| RRC ID |
55157
|
| Author |
Yoneda K, Sakuraba H, Araki T, Ohshima T.
|
| Title |
Crystal structure of the NADP+ and tartrate-bound complex of L-serine 3-dehydrogenase from the hyperthermophilic archaeon Pyrobaculum calidifontis.
|
| Journal |
Extremophiles
|
| 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.
|
| Volume |
22(3)
|
| Pages |
395-405
|
| Published |
2018-5-1
|
| DOI |
10.1007/s00792-018-1004-0
|
| PII |
10.1007/s00792-018-1004-0
|
| PMID |
29353380
|
| MeSH |
Alcohol Oxidoreductases / chemistry*
Alcohol Oxidoreductases / metabolism
Archaeal Proteins / chemistry*
Archaeal Proteins / metabolism
Catalytic Domain
Crystallography, X-Ray
Enzyme Stability
Hot Temperature
Molecular Docking Simulation*
NADP / chemistry
NADP / metabolism
Protein Binding
Pyrobaculum / enzymology*
Serine / chemistry
Serine / metabolism
Substrate Specificity
Tartrates / chemistry
Tartrates / metabolism
|
| IF |
2.046
|
| Times Cited |
1
|
| Resource |
| General Microbes |
JCM 11548 |
