3SS7

Crystal structure of holo D-serine dehydratase from Escherichia coli at 1.55 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of D-serine dehydratase from Escherichia coli.

Urusova, D.V.Isupov, M.N.Antonyuk, S.Kachalova, G.S.Oblomova, G.Vagin, A.A.Lebedev, A.A.Bourenko, G.P.Dauter, Z.Bartunik, H.D.Lamzin, V.S.Melik-Adamyan, W.R.Mueller, T.D.Schnackerz, K.D.

(2011) Biochim.Biophys.Acta 1824: 422-432

  • DOI: 10.1016/j.bbapap.2011.10.017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • D-Serine dehydratase from Escherichia coli is a member of the β-family (fold-type II) of the pyridoxal 5'-phosphate-dependent enzymes, catalyzing the conversion of D-serine to pyruvate and ammonia. The crystal structure of monomeric D-serine dehydrat ...

    D-Serine dehydratase from Escherichia coli is a member of the β-family (fold-type II) of the pyridoxal 5'-phosphate-dependent enzymes, catalyzing the conversion of D-serine to pyruvate and ammonia. The crystal structure of monomeric D-serine dehydratase has been solved to 1.97Å-resolution for an orthorhombic data set by molecular replacement. In addition, the structure was refined in a monoclinic data set to 1.55Å resolution. The structure of DSD reveals a larger pyridoxal 5'-phosphate-binding domain and a smaller domain. The active site of DSD is very similar to those of the other members of the β-family. Lys118 forms the Schiff base to PLP, the cofactor phosphate group is liganded to a tetraglycine cluster Gly279-Gly283, and the 3-hydroxyl group of PLP is liganded to Asn170 and N1 to Thr424, respectively. In the closed conformation the movement of the small domain blocks the entrance to active site of DSD. The domain movement plays an important role in the formation of the substrate recognition site and the catalysis of the enzyme. Modeling of D-serine into the active site of DSD suggests that the hydroxyl group of D-serine is coordinated to the carboxyl group of Asp238. The carboxyl oxygen of D-serine is coordinated to the hydroxyl group of Ser167 and the amide group of Leu171 (O1), whereas the O2 of the carboxyl group of D-serine is hydrogen-bonded to the hydroxyl group of Ser167 and the amide group of Thr168. A catalytic mechanism very similar to that proposed for L-serine dehydratase is discussed.


    Organizational Affiliation

    The Institute of Crystallography, Russian Academy of Sciences, Moscow, Russia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-serine dehydratase
X
442Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: dsdA
EC: 4.3.1.18
Find proteins for P00926 (Escherichia coli (strain K12))
Go to UniProtKB:  P00926
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
X
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
X
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
X
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 73.774α = 90.00
b = 47.806β = 104.96
c = 75.193γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
MOLREPphasing
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-18
    Type: Initial release
  • Version 1.1: 2012-02-08
    Type: Database references