The crystal structure of XdpB, the bacterial old yellow enzyme, in an FMN-free form
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388971%3A_____%2F18%3A00489548" target="_blank" >RIV/61388971:_____/18:00489548 - isvavai.cz</a>
Alternative codes found
RIV/86652036:_____/18:00499369 RIV/68407700:21340/18:00321219 RIV/00216208:11310/18:10375446
Result on the web
<a href="http://dx.doi.org/10.1371/journal.pone.0195299" target="_blank" >http://dx.doi.org/10.1371/journal.pone.0195299</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1371/journal.pone.0195299" target="_blank" >10.1371/journal.pone.0195299</a>
Alternative languages
Result language
angličtina
Original language name
The crystal structure of XdpB, the bacterial old yellow enzyme, in an FMN-free form
Original language description
Old Yellow Enzymes (OYES) are NAD(P)H dehydrogenases of not fully resolved physiological roles that are widespread among bacteria, plants, and fungi and have a great potential for biotechnological applications. We determined the apo form crystal structure of a member of the OYE class, glycerol trinitrate reductase XdpB, from Agrobacterium bohemicum R89-1 at 2.1 A resolution. In agreement with the structures of the related bacterial OYEs, the structure revealed the TIM barrel fold with an N-terminal beta-hairpin lid, but surprisingly, the structure did not contain its cofactor FMN. Its putative binding site was occupied by a pentapeptide TTSDN from the C-terminus of a symmetry related molecule. Biochemical experiments confirmed a specific concentration-dependent oligomerization and a low FMN content. The blocking of the FMN binding site can exist in vivo and regulates enzyme activity. Our bioinformatic analysis indicated that a similar self-inhibition could be expected in more OYEs which we designated as subgroup OYE C1. This subgroup is widespread among G-bacteria and can be recognized by the conserved sequence GxxDYP in proximity of the C termini. In proteobacteria, the C1 subgroup OYEs are typically coded in one operon with short-chain dehydrogenase. This operon is controlled by the tetR-like transcriptional regulator. OYEs coded in these operons are unlikely to be involved in the oxidative stress response as the other known members of the OYE family because no upregulation of XdpB was observed after exposing A. bohemicum R89-1 to oxidative stress.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10606 - Microbiology
Result continuities
Project
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Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2018
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
PLoS ONE
ISSN
1932-6203
e-ISSN
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Volume of the periodical
13
Issue of the periodical within the volume
4
Country of publishing house
US - UNITED STATES
Number of pages
18
Pages from-to
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UT code for WoS article
000429505000037
EID of the result in the Scopus database
2-s2.0-85045154045