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- Title
Crystal structure of the NADP<sup>+</sup> and tartrate-bound complex of l-serine 3-dehydrogenase from the hyperthermophilic archaeon <italic>Pyrobaculum calidifontis</italic>.
- Authors
Yoneda, Kazunari; Sakuraba, Haruhiko; Araki, Tomohiro; Ohshima, Toshihisa
- Abstract
A gene encoding l-serine dehydrogenase (l-SerDH) that exhibits extremely low sequence identity to the <italic>Agrobacterium tumefaciens</italic>l-SerDH was identified in the hyperthermophilic archaeon <italic>Pyrobaculum calidifontis</italic>. The predicted amino acid sequence showed 36% identity with that of <italic>Pseudomonas aeruginosa</italic>l-SerDH, suggesting that <italic>P. calidifontis</italic>l-SerDH is a novel type of l-SerDH, like <italic>Ps. aeruginosa</italic>l-SerDH. The overexpressed enzyme appears to be the most thermostable l-SerDH described to date, and no loss of activity was observed by incubation for 30 min at temperatures up to 100 °C. The enzyme showed substantial reactivity towards d-serine, in addition to l-serine. Two different crystal structures of <italic>P. calidifontis</italic>l-SerDH were determined using the Se-MAD and MR method: the structure in complex with NADP+/sulfate ion at 1.18 Å and the structure in complex with NADP+/l-tartrate (substrate analog) at 1.57 Å. The fold of the catalytic domain showed similarity with that of <italic>Ps. aeruginosa</italic>l-SerDH. However, the active site structure significantly differed between the two enzymes. Based on the structure of the tartrate, l- and d-serine and 3-hydroxypropionate molecules were modeled into the active site and the substrate binding modes were estimated. A structural comparison suggests that the wide cavity at the substrate binding site is likely responsible for the high reactivity of the enzyme toward both l- and d-serine enantiomers. This is the first description of the structure of the novel type of l-SerDH with bound NADP+ and substrate analog, and it provides new insight into the substrate binding mechanism of l-SerDH. The results obtained here may be very informative for the creation of l- or d-serine-specific SerDH by protein engineering.
- Subjects
THERMOPHILIC archaebacteria; DEHYDROGENASE genetics; NICOTINAMIDE adenine dinucleotide phosphate; CRYSTAL structure; TARTRATES; SERINE
- Publication
Extremophiles, 2018, Vol 22, Issue 3, p395
- ISSN
1431-0651
- Publication type
Article
- DOI
10.1007/s00792-018-1004-0