5VDB

Crystal structure of a GNAT superfamily acetyltransferase PA4794 in complex with bisubstrate analog 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.145 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Generating enzyme and radical-mediated bisubstrates as tools for investigating Gcn5-related N-acetyltransferases.

Reidl, C.Majorek, K.A.Dang, J.Tran, D.Jew, K.Law, M.Payne, Y.Minor, W.Becker, D.P.Kuhn, M.L.

(2017) FEBS Lett. 591: 2348-2361

  • DOI: 10.1002/1873-3468.12753
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Gcn5-related N-acetyltransferases (GNATs) are found in all kingdoms of life and catalyze important acyl transfer reactions in diverse cellular processes. While many 3D structures of GNATs have been determined, most do not contain acceptor substrates ...

    Gcn5-related N-acetyltransferases (GNATs) are found in all kingdoms of life and catalyze important acyl transfer reactions in diverse cellular processes. While many 3D structures of GNATs have been determined, most do not contain acceptor substrates in their active sites. To expand upon existing crystallographic strategies for improving acceptor-bound GNAT structures, we synthesized peptide substrate analogs and reacted them with CoA in PA4794 protein crystals. We found two separate mechanisms for bisubstrate formation: (a) a novel X-ray induced radical-mediated alkylation of CoA with an alkene peptide and (b) direct alkylation of CoA with a halogenated peptide. Our approach is widely applicable across the GNAT superfamily and can be used to improve the success rate of obtaining liganded structures of other acyltransferases.


    Related Citations: 
    • Structural, functional, and inhibition studies of a Gcn5-related N-acetyltransferase (GNAT) superfamily protein PA4794: a new C-terminal lysine protein acetyltransferase from pseudomonas aeruginosa.
      Majorek, K.A.,Kuhn, M.L.,Chruszcz, M.,Anderson, W.F.,Minor, W.
      (2013) J. Biol. Chem. 288: 30223


    Organizational Affiliation

    Department of Chemistry and Biochemistry, San Francisco State University, CA, USA.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.,Department of Chemistry, Loyola University Chicago, IL, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
acetyltransferase PA4794
A
161Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Find proteins for Q9HV14 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9HV14
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
93M
Query on 93M

Download SDF File 
Download CCD File 
A
(3R,5S,9R,26S)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-10,14,20-trioxo-26-({[(phenylacetyl)amino]acetyl}amino)-2,4,6-trioxa-18-thia-11,15,21-triaza-3,5-diphosphaheptacosan-27-oic acid 3,5-dioxide (non-preferred name)
C39 H59 N10 O21 P3 S
UWVFJLUZBIMSSQ-RYFVFCQRSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.145 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.335α = 90.00
b = 76.121β = 90.00
c = 39.149γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PDB_EXTRACTdata extraction
HKL-3000data scaling
HKL-2000data scaling
HKL-3000phasing
SCALEPACKdata scaling
HKL-3000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesU54 GM094585

Revision History 

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-08-23
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description