3SS9

Crystal structure of holo D-serine dehydratase from Escherichia coli at 1.97 A resolution

Summary for 3SS9

• Entry DOI: 10.2210/pdb3ss9/pdb
• Related: 3ANV 3AWN 3AWO 3ROX 3ROZ 3SS7
• Descriptor: D-serine dehydratase, PYRIDOXAL-5'-PHOSPHATE, POTASSIUM ION, ... (4 entities in total)
• Functional Keywords: d-serine dehydratase, type ii fold, alfa, beta elimination, pyridoxal-5'-phosphate, lyase
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 48236.61

Authors

Urusova, D.V.,Isupov, M.N.,Antonyuk, S.V.,Kachalova, G.S.,Vagin, A.A.,Lebedev, A.A.,Bourenkov, G.P.,Dauter, Z.,Bartunik, H.D.,Melik-Adamyan, W.R.,Mueller, T.D.,Schnackerz, K.D. (deposition date: 2011-07-08, release date: 2012-01-18, Last modification date: 2017-11-08)

Primary citation

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.
Crystal structure of D-serine dehydratase from Escherichia coli.
Biochim.Biophys.Acta, 1824:422-432, 2011

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.

PubMed: 22197591
DOI: 10.1016/j.bbapap.2011.10.017

Experimental method

X-RAY DIFFRACTION (1.97 Å)