5AYC

Crystal structure of Ruminococcus albus 4-O-beta-D-mannosyl-D-glucose phosphorylase (RaMP1) in complexes with sulfate and 4-O-beta-D-mannosyl-D-glucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into the difference in substrate recognition of two mannoside phosphorylases from two GH130 subfamilies.

Ye, Y.Saburi, W.Odaka, R.Kato, K.Sakurai, N.Komoda, K.Nishimoto, M.Kitaoka, M.Mori, H.Yao, M.

(2016) Febs Lett. 590: 828-837

  • DOI: 10.1002/1873-3468.12105
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In Ruminococcus albus, 4-O-β-D-mannosyl-D-glucose phosphorylase (RaMP1) and β-(1,4)-mannooligosaccharide phosphorylase (RaMP2) belong to two subfamilies of glycoside hydrolase family 130. The two enzymes phosphorolyze β-mannosidic linkages at the non ...

    In Ruminococcus albus, 4-O-β-D-mannosyl-D-glucose phosphorylase (RaMP1) and β-(1,4)-mannooligosaccharide phosphorylase (RaMP2) belong to two subfamilies of glycoside hydrolase family 130. The two enzymes phosphorolyze β-mannosidic linkages at the nonreducing ends of their substrates, and have substantially diverse substrate specificity. The differences in their mechanism of substrate binding have not yet been fully clarified. In the present study, we report the crystal structures of RaMP1 with/without 4-O-β-D-mannosyl-d-glucose and RaMP2 with/without β-(1→4)-mannobiose. The structures of the two enzymes differ at the +1 subsite of the substrate-binding pocket. Three loops are proposed to determine the different substrate specificities. One of these loops is contributed from the adjacent molecule of the oligomer structure. In RaMP1, His245 of loop 3 forms a hydrogen-bond network with the substrate through a water molecule, and is indispensible for substrate binding.


    Organizational Affiliation

    Graduate School of Life Science, Hokkaido University, Sapporo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
4-O-beta-D-mannosyl-D-glucose phosphorylase
A
386Ruminococcus albus (strain ATCC 27210 / DSM 20455 / JCM 14654 / NCDO 2250 / 7)Mutation(s): 0 
EC: 2.4.1.281
Find proteins for E6UIS7 (Ruminococcus albus (strain ATCC 27210 / DSM 20455 / JCM 14654 / NCDO 2250 / 7))
Go to UniProtKB:  E6UIS7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BGC
Query on BGC

Download SDF File 
Download CCD File 
A
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.153 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 87.700α = 90.00
b = 87.700β = 90.00
c = 283.874γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata processing
Cootrefinement
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-23
    Type: Initial release
  • Version 1.1: 2016-04-06
    Type: Database references