4TVW

Resorufin ligase with bound resorufin-AMP analog

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

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Literature

Computational design of a red fluorophore ligase for site-specific protein labeling in living cells.

Liu, D.S., Nivon, L.G., Richter, F., Goldman, P.J., Deerinck, T.J., Yao, J.Z., Richardson, D., Phipps, W.S., Ye, A.Z., Ellisman, M.H., Drennan, C.L., Baker, D., Ting, A.Y.

(2014) Proc Natl Acad Sci U S A 111: E4551-E4559

  • DOI: 10.1073/pnas.1404736111
  • Primary Citation of Related Structures:  
    4TVW, 4TVY

  • PubMed Abstract: 

    • Chemical fluorophores offer tremendous size and photophysical advantages over fluorescent proteins but are much more challenging to target to specific cellular proteins. Here, we used Rosetta-based computation to design a fluorophore ligase that accepts the red dye resorufin, starting from Escherichia coli lipoic acid ligase ...

    Chemical fluorophores offer tremendous size and photophysical advantages over fluorescent proteins but are much more challenging to target to specific cellular proteins. Here, we used Rosetta-based computation to design a fluorophore ligase that accepts the red dye resorufin, starting from Escherichia coli lipoic acid ligase. X-ray crystallography showed that the design closely matched the experimental structure. Resorufin ligase catalyzed the site-specific and covalent attachment of resorufin to various cellular proteins genetically fused to a 13-aa recognition peptide in multiple mammalian cell lines and in primary cultured neurons. We used resorufin ligase to perform superresolution imaging of the intermediate filament protein vimentin by stimulated emission depletion and electron microscopies. This work illustrates the power of Rosetta for major redesign of enzyme specificity and introduces a tool for minimally invasive, highly specific imaging of cellular proteins by both conventional and superresolution microscopies.

    Organizational Affiliation: 

    Departments of Chemistry and ating@mit.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lipoate-protein ligase AA, B, C, D341Escherichia coliMutation(s): 3 
Gene Names: lplA
EC: 2.7.7.63 (PDB Primary Data), 6.3.1.20 (UniProt)
UniProt
Find proteins for P32099 (Escherichia coli (strain K12))
Explore P32099 
Go to UniProtKB:  P32099
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32099
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
37P
Query on 37P
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C],
H [auth D]		5'-O-{[5-(7-hydroxy-3-oxo-3H-phenoxazin-2-yl)pentanoyl]sulfamoyl}adenosine
C27 H27 N7 O10 S
INHRVYHMUNZSSB-PKDYZCKRSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.354α = 90
b = 99.932β = 105.79
c = 107.284γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-22
    Type: Initial release
  • Version 1.1: 2014-11-05
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
  • Version 1.3: 2019-11-20
    Changes: Author supporting evidence