5H3Z

Crystal Structure of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Mechanistic insight into the substrate specificity of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans

Nakajima, M.Tanaka, N.Furukawa, N.Nihira, T.Kodutsumi, Y.Takahashi, Y.Sugimoto, N.Miyanaga, A.Fushinobu, S.Taguchi, H.Nakai, H.

(2017) Sci Rep 7: 42671-42671

  • DOI: 10.1038/srep42671
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glycoside phosphorylases catalyze the phosphorolysis of oligosaccharides into sugar phosphates. Recently, we found a novel phosphorylase acting on β-1,2-glucooligosaccharides with degrees of polymerization of 3 or more (1,2-β-oligoglucan phosphorylas ...

    Glycoside phosphorylases catalyze the phosphorolysis of oligosaccharides into sugar phosphates. Recently, we found a novel phosphorylase acting on β-1,2-glucooligosaccharides with degrees of polymerization of 3 or more (1,2-β-oligoglucan phosphorylase, SOGP) in glycoside hydrolase family (GH) 94. Here, we characterized SOGP from Lachnoclostridium phytofermentans (LpSOGP) and determined its crystal structure. LpSOGP is a monomeric enzyme that contains a unique β-sandwich domain (Ndom1) at its N-terminus. Unlike the dimeric GH94 enzymes possessing catalytic pockets at their dimer interface, LpSOGP has a catalytic pocket between Ndom1 and the catalytic domain. In the complex structure of LpSOGP with sophorose, sophorose binds at subsites +1 to +2. Notably, the Glc moiety at subsite +1 is flipped compared with the corresponding ligands in other GH94 enzymes. This inversion suggests the great distortion of the glycosidic bond between subsites -1 and +1, which is likely unfavorable for substrate binding. Compensation for this disadvantage at subsite +2 can be accounted for by the small distortion of the glycosidic bond in the sophorose molecule. Therefore, the binding mode at subsites +1 and +2 defines the substrate specificity of LpSOGP, which provides mechanistic insights into the substrate specificity of a phosphorylase acting on β-1,2-glucooligosaccharides.


    Organizational Affiliation

    Department of Biotechnology, The University of Tokyo, Tokyo, Japan.,Department of Chemistry, Tokyo Institute of Technology, Tokyo, Japan.,Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan.,Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan.,Graduate School of Science &Technology, Niigata University, Niigata, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
A, B
1122Lachnoclostridium phytofermentans (strain ATCC 700394 / DSM 18823 / ISDg)Mutation(s): 0 
Find proteins for A9KJS6 (Lachnoclostridium phytofermentans (strain ATCC 700394 / DSM 18823 / ISDg))
Go to UniProtKB:  A9KJS6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 87.761α = 90.00
b = 94.784β = 98.41
c = 157.943γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-01
    Type: Initial release