Crystal structure of a MurB family EP-UDP-N-acetylglucosamine reductase

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 

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This is version 1.3 of the entry. See complete history


LucY: A Versatile New Fluorescent Reporter Protein.

Auldridge, M.E.Cao, H.Sen, S.Franz, L.P.Bingman, C.A.Yennamalli, R.M.Phillips, G.N.Mead, D.Steinmetz, E.J.

(2015) PLoS One 10: e0124272-e0124272

  • DOI: https://doi.org/10.1371/journal.pone.0124272
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    We report on the discovery, isolation, and use of a novel yellow fluorescent protein. Lucigen Yellow (LucY) binds one FAD molecule within its core, thus shielding it from water and maintaining its structure so that fluorescence is 10-fold higher than freely soluble FAD. LucY displays excitation and emission spectra characteristic of FAD, with 3 excitation peaks at 276 nm, 377 nm, and 460 nm and a single emission peak at 530 nm. These excitation and emission maxima provide the large Stokes shift beneficial to fluorescence experimentation. LucY belongs to the MurB family of UDP-N-acetylenolpyruvylglucosamine reductases. The high resolution crystal structure shows that in contrast to other structurally resolved MurB enzymes, LucY does not contain a potentially quenching aromatic residue near the FAD isoalloxazine ring, which may explain its increased fluorescence over related proteins. Using E. coli as a system in which to develop LucY as a reporter, we show that it is amenable to circular permutation and use as a reporter of protein-protein interaction. Fragmentation between its distinct domains renders LucY non-fluorescent, but fluorescence can be partially restored by fusion of the fragments to interacting protein domains. Thus, LucY may find application in Protein-fragment Complementation Assays for evaluating protein-protein interactions.

  • Organizational Affiliation

    Lucigen Corp., Middleton, WI, United States of America.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-N-acetylenolpyruvoylglucosamine reductase309unidentifiedMutation(s): 0 
Find proteins for Q65JX9 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46))
Explore Q65JX9 
Go to UniProtKB:  Q65JX9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ65JX9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.786α = 90
b = 106.786β = 90
c = 201.085γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MD2data collection
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 1.1: 2015-08-12
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2023-03-22
    Changes: Database references, Derived calculations, Structure summary