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

Experimental Data Snapshot

  • Resolution: 1.55 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

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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: https://doi.org/10.1016/j.bbapap.2011.10.017
  • Primary Citation of Related Structures:  
    3SS7, 3SS9

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-serine dehydrataseA [auth X]442Escherichia coli K-12Mutation(s): 0 
Gene Names: b2366dsdAdsdA b2366JW2393JW2363
Find proteins for P00926 (Escherichia coli (strain K12))
Explore P00926 
Go to UniProtKB:  P00926
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00926
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.55 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.774α = 90
b = 47.806β = 104.96
c = 75.193γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

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