5epd | pdb_00005epd

Crystal structure of Glycerol Trinitrate Reductase XdpB from Agrobacterium sp. R89-1 (Apo form)

spinqualitylabelsall models 5epd, resolution 2.10Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5epd is a 1 chain structure with sequence from "achromobacter_radiobacter"_(beijerinck_and_van_delden_1902)_bergey_et_al._1934 "achromobacter radiobacter" (beijerinck and van delden 1902) bergey et al. 1934. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Related: 4jic Gene: xdpB ("Achromobacter radiobacter" (Beijerinck and van Delden 1902) Bergey et al. 1934) Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed 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. The crystal structure of XdpB, the bacterial old yellow enzyme, in an FMN-free form.,Zahradnik J, Kolenko P, Palyzova A, Cerny J, Kolarova L, Kyslikova E, Maresova H, Grulich M, Nunvar J, Sulc M, Kyslik P, Schneider B PLoS One. 2018 Apr 9;13(4):e0195299. doi: 10.1371/journal.pone.0195299., eCollection 2018. PMID:29630677 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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