3WAT

Crystal structure of 4-O-beta-D-mannosyl-D-glucose phosphorylase MGP complexed with Man+Glc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

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This is version 1.2 of the entry. See complete history


Literature

Structure of Novel Enzyme in Mannan Biodegradation Process 4-O-beta-d-Mannosyl-d-Glucose Phosphorylase MGP

Nakae, S.Ito, S.Higa, M.Senoura, T.Wasaki, J.Hijikata, A.Shionyu, M.Ito, S.Shirai, T.

(2013) J Mol Biol 425: 4468-4478

  • DOI: 10.1016/j.jmb.2013.08.002
  • Primary Citation of Related Structures:  
    3WAS, 3WAT, 3WAU, 4KMI

  • PubMed Abstract: 
  • The crystal structure of a novel component of the mannan biodegradation system, 4-O-β-D-mannosyl-D-glucose phosphorylase (MGP), was determined to a 1.68-Å resolution. The structure of the enzyme revealed a unique homohexameric structure, which was formed by using two helices attached to the N-terminus and C-terminus as a tab for sticking between subunits ...

    The crystal structure of a novel component of the mannan biodegradation system, 4-O-β-D-mannosyl-D-glucose phosphorylase (MGP), was determined to a 1.68-Å resolution. The structure of the enzyme revealed a unique homohexameric structure, which was formed by using two helices attached to the N-terminus and C-terminus as a tab for sticking between subunits. The structures of MGP complexes with genuine substrates, 4-O-β-D-mannosyl-D-glucose and phosphate, and the product D-mannose-1-phosphate were also determined. The complex structures revealed that the invariant residue Asp131, which is supposed to be the general acid/base, did not exist close to the glycosidic Glc-O4 atom, which should be protonated in the catalytic reaction. Also, no solvent molecule that might mediate a proton transfer from Asp131 was observed in the substrate complex structure, suggesting that the catalytic mechanism of MGP is different from those of known disaccharide phosphorylases.


    Organizational Affiliation

    Department of Bioscience, Nagahama Institute of Bio-science and Technology, and Japan Science and Technology Agency Institute for Bioinformatics Research and Development, 1266 Tamura, Nagahama 526-0829, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
4-O-beta-D-mannosyl-D-glucose phosphorylaseA, B390Bacteroides fragilis NCTC 9343Mutation(s): 0 
Gene Names: BF0772BF9343_0737
EC: 2.4.1.281
UniProt
Find proteins for Q5LH68 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / NCTC 9343 / Onslow))
Explore Q5LH68 
Go to UniProtKB:  Q5LH68
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5LH68
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.54α = 90
b = 82.54β = 90
c = 307.48γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SOLVEphasing
PHENIXrefinement
MOSFLMdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-04
    Type: Initial release
  • Version 1.1: 2013-11-20
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary