1V7V

Crystal structure of Vibrio proteolyticus chitobiose phosphorylase

• PDB DOI:  https://doi.org/10.2210/pdb1V7V/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio proteolyticus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-12-24 Released: 2004-06-22 
• Deposition Author(s): Hidaka, M., Honda, Y., Nirasawa, S., Kitaoka, M., Hayashi, K., Wakagi, T., Shoun, H., Fushinobu, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.186 
• R-Value Work: 0.162 
• R-Value Observed: 0.162 

Literature

Chitobiose phosphorylase from Vibrio proteolyticus, a member of glycosyl transferase family 36, has a clan GH-L-like (alpha/alpha)(6) barrel fold.

Hidaka, M., Honda, Y., Kitaoka, M., Nirasawa, S., Hayashi, K., Wakagi, T., Shoun, H., Fushinobu, S.

(2004) Structure 12: 937-947

• PubMed: 15274915 
• DOI: https://doi.org/10.1016/j.str.2004.03.027
• Primary Citation of Related Structures:  
  1V7V, 1V7W, 1V7X


• PubMed Abstract: 
  

Vibrio proteolyticus chitobiose phosphorylase (ChBP) belongs to glycosyl transferase family 36 (GT-36), and catalyzes the reversible phosphorolysis of chitobiose into alpha-GlcNAc-1-phosphate and GlcNAc with inversion of the anomeric configuration. As the first known structures of a GT-36 enzyme, we determined the crystal structure of ChBP in a ternary complex with GlcNAc and SO(4). It is also the first structures of an inverting phosphorolytic enzyme in a complex with a sugar and a sulfate ion, and reveals a pseudo-ternary complex structure of enzyme-sugar-phosphate. ChBP comprises a beta sandwich domain and an (alpha/alpha)(6) barrel domain, constituting a distinctive structure among GT families. Instead, it shows significant structural similarity with glycoside hydrolase (GH) enzymes, glucoamylases (GH-15), and maltose phosphorylase (GH-65) in clan GH-L. The structural similarity reported here, together with distant sequence similarities between ChBP and GHs, led to the reclassification of family GT-36 into a novel GH family, namely GH-94.

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Related Citations: 

• Reaction mechanism of chitobiose phosphorylase from Vibrio proteolyticus: identification of family 36 glycosyltransferase in Vibrio
  Honda, Y., Kitaoka, M., Hayashi, K.
  (2004) Biochem J 377: 225

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Organizational Affiliation: 

Department of Biotechnology, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 91.41 kDa 
• Atom Count: 6,901 
• Modelled Residue Count: 779 
• Deposited Residue Count: 807 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
chitobiose phosphorylase	A	807	Vibrio proteolyticus	Mutation(s): 0  Gene Names: chbP EC: 2.4.1 (PDB Primary Data), 2.4.1.280 (UniProt)
UniProt
Find proteins for Q76IQ9 (Vibrio proteolyticus) Explore Q76IQ9  Go to UniProtKB:  Q76IQ9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.186 
• R-Value Work: 0.162 
• R-Value Observed: 0.162 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.946	α = 90
b = 70.58	β = 98.4
c = 80.045	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-06-22 
Deposition Author(s): Hidaka, M., Honda, Y., Nirasawa, S., Kitaoka, M., Hayashi, K., Wakagi, T., Shoun, H., Fushinobu, S.

Revision History  

• Version 1.0: 2004-06-22
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance