PDBsum entry 1wpq

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Oxidoreductase PDB id
Protein chain
348 a.a.
SO4 ×7
13P ×2
NAD ×2
Waters ×602

References listed in PDB file
Key reference
Title Crystal structures of human glycerol 3-Phosphate dehydrogenase 1 (gpd1).
Authors X.Ou, C.Ji, X.Han, X.Zhao, X.Li, Y.Mao, L.L.Wong, M.Bartlam, Z.Rao.
Ref. J Mol Biol, 2006, 357, 858-869. [DOI no: 10.1016/j.jmb.2005.12.074]
PubMed id 16460752
Homo sapiensl-alpha-glycerol-3-phosphate dehydrogenase 1 (GPD1) catalyzes the reversible biological conversion of dihydroxyacetone (DHAP) to glycerol-3-phosphate. The GPD1 protein was expressed in Escherichia coli, and purified as a fusion protein with glutathione S-transferase. Here we report the apoenzyme structure of GPD1 determined by multiwavelength anomalous diffraction phasing, and other complex structures with small molecules (NAD(+) and DHAP) by the molecular replacement method. This enzyme structure is organized into two distinct domains, the N-terminal eight-stranded beta-sheet sandwich domain and the C-terminal helical substrate-binding domain. An electrophilic catalytic mechanism by the epsilon-NH(3)(+) group of Lys204 is proposed on the basis of the structural analyses. In addition, the inhibitory effects of zinc and sulfate on GPDHs are assayed and discussed.
Figure 4.
Figure 4. The putative active site. The phosphate group of DHAP is half-encircled by the side-chain of Arg269, and interacts with Arg269 and Gly268 directly by hydrogen bonds (not shown). The conserved residues Lys204, Asn205, Asp260 and Thr264 form a stable hydrogen bonding network. The other hydrogen bonding network includes residues Lys120 and Asp260, as well as an ordered water molecule (with a B-factor of 16.4 Å2) which hydrogen bonds to Gly149 and Asn151 (not shown). In these two electrostatic networks, only the e-NH3+ group of Lys204 is the nearest to the C[2] atom of DHAP (3.4 Å).
Figure 7.
Figure 7. (a) and (b) Superposition of the human GPD1 apoenzyme structure (red) with the L. mexicana GPDH structures in complex with NAD (blue, PDB code: 1EVZ), and in complex with both NAD and DHAP (green, PDB code: 1N1E). (b) An enlarged image of the shaded area in (a). The structure of human apo-GPD1 is structurally closer to the 1N1E structure (closed form) of L. mexicana than the 1EVZ structure (open form) of L. mexicana.
The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 357, 858-869) copyright 2006.
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