3WFZ

Crystal structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase C236Y Mutant

• PDB DOI: https://doi.org/10.2210/pdb3WFZ/pdb

• Classification: TRANSFERASE
• Organism(s): Bifidobacterium longum subsp. longum JCM 1217
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-07-25 Released: 2013-10-09 
• Deposition Author(s): Koyama, Y., Hidaka, M., Kawakami, M., Nishimoto, M., Kitaoka, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.249 
• R-Value Work: 0.179 
• R-Value Observed: 0.183 

Starting Model: experimental

Literature

Directed evolution to enhance thermostability of galacto-N-biose/lacto-N-biose I phosphorylase.

Koyama, Y., Hidaka, M., Nishimoto, M., Kitaoka, M.

(2013) Protein Eng Des Sel 26: 755-761

• PubMed: 24065834 
• DOI: https://doi.org/10.1093/protein/gzt049
• Primary Citation of Related Structures:  
  3WFZ


• PubMed Abstract: 
  

  Galacto-N-biose/lacto-N-biose I phosphorylase (GLNBP) is the key enzyme in the enzymatic production of lacto-N-biose I. For the purpose of industrial use, we improved the thermostability of GLNBP by evolutionary engineering in which five substitutions in the amino acid sequence were selected from a random mutagenesis GLNBP library constructed using error-prone polymerase chain reaction. Among them, C236Y and D576V mutants showed considerably improved thermostability. Structural analysis of C236Y revealed that the hydroxyl group of Tyr236 forms a hydrogen bond with the carboxyl group of E319. The C236Y and D576V mutations together contributed to the thermostability. The C236Y/D576V mutant exhibited 20°C higher thermostability than the wild type.

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Organizational Affiliation: 

National Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 343.06 kDa 
• Atom Count: 24,550 
• Modelled Residue Count: 2,961 
• Deposited Residue Count: 3,036 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lacto-N-biose phosphorylase	A, B, C, D	759	Bifidobacterium longum subsp. longum JCM 1217	Mutation(s): 1  Gene Names: BLLJ_1623, lnpA EC: 2.4.1.211
UniProt
Find proteins for E8MF13 (Bifidobacterium longum subsp. longum (strain ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194b)) Explore E8MF13  Go to UniProtKB:  E8MF13

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDG	E [auth A], F [auth B], G [auth C], H [auth D]	2-acetamido-2-deoxy-alpha-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.249 
• R-Value Work: 0.179 
• R-Value Observed: 0.183 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.617	α = 105.48
b = 112.996	β = 90.88
c = 118.934	γ = 106.73

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-09 
Deposition Author(s): Koyama, Y., Hidaka, M., Kawakami, M., Nishimoto, M., Kitaoka, M.

Revision History  

• Version 1.0: 2013-10-09
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2022-08-24
  Changes: Database references, Structure summary
• Version 2.2: 2023-11-08
  Changes: Data collection, Refinement description