2ZZD | pdb_00002zzd

Recombinant thiocyanate hydrolase, air-oxidized form of holo-enzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 
    0.159 (Depositor), 0.161 (DCC) 
  • R-Value Work: 
    0.150 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.150 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1021/ja903979s
  • Primary Citation Related Structures: 
    2DXB, 2DXC, 2ZZD

  • 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)), 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.

Macromolecule Content 

  • Total Structure Weight: 242.39 kDa 
  • Atom Count: 19,243 
  • Modeled Residue Count: 1,959 
  • Deposited Residue Count: 2,104 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Thiocyanate hydrolase subunit alpha
A, D, G, J
126Thiobacillus thioparusMutation(s): 0 
Gene Names: scnA
EC: 3.5.5.8
UniProt
Find proteins for O66187 (Thiobacillus thioparus)
Explore O66187 
Go to UniProtKB:  O66187
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66187
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Thiocyanate hydrolase subunit beta
B, E, H, K
157Thiobacillus thioparusMutation(s): 0 
Gene Names: scnB
EC: 3.5.5.8
UniProt
Find proteins for O66186 (Thiobacillus thioparus)
Explore O66186 
Go to UniProtKB:  O66186
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66186
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Thiocyanate hydrolase subunit gamma
C, F, I, L
243Thiobacillus thioparusMutation(s): 0 
Gene Names: scnC
EC: 3.5.5.8
UniProt
Find proteins for O66188 (Thiobacillus thioparus)
Explore O66188 
Go to UniProtKB:  O66188
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66188
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FRU

Query on FRU



Download:Ideal Coordinates CCD File
M [auth B],
W [auth L],
X [auth L]
beta-D-fructofuranose
C6 H12 O6
RFSUNEUAIZKAJO-ARQDHWQXSA-N
BGC

Query on BGC



Download:Ideal Coordinates CCD File
R [auth F]beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
TLA

Query on TLA



Download:Ideal Coordinates CCD File
O [auth C],
Q [auth F],
T [auth I],
V [auth L]
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
3CO

Query on 3CO



Download:Ideal Coordinates CCD File
N [auth C],
P [auth F],
S [auth I],
U [auth L]
COBALT (III) ION
Co
JAWGVVJVYSANRY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSD
Query on CSD
C, F, I, L
L-PEPTIDE LINKINGC3 H7 N O4 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free:  0.159 (Depositor), 0.161 (DCC) 
  • R-Value Work:  0.150 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.150 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.012α = 90
b = 170.756β = 90
c = 175.176γ = 90
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.4: 2024-11-13
    Changes: Structure summary