1L8L

Molecular basis for the local confomational rearrangement of human phosphoserine phosphatase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular basis for the local conformational rearrangement of human phosphoserine phosphatase.

Kim, H.Y.Heo, Y.S.Kim, J.H.Park, M.H.Moon, J.Kim, E.Kwon, D.Yoon, J.Shin, D.Jeong, E.J.Park, S.Y.Lee, T.G.Jeon, Y.H.Ro, S.Cho, J.M.Hwang, K.Y.

(2002) J Biol Chem 277: 46651-46658

  • DOI: 10.1074/jbc.M204866200
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Human phosphoserine phosphatase (HPSP) regulates the levels of glycine and d-serine, the putative co-agonists for the glycine site of the NMDA receptor in the brain. Here, we describe the first crystal structures of the HPSP in complexes with the com ...

    Human phosphoserine phosphatase (HPSP) regulates the levels of glycine and d-serine, the putative co-agonists for the glycine site of the NMDA receptor in the brain. Here, we describe the first crystal structures of the HPSP in complexes with the competitive inhibitor 2-amino-3-phosphonopropionic acid (AP3) at 2.5 A, and the phosphate ion (Pi) and the product uncompetitive inhibitor l-serine (HPSP.l-Ser.Pi) at 2.8 A. The complex structures reveal that the open-closed environmental change of the active site, generated by local rearrangement of the alpha-helical bundle domain, is important to substrate recognition and hydrolysis. The maximal extent of this structural rearrangement is shown to be about 13 A at the L4 loop and about 25 degrees at the helix alpha3. Both the structural change and mutagenesis data suggest that Arg-65 and Glu-29 play an important role in the binding of the substrate. Interestingly, the AP3 binding mode turns out to be significantly different from that of the natural substrate, phospho-l-serine, and the HPSP.l-Ser.Pi structure provides a structural basis for the feedback control mechanism of serine. These analyses allow us to provide a clear model for the mechanism of HPSP and a framework for structure-based drug development.


    Organizational Affiliation

    Divison of Drug Discovery, CrystalGenomics Incorporated, Daeduck Biocommunity, Jeonmin-dong, Yuseong-gu, Taejeon City, South Korea 305-600.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-3-phosphoserine phosphatase
A, B
225Homo sapiensMutation(s): 1 
Gene Names: PSPH
EC: 3.1.3.3
Find proteins for P78330 (Homo sapiens)
Go to UniProtKB:  P78330
NIH Common Fund Data Resources
PHAROS  P78330
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APO
Query on APO

Download CCD File 
A, B
D-2-AMINO-3-PHOSPHONO-PROPIONIC ACID
C3 H8 N O5 P
LBTABPSJONFLPO-UWTATZPHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.213α = 90
b = 106.213β = 90
c = 87.812γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-04-01
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance