Escherichia coli GlpE sulfurtransferase soaked with KCN

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Escherichia Coli Glpe is a Prototype Sulfurtransferase for the Single-Domain Rhodanese Homology Superfamily

Spallarossa, A.Donahue, J.T.Larson, T.J.Bolognesi, M.Bordo, D.

(2001) Structure 9: 1117

  • DOI: https://doi.org/10.1016/s0969-2126(01)00666-9
  • Primary Citation of Related Structures:  
    1GMX, 1GN0

  • PubMed Abstract: 

    Rhodanese domains are structural modules occurring in the three major evolutionary phyla. They are found as single-domain proteins, as tandemly repeated modules in which the C-terminal domain only bears the properly structured active site, or as members of multidomain proteins. Although in vitro assays show sulfurtransferase or phosphatase activity associated with rhodanese or rhodanese-like domains, specific biological roles for most members of this homology superfamily have not been established. Eight ORFs coding for proteins consisting of (or containing) a rhodanese domain bearing the potentially catalytic Cys have been identified in the Escherichia coli K-12 genome. One of these codes for the 12-kDa protein GlpE, a member of the sn-glycerol 3-phosphate (glp) regulon. The crystal structure of GlpE, reported here at 1.06 A resolution, displays alpha/beta topology based on five beta strands and five alpha helices. The GlpE catalytic Cys residue is persulfurated and enclosed in a structurally conserved 5-residue loop in a region of positive electrostatic field. Relative to the two-domain rhodanese enzymes of known three-dimensional structure, GlpE displays substantial shortening of loops connecting alpha helices and beta sheets, resulting in radical conformational changes surrounding the active site. As a consequence, GlpE is structurally more similar to Cdc25 phosphatases than to bovine or Azotobacter vinelandii rhodaneses. Sequence searches through completed genomes indicate that GlpE can be considered to be the prototype structure for the ubiquitous single-domain rhodanese module.

  • Organizational Affiliation

    Department of Pharmaceutical Sciences, University of Genova, Viale Benedetto XV, 3, 16132, Genova, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
THIOSULFATE SULFURTRANSFERASE GLPE108Escherichia coli BL21(DE3)Mutation(s): 0 
Find proteins for P0A6V5 (Escherichia coli (strain K12))
Explore P0A6V5 
Go to UniProtKB:  P0A6V5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6V5
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.177 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.796α = 90
b = 53.796β = 90
c = 30.346γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-11-29
    Type: Initial release
  • Version 1.1: 2012-08-01
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other