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

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.183 

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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

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

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lacto-N-biose phosphorylase
A, B, C, D
759Bifidobacterium longum subsp. longum JCM 1217Mutation(s): 1 
Gene Names: BLLJ_1623lnpA
Find proteins for E8MF13 (Bifidobacterium longum subsp. longum (strain ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194b))
Explore E8MF13 
Go to UniProtKB:  E8MF13
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE8MF13
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • 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 = 68.617α = 105.48
b = 112.996β = 90.88
c = 118.934γ = 106.73
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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