4TVY | pdb_00004tvy

Apo resorufin ligase

• PDB DOI: https://doi.org/10.2210/pdb4TVY/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-06-28 Released: 2014-10-22 
• Deposition Author(s): Goldman, P.J., Drennan, C.L.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.262 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

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

• PubMed: 25313043 
• DOI: https://doi.org/10.1073/pnas.1404736111
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Departments of Chemistry and.
Department of Biochemistry.
Department of Biochemistry, Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA 98195;
National Center for Microscopy and Imaging Research, Center for Research on Biological Systems and.
Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
National Center for Microscopy and Imaging Research, Center for Research on Biological Systems and Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093; and.
Departments of Chemistry and Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139;
Department of Biochemistry, Howard Hughes Medical Institute, and.
Departments of Chemistry and [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 77.34 kDa 
• Atom Count: 5,379 
• Modeled Residue Count: 650 
• Deposited Residue Count: 682 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoate-protein ligase A	A, B	341	Escherichia coli K-12	Mutation(s): 3  Gene Names: lplA, yjjF, b4386, JW4349 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
37R	C [auth A], D [auth A], E [auth B], F [auth B]	5-(3,7-dihydroxy-10H-phenoxazin-2-yl)pentanamide C17 H18 N2 O4 NQCQIFYOQVPSOG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.262 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.117	α = 90
b = 89.951	β = 90
c = 108.89	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-10-22 
Deposition Author(s): Goldman, P.J., Drennan, C.L.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• 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, Refinement description, Source and taxonomy
• Version 1.3: 2017-11-22
  Changes: Refinement description
• Version 1.4: 2019-11-20
  Changes: Author supporting evidence
• Version 1.5: 2023-09-27
  Changes: Data collection, Database references, Refinement description