6Q2F

Structure of Rhamnosidase from Novosphingobium sp. PP1Y


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


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Literature

The crystal structure and insight into the substrate specificity of the alpha-L rhamnosidase RHA-P from Novosphingobium sp. PP1Y.

Terry, B.Ha, J.De Lise, F.Mensitieri, F.Izzo, V.Sazinsky, M.H.

(2019) Arch.Biochem.Biophys. --: 108189-108189

  • DOI: 10.1016/j.abb.2019.108189

  • PubMed Abstract: 
  • Flavonoid natural products are well known for their beneficial antimicrobial, antitumor, and anti-inflammatory properties, however, some of these natural products often are rhamnosylated, which severely limits their bioavailability. The lack of endog ...

    Flavonoid natural products are well known for their beneficial antimicrobial, antitumor, and anti-inflammatory properties, however, some of these natural products often are rhamnosylated, which severely limits their bioavailability. The lack of endogenous rhamnosidases in the human GI tract not only prevents many of these glycosylated compounds from being of value in functional foods but also limits the modification of natural product libraries being tested for drug discovery. RHA-P is a catalytically efficient, thermostable α-l-rhamnosidase from the marine bacterium Novosphingobium sp. PP1Y that selectively hydrolyzes α-1,6 and α-1,2 glycosidic linkages between a terminal rhamnose and a flavonoid moiety. This work reports the 2.2 Å resolution crystal structure of RHA-P, which is an essential step forward in the characterization of RHA-P as a potential catalyst to increase the bioavailability of rhamnosylated natural compounds. The structure shows highly conserved rhamnose- and calcium-binding residues in a shallow active site that is housed in the (α/β) 8 barrel domain. In comparison to BT0986 (pdbID: 5MQN), the only known structure of an RHA-P homolog, the morphology, electrostatic potentials and amino acid composition of the substrate binding pocket are significantly different, offering insight into the substrate preference of RHA-P for glycosylated aryl compounds such as hesperidin, naringin, rutin, and quercitrin, over polysaccharides, which are preferred by BT0986. These preferences were further explored by using in silico docking, the results of which are consistent with the known kinetic data for RHA-P acting on different rhamnosylated flavonoids. Due to its promiscuity, relative thermostability compared to other known rhamnosidases, and catalytic efficiency even in significant concentrations of organic solvents, RHA-P continues to show potential for biocatalytic applications.


    Organizational Affiliation

    Department of Chemistry, Pomona College, 645 N. College Ave Claremont, CA, 91711, USA.,Department of Biology of the University Federico II, via Cinthia 4, Naples, Italy.,Dipartimento di Medicina, Chirurgia e Odontoiatria "Scuola Medica Salernitana", Università degli Studi di Salerno, via S. Allende, 84081, Baronissi, SA, Italy. Electronic address: vizzo@unisa.it.,Department of Chemistry, Pomona College, 645 N. College Ave Claremont, CA, 91711, USA. Electronic address: matthew.sazinsky@pomona.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycoside hydrolase family protein
A
1151Novosphingobium sp. PP1YMutation(s): 0 
Find proteins for F6IEX3 (Novosphingobium sp. PP1Y)
Go to UniProtKB:  F6IEX3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.163 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 80.809α = 90.00
b = 114.570β = 90.00
c = 158.797γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-11-27
    Type: Initial release