3W6U

Crystal structure of NADP bound L-serine 3-dehydrogenase from Hyperthermophilic Archaeon Pyrobaculum calidifontis

Summary for 3W6U

• Entry DOI: 10.2210/pdb3w6u/pdb
• Descriptor: 6-phosphogluconate dehydrogenase, NAD-binding protein, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (3 entities in total)
• Functional Keywords: hyperthermophilic archaeon, rossmann fold, l-serine 3-dehydrogenase, nad(p) binding, oxidoreductase
• Biological source: Pyrobaculum calidifontis
• Total number of polymer chains: 1
• Total formula weight: 34186.28

Authors

Yoneda, K.,Sakuraba, H.,Ohshima, T. (deposition date: 2013-02-22, release date: 2014-01-15, Last modification date: 2024-11-13)

Primary citation

Yoneda, K.,Sakuraba, H.,Araki, T.,Ohshima, T.
Crystal structure of the NADP+and tartrate-bound complex of L-serine 3-dehydrogenase from the hyperthermophilic archaeon Pyrobaculum calidifontis.
Extremophiles, 22:395-405, 2018

PubMed Abstract: A gene encoding L-serine dehydrogenase (L-SerDH) that exhibits extremely low sequence identity to the Agrobacterium tumefaciens L-SerDH was identified in the hyperthermophilic archaeon Pyrobaculum calidifontis. The predicted amino acid sequence showed 36% identity with that of Pseudomonas aeruginosa L-SerDH, suggesting that P. calidifontis L-SerDH is a novel type of L-SerDH, like Ps. aeruginosa 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 P. calidifontis 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 Ps. aeruginosa 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.

PubMed: 29353380
DOI: 10.1007/s00792-018-1004-0

Experimental method

X-RAY DIFFRACTION (2 Å)