Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.70 kDa 
• Atom Count: 3059 
• Modelled Residue Count: 386 
• Deposited Residue Count: 386 
• Unique protein chains: 1

5AY9

Crystal structure of Ruminococcus albus 4-O-beta-D-mannosyl-D-glucose phosphorylase (RaMP1)

• PDB DOI: 10.2210/pdb5AY9/pdb

• Classification: TRANSFERASE
• Organism(s): Ruminococcus albus 7 = DSM 20455
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-08-11 Released: 2016-03-23 
• Deposition Author(s): Ye, Y., Saburi, W., Kato, K., Yao, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.281 
• R-Value Work: 0.239 
• R-Value Observed: 0.241 

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

• PubMed: 26913570 
• DOI: 10.1002/1873-3468.12105
• Primary Citation of Related Structures:  
  5AY9, 5AYC, 5AYD, 5AYE


• 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 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.

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Organizational Affiliation: 

Department of Pharmacology, Basic Medical College of Zhengzhou University, Zhengzhou, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-O-beta-D-mannosyl-D-glucose phosphorylase	A	386	Ruminococcus albus 7 = DSM 20455	Mutation(s): 0  Gene Names: Rumal_0852 EC: 2.4.1.281
UniProt
Find proteins for E6UIS7 (Ruminococcus albus (strain ATCC 27210 / DSM 20455 / JCM 14654 / NCDO 2250 / 7)) Explore E6UIS7  Go to UniProtKB:  E6UIS7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.281 
• R-Value Work: 0.239 
• R-Value Observed: 0.241 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.9	α = 90
b = 88.9	β = 90
c = 286.857	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-08-11 
• Released Date: 2016-03-23 
Deposition Author(s): Ye, Y., Saburi, W., Kato, K., Yao, M.

Revision History  

• Version 1.0: 2016-03-23
  Type: Initial release
  
• Version 1.1: 2016-04-06
  Changes: Database references
• Version 1.2: 2020-02-26
  Changes: Data collection, Database references, Derived calculations