3X43

Crystal structure of O-ureido-L-serine synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The structural and mutational analyses of O-ureido-L-serine synthase necessary for D-cycloserine biosynthesis

Uda, N.Matoba, Y.Oda, K.Kumagai, T.Sugiyama, M.

(2015) FEBS J 

  • DOI: 10.1111/febs.13386
  • Primary Citation of Related Structures:  
    3X43, 3X44

  • PubMed Abstract: 
  • We have recently been successful in cloning a gene cluster necessary for the biosynthesis of D-cycloserine (D-CS) from D-CS-producing Streptomyces lavendulae ATCC11924. Although dcsD, one of the ORFs located on the gene cluster, encodes a protein hom ...

    We have recently been successful in cloning a gene cluster necessary for the biosynthesis of D-cycloserine (D-CS) from D-CS-producing Streptomyces lavendulae ATCC11924. Although dcsD, one of the ORFs located on the gene cluster, encodes a protein homologous to O-acetylserine sulfhydrylase that synthesizes L-cysteine using O-acetyl-L-serine together with sulfide, it functions to form O-ureido-L-serine as a D-CS biosynthetic intermediate, using O-acetyl-L-serine together with hydroxyurea (HU). In the present study, using crystallographic and mutational studies, three amino acid residues in DcsD that are important for the substrate preference toward HU were determined. We showed that two of the three residues are important for the binding of HU into the substrate-binding pocket. The other residue contributes to the formation of a loose hydrogen-bond network during the catalytic reaction. Information regarding the amino acid residues will be very useful in the design of a new catalyst for synthesizing the β-substituted-L-alanine derivatives.


    Organizational Affiliation

    Department of Molecular Microbiology and Biotechnology, Graduate School of Biomedical & Health Sciences, Hiroshima University, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
O-ureido-L-serine synthaseABCDEFGH332Streptomyces lavendulaeMutation(s): 0 
Gene Names: dcsD
EC: 2.6.99.3 (PDB Primary Data), 2.5.1.47 (PDB Primary Data)
Find proteins for D2Z027 (Streptomyces lavendulae)
Explore D2Z027 
Go to UniProtKB:  D2Z027
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download CCD File 
A, B, C, D, E, F, G, H
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.48α = 90
b = 154.13β = 90.48
c = 118.52γ = 90
Software Package:
Software NamePurpose
BSSdata collection
MOLREPphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-29
    Type: Initial release
  • Version 1.1: 2015-08-12
    Changes: Database references