6HYY

Human phosphoserine phosphatase with serine and phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structures and snapshots along the reaction pathway of human phosphoserine phosphatase.

Haufroid, M.Mirgaux, M.Leherte, L.Wouters, J.

(2019) Acta Crystallogr D Struct Biol 75: 592-604

  • DOI: 10.1107/S2059798319006867
  • Primary Citation of Related Structures:  
    6HYJ, 6HYY, 6Q6J

  • PubMed Abstract: 
  • The equilibrium between phosphorylation and dephosphorylation is one of the most important processes that takes place in living cells. Human phosphoserine phosphatase (hPSP) is a key enzyme in the production of serine by the dephosphorylation of phospho-L-serine ...

    The equilibrium between phosphorylation and dephosphorylation is one of the most important processes that takes place in living cells. Human phosphoserine phosphatase (hPSP) is a key enzyme in the production of serine by the dephosphorylation of phospho-L-serine. It is directly involved in the biosynthesis of other important metabolites such as glycine and D-serine (a neuromodulator). hPSP is involved in the survival mechanism of cancer cells and has recently been found to be an essential biomarker. Here, three new high-resolution crystal structures of hPSP (1.5-2.0 Å) in complexes with phosphoserine and with serine, which are the substrate and the product of the reaction, respectively, and in complex with a noncleavable substrate analogue (homocysteic acid) are presented. New types of interactions take place between the enzyme and its ligands. Moreover, the loop involved in the open/closed state of the enzyme is fully refined in a totally unfolded conformation. This loop is further studied through molecular-dynamics simulations. Finally, all of these analyses allow a more complete reaction mechanism for this enzyme to be proposed which is consistent with previous publications on the subject.


    Organizational Affiliation

    Namur Medicine and Drug Innovation Center, Namur Research Institute for Life Science (NAMEDIC-NARILIS), Department of Chemistry, Laboratoire de Chimie Biologique Structurale (CBS), University of Namur (UNamur), 61 Rue de Bruxelles, 5000 Namur, Belgium.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphoserine phosphataseA, B221Homo sapiensMutation(s): 0 
Gene Names: PSPH
EC: 3.1.3.3
UniProt & NIH Common Fund Data Resources
Find proteins for P78330 (Homo sapiens)
Explore P78330 
Go to UniProtKB:  P78330
PHAROS:  P78330
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP78330
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SER
Query on SER

Download Ideal Coordinates CCD File 
E [auth A]SERINE
C3 H7 N O3
MTCFGRXMJLQNBG-REOHCLBHSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.14α = 90
b = 129.14β = 90
c = 155.79γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2019-06-26
    Changes: Data collection, Database references