6S9U | pdb_00006s9u

Crystal structure of sucrose 6F-phosphate phosphorylase from Ilumatobacter coccineus

• PDB DOI: https://doi.org/10.2210/pdb6S9U/pdb

• Classification: TRANSFERASE
• Organism(s): Ilumatobacter coccineus YM16-304
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2019-07-15 Released: 2019-08-28 
• Deposition Author(s): Capra, N., Franceus, J., Desmet, T., Thunnissen, A.M.W.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.200 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Literature

Structural Comparison of a Promiscuous and a Highly Specific Sucrose 6 F -Phosphate Phosphorylase.

Franceus, J., Capra, N., Desmet, T., Thunnissen, A.W.H.

(2019) Int J Mol Sci 20

• PubMed: 31405215 
• DOI: https://doi.org/10.3390/ijms20163906
• Primary Citation Related Structures: 
  6S9U, 6S9V


• PubMed Abstract: 
  

  In family GH13 of the carbohydrate-active enzyme database, subfamily 18 contains glycoside phosphorylases that act on α-sugars and glucosides. Because their phosphorolysis reactions are effectively reversible, these enzymes are of interest for the biocatalytic synthesis of various glycosidic compounds. Sucrose 6 ^F -phosphate phosphorylases (SPPs) constitute one of the known substrate specificities. Here, we report the characterization of an SPP from Ilumatobacter coccineus with a far stricter specificity than the previously described promiscuous SPP from Thermoanaerobacterium thermosaccharolyticum . Crystal structures of both SPPs were determined to provide insight into their similarities and differences. The residues responsible for binding the fructose 6-phosphate group in subsite +1 were found to differ considerably between the two enzymes. Furthermore, several variants that introduce a higher degree of substrate promiscuity in the strict SPP from I. coccineus were designed. These results contribute to an expanded structural knowledge of enzymes in subfamily GH13_18 and facilitate their rational engineering.

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Organizational Affiliation: 
• Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium. [e-mail].
Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 60.75 kDa 
• Atom Count: 4,505 
• Modeled Residue Count: 520 
• Deposited Residue Count: 531 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative sucrose phosphorylase	A	531	Ilumatobacter coccineus YM16-304	Mutation(s): 0  Gene Names: YM304_32550 EC: 2.4.1.7 (PDB Primary Data), 2.4.1.329 (UniProt)
UniProt
Find proteins for A0A6C7EEG6 (Ilumatobacter coccineus (strain NBRC 103263 / KCTC 29153 / YM16-304)) Explore A0A6C7EEG6  Go to UniProtKB:  A0A6C7EEG6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B3P	C [auth A], D [auth A]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C11 H26 N2 O6 HHKZCCWKTZRCCL-UHFFFAOYSA-N
TRS	E [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.200 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.434	α = 90
b = 92.054	β = 90
c = 179.971	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-08-28 
Deposition Author(s): Capra, N., Franceus, J., Desmet, T., Thunnissen, A.M.W.H.

Revision History  

• Version 1.0: 2019-08-28
  Type: Initial release
  
• Version 1.1: 2020-09-30
  Changes: Database references
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references