7OSO

The crystal structure of Erwinia tasmaniensis levansucrase in complex with (S)-1,2,4-butanentriol

PDB DOI: https://doi.org/10.2210/pdb7OSO/pdb

Classification: TRANSFERASE
Organism(s): Erwinia tasmaniensis Et1/99
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2021-06-09 Released: 2022-06-22
Deposition Author(s): Polsinelli, I., Salomone-Stagni, M., Benini, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.164
R-Value Work: 0.133
R-Value Observed: 0.134

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Erwinia tasmaniensis levansucrase shows enantiomer selection for (S)-1,2,4-butanetriol.

Polsinelli, I., Salomone-Stagni, M., Benini, S.

(2022) Acta Crystallogr F Struct Biol Commun 78: 289-296

PubMed: 35924596 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S2053230X2200680X
Primary Citation of Related Structures:
7OSO

PubMed Abstract:
Levansucrases are biotechnologically interesting fructosyltransferases due to their potential use in the enzymatic or chemo-enzymatic synthesis of glycosides of non-natural substrates relevant to pharmaceutical applications. The structure of Erwinia tasmaniensis levansucrase in complex with (S)-1,2,4-butanetriol and its biochemical characterization suggests the possible application of short aliphatic moieties containing polyols with defined stereocentres in fructosylation biotechnology. The structural information revealed that (S)-1,2,4-butanetriol mimics the natural substrate. The preference of the protein towards a specific 1,2,4-butanetriol enantiomer was assessed using microscale thermophoresis binding assays. Furthermore, the results obtained and the structural comparison of levansucrases and inulosucrases suggest that the fructose binding modes could differ in fructosyltransferases from Gram-positive and Gram-negative bacteria.

Organizational Affiliation

Bioorganic Chemistry and Bio-Crystallography Laboratory (B2Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Universita 5, 39100 Bolzano, Italy.

Macromolecule Content

Total Structure Weight: 46.44 kDa
Atom Count: 3,789
Modelled Residue Count: 412
Deposited Residue Count: 412
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Levansucrase (Beta-D-fructofuranosyl transferase)	A	412	Erwinia tasmaniensis Et1/99	Mutation(s): 0 Gene Names: lsc, ETA_34670 EC: 2.4.1.10
UniProt
Find proteins for B2VCC3 (Erwinia tasmaniensis (strain DSM 17950 / CFBP 7177 / CIP 109463 / NCPPB 4357 / Et1/99)) Explore B2VCC3 Go to UniProtKB: B2VCC3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B2VCC3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0V1 (Subject of Investigation/LOI) Query on 0V1 Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	(2~{S})-butane-1,2,4-triol C₄ H₁₀ O₃ ARXKVVRQIIOZGF-BYPYZUCNSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]