5MAN | pdb_00005man

Structure of sucrose phosphorylase from Bifidobacterium adolescentis bound to nigerose

• PDB DOI: https://doi.org/10.2210/pdb5MAN/pdb

• Classification: TRANSFERASE
• Organism(s): Bifidobacterium adolescentis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-11-03 Released: 2017-12-20 
• Deposition Author(s): Grimm, C., Kraus, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.262 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Literature

Switching enzyme specificity from phosphate to resveratrol glucosylation.

Kraus, M., Grimm, C., Seibel, J.

(2017) Chem Commun (Camb) 53: 12181-12184

• PubMed: 29057405 
• DOI: https://doi.org/10.1039/c7cc05993k
• Primary Citation Related Structures: 
  5M9X, 5MAN


• PubMed Abstract: 
  

  Here we present a point mutation-triggered domain shift which switches the acceptor preference of a sucrose phosphorylase from phosphate to a variety of large polyphenolic compounds including resveratrol and quercetin, enabling their efficient glucosylation. The variant possesses a high affinity for aromatic substrates due to newly introduced π-π- and hydrophobic interactions in the altered active site. The domain shift brings about a substantially enlarged and multifunctional active site for polyphenol glucosylation and rare disaccharide production. The crystal structure of the variant with its product resveratrol-3-α-d-glucoside allows the prediction of the substrate scope and regioselectivity of the aromatic compounds' glucosylation sites.

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Organizational Affiliation: 
• Department of Organic Chemistry, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.61 kDa 
• Atom Count: 4,103 
• Modeled Residue Count: 504 
• Deposited Residue Count: 504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sucrose phosphorylase	A [auth B]	504	Bifidobacterium adolescentis	Mutation(s): 0  Gene Names: sucP EC: 2.4.1.7
UniProt
Find proteins for A0ZZH6 (Bifidobacterium adolescentis (strain ATCC 15703 / DSM 20083 / NCTC 11814 / E194a)) Explore A0ZZH6  Go to UniProtKB:  A0ZZH6

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose	B [auth A]	2		N/A
Glycosylation Resources
GlyTouCan: G81189IV GlyCosmos: G81189IV

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900052	B [auth A]	alpha-nigerose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.262 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.445	α = 90
b = 82.445	β = 90
c = 154.864	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): Grimm, C., Kraus, M.

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-05-08
  Changes: Data collection, Database references, Structure summary