4RBN

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1128/JB.00110-15

  • 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 A ...

    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.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois, USA Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral and Consejo Nacional de Investigaciones Científicas y Técnicas, Centro Científico Tecnológico Santa Fe, Santa Fe, Argentina.,Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois, USA dliu@luc.edu.,Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois, USA.,Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral and Consejo Nacional de Investigaciones Científicas y Técnicas, Centro Científico Tecnológico Santa Fe, Santa Fe, Argentina.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sucrose synthase:Glycosyl transferases group 1
A, C, B, D
794Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)Mutation(s): 0 
Gene Names: ss2
EC: 2.4.1.13
Find proteins for Q820M5 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298))
Go to UniProtKB:  Q820M5
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.176 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 236.899α = 90.00
b = 236.899β = 90.00
c = 213.442γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
SCALAdata scaling
HKL-2000data collection
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-08-26
    Type: Database references