2ZPU

Crystal Structure of Modified Serine Racemase from S.pombe.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1093/jb/mvp010
  • Primary Citation of Related Structures:  
    2ZPU

  • 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 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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein C320.14323Schizosaccharomyces pombeMutation(s): 0 
Gene Names: SPCC320.14, SPCC330.15c
EC: 5.1.1.18
UniProt
Find proteins for O59791 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O59791 
Go to UniProtKB:  O59791
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO59791
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PDD
Query on PDD
Download Ideal Coordinates CCD File 
C [auth A]N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE
C11 H17 N2 O7 P
WACJCHFWJNNBPR-SSDOTTSWSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.74α = 90
b = 72.99β = 102.41
c = 65.07γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-11
    Changes: Refinement description
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description