8UMC

Deinococcus aerius TR0125 C-glucosyl deglycosidase (CGD), cryo-EM


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural and Functional Characterization of a Gene Cluster Responsible for Deglycosylation of C-glucosyl Flavonoids and Xanthonoids by Deinococcus aerius.

Furlanetto, V.Kalyani, D.C.Kostelac, A.Puc, J.Haltrich, D.Hallberg, B.M.Divne, C.

(2024) J Mol Biol 436: 168547-168547

  • DOI: https://doi.org/10.1016/j.jmb.2024.168547
  • Primary Citation of Related Structures:  
    8QVC, 8QVD, 8QVE, 8UMC

  • PubMed Abstract: 

    Plant C-glycosylated aromatic polyketides are important for plant and animal health. These are specialized metabolites that perform functions both within the plant, and in interaction with soil or intestinal microbes. Despite the importance of these plant compounds, there is still limited knowledge of how they are metabolized. The Gram-positive aerobic soil bacterium Deinococcus aerius strain TR0125 and other Deinococcus species thrive in a wide range of harsh environments. In this work, we identified a C-glycoside deglycosylation gene cluster in the genome of D. aerius. The cluster includes three genes coding for a GMC-type oxidoreductase (DaCGO1) that oxidizes the glucosyl C3 position in aromatic C-glucosyl compounds, which in turn provides the substrate for the C-glycoside deglycosidase (DaCGD; composed of α+β subunits) that cleaves the glucosyl-aglycone C-C bond. Our results from size-exclusion chromatography, single particle cryo-electron microscopy and X-ray crystallography show that DaCGD is an α 2 β 2 heterotetramer, which represents a novel oligomeric state among bacterial CGDs. Importantly, the high-resolution X-ray structure of DaCGD provides valuable insights into the activation of the catalytic hydroxide ion by Lys261. DaCGO1 is specific for the 6-C-glucosyl flavones isovitexin, isoorientin and the 2-C-glucosyl xanthonoid mangiferin, and the subsequent C-C-bond cleavage by DaCGD generated apigenin, luteolin and norathyriol, respectively. Of the substrates tested, isovitexin was the preferred substrate (DaCGO1, K m 0.047 mM, k cat 51 min -1 ; DaCGO1/DaCGD, K m 0.083 mM, k cat 0.42 min -1 ).


  • Organizational Affiliation

    School of Engineering Sciences in Chemistry, Biotechnology, and Health, CBH, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Xylose isomerase-like TIM barrel domain-containing protein
A, C
347Deinococcus aeriusMutation(s): 0 
Gene Names: DAERI_200053
UniProt
Find proteins for A0A2I9DAN1 (Deinococcus aerius)
Explore A0A2I9DAN1 
Go to UniProtKB:  A0A2I9DAN1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2I9DAN1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DUF6379 domain-containing protein
B, D
123Deinococcus aeriusMutation(s): 0 
Gene Names: DAERI_200052
UniProt
Find proteins for A0A2I9E2I0 (Deinococcus aerius)
Explore A0A2I9E2I0 
Go to UniProtKB:  A0A2I9E2I0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2I9E2I0
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentSwedenFormas 2017-00983
Other governmentSwedenVR 2017-03877
Other privateSwedenOscar and Lili Lamm Memorial Foundation DO2017-0020
Austrian Science FundAustriaFWF P33545
Austrian Science FundAustriaFWF W1224

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-29
    Type: Initial release