10 O5
PYMYPHUHKUWMLA-MROZADKFSA-N
CO
Query on CO

Download Ideal Coordinates CCD File 
B [auth A]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.73α = 90
b = 107.06β = 90
c = 118.89γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
CNSrefinement
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-28
    Type: Initial release
  • Version 1.1: 2014-06-11
    Changes: Database references
  • Version 2.0: 2020-07-01
    Changes: Atomic model, Data collection, Database references, Derived calculations
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.1: 2022-08-24
    Changes: Database references, Structure summary
  • Version 3.2: 2023-11-08
    Changes: Data collection, Refinement description