4KLV

Crystal structure of a GNAT superfamily acetyltransferase PA4794 in complex with 4-methylumbelliferyl phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.122 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 30223-30235

  • DOI: 10.1074/jbc.M113.501353
  • Primary Citation of Related Structures:  3PGP, 4KLW, 4KOR, 4KOS, 4KOT, 4KOU, 4KOV, 4KOW, 4KOX, 4KOY, 4KUA, 4KUB, 4L89, 4L8A
  • Also Cited By: 5VDB

  • PubMed Abstract: 
  • The Gcn5-related N-acetyltransferase (GNAT) superfamily is a large group of evolutionarily related acetyltransferases, with multiple paralogs in organisms from all kingdoms of life. The functionally characterized GNATs have been shown to catalyze the ...

    The Gcn5-related N-acetyltransferase (GNAT) superfamily is a large group of evolutionarily related acetyltransferases, with multiple paralogs in organisms from all kingdoms of life. The functionally characterized GNATs have been shown to catalyze the transfer of an acetyl group from acetyl-coenzyme A (Ac-CoA) to the amine of a wide range of substrates, including small molecules and proteins. GNATs are prevalent and implicated in a myriad of aspects of eukaryotic and prokaryotic physiology, but functions of many GNATs remain unknown. In this work, we used a multi-pronged approach of x-ray crystallography and biochemical characterization to elucidate the sequence-structure-function relationship of the GNAT superfamily member PA4794 from Pseudomonas aeruginosa. We determined that PA4794 acetylates the Nε amine of a C-terminal lysine residue of a peptide, suggesting it is a protein acetyltransferase specific for a C-terminal lysine of a substrate protein or proteins. Furthermore, we identified a number of molecules, including cephalosporin antibiotics, which are inhibitors of PA4794 and bind in its substrate-binding site. Often, these molecules mimic the conformation of the acetylated peptide product. We have determined structures of PA4794 in the apo-form, in complexes with Ac-CoA, CoA, several antibiotics and other small molecules, and a ternary complex with the products of the reaction: CoA and acetylated peptide. Also, we analyzed PA4794 mutants to identify residues important for substrate binding and catalysis.


    Organizational Affiliation

    From the Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
A
162Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)N/A
Find proteins for Q9HV14 (Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228))
Go to UniProtKB:  Q9HV14
Small Molecules
Ligands 3 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
KLV
Query on KLV

Download SDF File 
Download CCD File 
A
4-methylumbelliferyl phosphate
4-methyl-2-oxo-2H-chromen-7-yl dihydrogen phosphate
C10 H9 O6 P
BCHIXGBGRHLSBE-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KLVKd: 165000 nM BINDINGMOAD
KLVKd: 165300 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.122 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.340α = 90.00
b = 76.486β = 90.00
c = 39.336γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000data scaling
HKL-3000phasing
REFMACrefinement
Cootmodel building
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2013-09-18
    Type: Database references
  • Version 1.2: 2013-11-13
    Type: Database references