9FQ5 | pdb_00009fq5

Crystal structure of phosphoserine phosphatase (SerB) from Brucella melitensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.224 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Structural and Enzymological Characterization of Phosphoserine Phosphatase From Brucella melitensis.

Scaillet, T.Pierson, E.Fillet, M.Wouters, J.

(2025) Proteins 

  • DOI: https://doi.org/10.1002/prot.70027
  • Primary Citation of Related Structures:  
    8Q4S, 8QOB, 9FQ5, 9FQC, 9FQN

  • PubMed Abstract: 

    Amino acid L-serine (L-Ser) is a precursor of various biomolecules, including other amino acids, glutathione, and nucleotides. The metabolism of this amino acid is crucial in diseases such as brucellosis. Previous studies have revealed that the enzymes involved in L-Ser biosynthesis are essential for Brucella replication, making them potential targets for the development of new drugs. Here, we focus on Brucella melitensis phosphoserine phosphatase (BmPSP), which catalyzes the dephosphorylation of phosphoserine in L-Ser. The enzyme is characterized through enzymatic and structural studies, leading to the discovery of its first crystallographic structures. The interactions of BmPSP with different ligands are also investigated. We demonstrate that the substitution of its Mg 2+ cofactor with Ca 2+ inhibits the enzyme and results in a slight movement of catalytic residues in the active site. Crystallographic structures of BmPSP in complex with substrate, reaction products, and substrate analogs are also detailed, revealing the interaction between these molecules and the active site residues. This structural study provides a better understanding of phosphoserine phosphatases, highlighting the involvement of two highly conserved residues in the mechanism of substrate entry into the active site.


  • Organizational Affiliation

    Department of Chemistry, Laboratoire de Chimie Biologique Structurale (CBS), University of Namur (UNamur), Namur Research Institute for Life Sciences (NARILIS), Namur Institute of Structural Matter (NISM), Namur, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoserine phosphatase307Brucella melitensisMutation(s): 0 
Gene Names: BMEI0615
EC: 3.1.3.3
UniProt
Find proteins for Q8YI30 (Brucella melitensis biotype 1 (strain ATCC 23456 / CCUG 17765 / NCTC 10094 / 16M))
Explore Q8YI30 
Go to UniProtKB:  Q8YI30
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8YI30
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
B [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
F [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.224 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.1α = 90
b = 143.1β = 90
c = 143.1γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MxCuBEdata collection
XSCALEdata scaling
XDSdata reduction
PHASERphasing
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release
  • Version 1.1: 2025-08-06
    Changes: Database references