4AZJ

Structural basis of L-phosphoserine binding to Bacillus alcalophilus phosphoserine aminotransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis of L-Phosphoserine Binding to Bacillus Alcalophilus Phosphoserine Aminotransferase

Battula, P.Dubnovitsky, A.P.Papageorgiou, A.C.

(2013) Acta Crystallogr.,Sect.D 69: 804

  • DOI: 10.1107/S0907444913002096
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Phosphoserine aminotransferase is a vitamin B6-dependent enzyme that catalyzes the reversible conversion of 3-phosphohydroxypyruvate to L-phosphoserine using glutamate as an amine donor. In an effort to gain insight into the substrate-recognition mec ...

    Phosphoserine aminotransferase is a vitamin B6-dependent enzyme that catalyzes the reversible conversion of 3-phosphohydroxypyruvate to L-phosphoserine using glutamate as an amine donor. In an effort to gain insight into the substrate-recognition mechanism of the enzyme, crystal structures of Bacillus alcalophilus phosphoserine aminotransferase in the presence or absence of L-phosphoserine were determined to resolutions of 1.5 and 1.6 Å, respectively. Local conformational changes induced upon substrate binding were identified. However, in contrast to other aminotransferases, no domain or subunit movements were observed. Two Arg residues (Arg42 and Arg328) and two His residues (His41 and His327) were found to form a tight binding site for the phosphate group of L-phosphoserine. Comparison with Escherichia coli phosphoserine aminotransferase in complex with the substrate analogue α-methylglutamate revealed more extensive structural changes in the case of L-phosphoserine binding. Based on the structural analysis, the flexibility of Arg328 is proposed to be critical for substrate recognition.


    Organizational Affiliation

    Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, BioCity, FIN-20521 Turku, Finland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOSERINE AMINOTRANSFERASE
A, B
360Bacillus alcalophilusMutation(s): 0 
Gene Names: serC
EC: 2.6.1.52
Find proteins for Q9RME2 (Bacillus alcalophilus)
Go to UniProtKB:  Q9RME2
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SEP
Query on SEP

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Download CCD File 
A, B
PHOSPHOSERINE
PHOSPHONOSERINE
C3 H8 N O6 P
BZQFBWGGLXLEPQ-REOHCLBHSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PLP
Query on PLP

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Download CCD File 
A, B
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.146 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 104.692α = 90.00
b = 136.194β = 90.00
c = 151.283γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-01
    Type: Initial release
  • Version 1.1: 2013-05-15
    Type: Database references
  • Version 1.2: 2018-01-17
    Type: Data collection