The crystal structure of Nitrosomonas europaea sucrose synthase: Insights into the evolutionary origin of sucrose metabolism in prokaryotes

Experimental Data Snapshot

  • Resolution: 3.05 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


The Crystal Structure of Nitrosomonas europaea Sucrose Synthase Reveals Critical Conformational Changes and Insights into Sucrose Metabolism in Prokaryotes.

Wu, R.Asencion Diez, M.D.Figueroa, C.M.Machtey, M.Iglesias, A.A.Ballicora, M.A.Liu, D.

(2015) J Bacteriol 197: 2734-2746

  • DOI: https://doi.org/10.1128/JB.00110-15
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    In this paper we report the first crystal structure of a prokaryotic sucrose synthase from the nonphotosynthetic bacterium Nitrosomonas europaea. The obtained structure was in an open form, whereas the only other available structure, from the plant Arabidopsis thaliana, was in a closed conformation. Comparative structural analysis revealed a "hinge-latch" combination, which is critical to transition between the open and closed forms of the enzyme. The N. europaea sucrose synthase shares the same fold as the GT-B family of the retaining glycosyltransferases. In addition, a triad of conserved homologous catalytic residues in the family was shown to be functionally critical in the N. europaea sucrose synthase (Arg567, Lys572, and Glu663). This implies that sucrose synthase shares not only a common origin with the GT-B family but also a similar catalytic mechanism. The enzyme preferred transferring glucose from ADP-glucose rather than UDP-glucose like the eukaryotic counterparts. This predicts that these prokaryotic organisms have a different sucrose metabolic scenario from plants. Nucleotide preference determines where the glucose moiety is targeted after sucrose is degraded. We obtained biochemical and structural evidence of sucrose metabolism in nonphotosynthetic bacteria. Until now, only sucrose synthases from photosynthetic organisms have been characterized. Here, we provide the crystal structure of the sucrose synthase from the chemolithoautotroph N. europaea. The structure supported that the enzyme functions with an open/close induced fit mechanism. The enzyme prefers as the substrate adenine-based nucleotides rather than uridine-based like the eukaryotic counterparts, implying a strong connection between sucrose and glycogen metabolism in these bacteria. Mutagenesis data showed that the catalytic mechanism must be conserved not only in sucrose synthases but also in all other retaining GT-B glycosyltransferases.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sucrose synthase:Glycosyl transferases group 1A,
B [auth C],
C [auth B],
794Nitrosomonas europaeaMutation(s): 0 
Gene Names: ss2NE1214
Find proteins for Q820M5 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298))
Explore Q820M5 
Go to UniProtKB:  Q820M5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ820M5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.05 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 236.899α = 90
b = 236.899β = 90
c = 213.442γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-08-26
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references