5B3A

Crystal Structure of O-Phoshoserine Sulfhydrylase from Aeropyrum pernix in Complexed with the alpha-Aminoacrylate Intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.145 

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This is version 1.4 of the entry. See complete history


Literature

Role of F225 in O-phosphoserine sulfhydrylase from Aeropyrum pernix K1

Takeda, E.Kunimoto, K.Kawai, Y.Kataoka, M.Ishikawa, K.Nakamura, T.

(2016) Extremophiles 20: 733-745

  • DOI: https://doi.org/10.1007/s00792-016-0862-6
  • Primary Citation of Related Structures:  
    5B36, 5B3A

  • PubMed Abstract: 

    O-Phosphoserine sulfhydrylase (OPSS) synthesizes cysteine from O-phospho-L-serine (OPS) and sulfide. We have determined the three-dimensional structures of OPSS from hyperthermophilic archaeon Aeropyrum pernix K1 (ApOPSS) in complex with aminoacrylate intermediate (AA) formed from pyridoxal 5'-phosphate with OPS or in complex with cysteine and compared them with that of ApOPSS. We found an orientational change of F225 at the active-site entrance and constructed an F225A mutant to examine its activities and AA stability and clarify the role of F225 in ApOPSS. The OPS and O-acetyl-L-serine (OAS) sulfhydrylase activities of the F225A mutant decreased by 4.2- and 15-fold compared to those of the wild-type (wt) ApOPSS, respectively. The ability of OPS and OAS to form AA also decreased by 12- and 27-fold, respectively. AA was less stable in the F225A mutant than in the wt ApOPSS. Simulated docking showed that leaving groups, such as phosphate and acetate, were oriented to the inside of the active site in the F225A mutant, whereas they were oriented to the entrance in the wt ApOPSS. These results suggest that F225 in ApOPSS plays important roles in maintaining the hydrophobic environment of AA from solvent water and in controlling the orientation of leaving groups.


  • Organizational Affiliation

    Laboratory of Molecular Biochemistry, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga, 526-0829, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein CysO
A, B
389Aeropyrum pernix K1Mutation(s): 0 
Gene Names: cysOAPE_1586
EC: 4.2.1.22 (PDB Primary Data), 2.5.1.47 (PDB Primary Data), 2.5.1.65 (PDB Primary Data)
UniProt
Find proteins for Q9YBL2 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1))
Explore Q9YBL2 
Go to UniProtKB:  Q9YBL2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9YBL2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.145 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.151α = 90
b = 74.151β = 90
c = 275.961γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2016-07-20
    Changes: Database references
  • Version 1.2: 2016-09-07
    Changes: Database references
  • Version 1.3: 2017-05-10
    Changes: Non-polymer description
  • Version 1.4: 2023-11-08
    Changes: Data collection, Database references, Refinement description