1H4M

Sulfurtransferase from Azotobacter vinelandii in complex with phosphate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


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


Literature

A Persulfurated Cysteine Promotes Active Site Reactivity in Azotobacter Vinelandii Rhodanse

Bordo, D., Forlani, F., Spallarossa, A., Colnaghi, R., Carpen, A., Bolognesi, M., Pagani, S.

(2001) Biol Chem 382: 1245

  • DOI: 10.1515/BC.2001.155
  • Primary Citation of Related Structures:  
    1H4M, 1H4K

  • PubMed Abstract: 

    • Active site reactivity and specificity of RhdA, a thiosulfate:cyanide sulfurtransferase (rhodanese) from Azotobacter vinelandii, have been investigated through ligand binding, site-directed mutagenesis, and X-ray crystallographic techniques, in a combined approach ...

    Active site reactivity and specificity of RhdA, a thiosulfate:cyanide sulfurtransferase (rhodanese) from Azotobacter vinelandii, have been investigated through ligand binding, site-directed mutagenesis, and X-ray crystallographic techniques, in a combined approach. In native RhdA the active site Cys230 is found persulfurated; fluorescence and sulfurtransferase activity measurements show that phosphate anions interact with Cys230 persulfide sulfur atom and modulate activity. Crystallographic analyses confirm that phosphate and hypophosphite anions react with native RhdA, removing the persulfide sulfur atom from the active site pocket. Considering that RhdA and the catalytic subunit of Cdc25 phosphatases share a common three-dimensional fold as well as active site Cys (catalytic) and Arg residues, two RhdA mutants carrying a single amino acid insertion at the active site loop were designed and their phosphatase activity tested. The crystallographic and functional results reported here show that specific sulfurtransferase or phosphatase activities are strictly related to precise tailoring of the catalytic loop structure in RhdA and Cdc25 phosphatase, respectively.

    Related Citations: 
    • The Crystal Structure of a Sulfurtransferase from Azotobacter Vinelandii Highliths the Evolutionary Relationship between the Rhodanese and Phosphatase Enzyme Families
      Bordo, D., Deriu, D., Colnaghi, R., Carpen, A., Pagani, S., Bolognesi, M.
      (2000) J Mol Biol 298: 691
    Organizational Affiliation: 

    National Cancer Research Institute, Advanced Biotechnology Center, Genova, Italy.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PUTATIVE THIOSULFATE SULFURTRANSFERASE X271Azotobacter vinelandiiMutation(s): 0 
Gene Names: rhdA
EC: 2.8.1.1
Find proteins for P52197 (Azotobacter vinelandii)
Explore P52197 
Go to UniProtKB:  P52197
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO
Download Ideal Coordinates CCD File 
X
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.41α = 90
b = 151.469β = 90
c = 53.609γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-05-16
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection