1ORB

ACTIVE SITE STRUCTURAL FEATURES FOR CHEMICALLY MODIFIED FORMS OF RHODANESE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Active site structural features for chemically modified forms of rhodanese.

Gliubich, F.Gazerro, M.Zanotti, G.Delbono, S.Bombieri, G.Berni, R.

(1996) J Biol Chem 271: 21054-21061

  • DOI: 10.1074/jbc.271.35.21054
  • Primary Citation of Related Structures:  
    2ORA, 1ORB

  • PubMed Abstract: 
  • In the course of the reaction catalyzed by rhodanese, the enzyme cycles between two catalytic intermediates, the sulfur-free and the sulfur-substituted (persulfide-containing) forms. The crystal structure of sulfur-free rhodanese, which was prepared in solution and then crystallized, is highly similar to that of sulfur-substituted enzyme ...

    In the course of the reaction catalyzed by rhodanese, the enzyme cycles between two catalytic intermediates, the sulfur-free and the sulfur-substituted (persulfide-containing) forms. The crystal structure of sulfur-free rhodanese, which was prepared in solution and then crystallized, is highly similar to that of sulfur-substituted enzyme. The inactivation of sulfur-free rhodanese with a small molar excess of hydrogen peroxide relies essentially on a modification limited to the active site, consisting of the oxidation of the essential sulfhydryl to sulfenyl group (-S-OH). Upon reaction of the sulfur-free enzyme with monoiodoacetate in the crystal, the Cys-247 side chain with the bound carboxymethyl group is forced into a conformation that allows favorable interactions of the carboxylate with the four peptide NH groups that participate in hydrogen bonding interactions with the transferable sulfur atom of the persulfide group in the sulfur-substituted rhodanese. It is concluded that active site-specific chemical modifications of sulfur-free rhodanese do not lead to significant changes of the protein structure, consistent with a high degree of similarity of the structures of the sulfur-free and sulfur-substituted forms of the enzyme both in solution and in the crystal.


    Related Citations: 
    • The High Resolution Three-Dimensional Structure of Bovine Liver Rhodanese
      Hol, W.G.J., Lijk, L.J., Kalk, K.H.
      (1983) Fundam Appl Toxicol 3: 370
    • The Structure of Bovine Liver Rhodanese: The Active Site in the Sulfur-Substituted and the Sulfur-Free Enzyme
      Ploegman, J.H., Drent, G., Kalk, K.H., Hol, W.G.J.
      (1979) J Mol Biol 127: 149
    • The Covalent and Tertiary Structure of Bovine Liver Rhodanese
      Ploegman, J.H., Drent, G., Kalk, K.H., Hol, W.G.J., Heinrikson, W.G.J., Keim, R.L., Weng, P.S., Russel, J.
      (1978) Nature 273: 124

    Organizational Affiliation

    Department of Organic Chemistry, University of Padova and Biopolymer Research Center, Consiglio Nazionale delle Ricerche, 35131 Padova, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CARBOXYMETHYLATED RHODANESEA296Bos taurusMutation(s): 0 
Gene Names: TST
EC: 2.8.1.1
UniProt
Find proteins for P00586 (Bos taurus)
Explore P00586 
Go to UniProtKB:  P00586
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download Ideal Coordinates CCD File 
B [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.23α = 90
b = 49.04β = 98.6
c = 42.25γ = 90
Software Package:
Software NamePurpose
TNTrefinement
SAINTdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-10-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance