5EPD

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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.

(2018) PLoS ONE 13: e0195299-e0195299

  • DOI: 10.1371/journal.pone.0195299

  • PubMed Abstract: 
  • 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 stru ...

    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 Å resolution. In agreement with the structures of the related bacterial OYEs, the structure revealed the TIM barrel fold with an N-terminal β-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.


    Organizational Affiliation

    Dept. of Solid State Engineering, FNSPE Czech Technical University, Prague, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University Prague, Czech Republic.,Institute of Biotechnology CAS, v. v. i., BIOCEV, Vestec, Prague West, Czech Republic.,Institute of Microbiology CAS, v. v. i., Prague, Czech Republic.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycerol trinitrate reductase
A
385Rhizobium radiobacterMutation(s): 0 
Gene Names: xdpB
Find proteins for A0A0A0VDJ9 (Rhizobium radiobacter)
Go to UniProtKB:  A0A0A0VDJ9
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.885α = 90.00
b = 68.599β = 90.00
c = 93.677γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
BALBESphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Charles UniversityCzech Republic720414

Revision History 

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 1.1: 2019-02-27
    Type: Data collection, Database references