2DXB

Recombinant thiocyanate hydrolase comprising partially-modified cobalt centers


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Basis for Catalytic Activation of Thiocyanate Hydrolase Involving Metal-Ligated Cysteine Modification

Arakawa, T.Kawano, Y.Katayama, Y.Nakayama, H.Dohmae, N.Yohda, M.Odaka, M.

(2009) J Am Chem Soc 131: 14838-14843

  • DOI: 10.1021/ja903979s
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Thiocyanate hydrolase (SCNase) is a member of a family of nitrile hydratase proteins, each of which contains a unique noncorrin cobalt center with two post-translationally modified cysteine ligands, cysteine-sulfenic acid or -sulfenate (Cys-SO(H)), a ...

    Thiocyanate hydrolase (SCNase) is a member of a family of nitrile hydratase proteins, each of which contains a unique noncorrin cobalt center with two post-translationally modified cysteine ligands, cysteine-sulfenic acid or -sulfenate (Cys-SO(H)), and cysteine-sulfininate (Cys-SO(2)(-)), respectively. We have found that a partially matured recombinant SCNase was activated during storage. The crystal structures of SCNase before and after storage demonstrated that Cys-SO(2)(-) modification of gammaCys131 proceeded to completion prior to storage, while Cys-SO(H) modification of gammaCys133 occurred during storage. SCNase activity was suppressed when gammaCys133 was further oxidized to Cys-SO(2)(-). The correlation between the catalytic activity and the extent of the gammaCys133 modification indicates that the cysteine sulfenic acid modification of gammaCys133 is of primary importance in determining the activity of SCNase.


    Organizational Affiliation

    Department of Biotechnology and Life Science, Graduate School of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thiocyanate hydrolase subunit alpha
A, D, G, J, M, P, S, V
126Thiobacillus thioparusMutation(s): 0 
Gene Names: scnA
EC: 3.5.5.8
Find proteins for O66187 (Thiobacillus thioparus)
Go to UniProtKB:  O66187
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Thiocyanate hydrolase subunit beta
B, E, H, K, N, Q, T, W
157Thiobacillus thioparusMutation(s): 0 
Gene Names: scnB
EC: 3.5.5.8
Find proteins for O66186 (Thiobacillus thioparus)
Go to UniProtKB:  O66186
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Thiocyanate hydrolase subunit gamma
C, F, I, L, O, R, U, X
243Thiobacillus thioparusMutation(s): 0 
Gene Names: scnC
EC: 3.5.5.8
Find proteins for O66188 (Thiobacillus thioparus)
Go to UniProtKB:  O66188
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download CCD File 
C, F, I, L, O, R, U, X
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
3CO
Query on 3CO

Download CCD File 
C, F, I, L, O, R, U, X
COBALT (III) ION
Co
JAWGVVJVYSANRY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
C,F,I,L,O,R,U,XL-PEPTIDE LINKINGC3 H7 N O4 SCYS
CSO
Query on CSO
C,F,I,L,O,R,U,XL-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.874α = 90
b = 245.141β = 90
c = 244.653γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-08-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance