2ZPU

Crystal Structure of Modified Serine Racemase from S.pombe.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Serine racemase with catalytically active lysinoalanyl residue.

Yamauchi, T.Goto, M.Wu, H.Y.Uo, T.Yoshimura, T.Mihara, H.Kurihara, T.Miyahara, I.Hirotsu, K.Esaki, N.

(2009) J.Biochem. 145: 421-424

  • DOI: 10.1093/jb/mvp010

  • PubMed Abstract: 
  • Serine racemase synthesizes d-serine, a physiological agonist of the NMDA receptor in mammalian brains. Schizosaccharomyces pombe produces serine racemase (spSR) that is highly similar to the brain enzyme. Our mass-spectrometric and X-ray studies rev ...

    Serine racemase synthesizes d-serine, a physiological agonist of the NMDA receptor in mammalian brains. Schizosaccharomyces pombe produces serine racemase (spSR) that is highly similar to the brain enzyme. Our mass-spectrometric and X-ray studies revealed that spSR is modified with its natural substrate serine. spSR remains partially active even though its essential Lys57 inherently forming a Schiff base with the coenzyme pyridoxal 5'-phosphate is converted to N(6)-(R-2-amino-2-carboxyethyl)-l-lysyl (lysino-d-alanyl) residue. This indicates that the alpha-amino group of the d-alanyl moiety of the lysino-d-alanyl residue serves as a catalytic base in the same manner as the epsilon-amino group of Lys57 of the original spSR.


    Organizational Affiliation

    Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein C320.14
A
323Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: SRR
EC: 4.3.1.17, 4.3.1.18, 5.1.1.18
Find proteins for O59791 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to Gene View: SRR
Go to UniProtKB:  O59791
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PDD
Query on PDD

Download SDF File 
Download CCD File 
A
N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE
C11 H17 N2 O7 P
WACJCHFWJNNBPR-SSDOTTSWSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.183 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 59.740α = 90.00
b = 72.990β = 102.41
c = 65.070γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
MAR345data collection
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-07-29 
  • Released Date: 2009-04-28 
  • Deposition Author(s): Goto, M.

Revision History 

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-11
    Type: Refinement description