2IL4

Crystal structure of At1g77540-Coenzyme A Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.054 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of Arabidopsis thaliana At1g77540 Protein, a Minimal Acetyltransferase from the COG2388 Family.

Tyler, R.C.Bitto, E.Berndsen, C.E.Bingman, C.A.Singh, S.Lee, M.S.Wesenberg, G.E.Denu, J.M.Phillips, G.N.Markley, J.L.

(2006) Biochemistry 45: 14325-14336

  • DOI: 10.1021/bi0612059
  • Primary Citation of Related Structures:  
  • Also Cited By: 2Q44

  • PubMed Abstract: 
  • We describe X-ray crystal and NMR solution structures of the protein coded for by Arabidopsis thaliana gene At1g77540.1 (At1g77540). The crystal structure was determined to 1.15 A with an R factor of 14.9% (Rfree = 17.0%) by multiple-wavelength anoma ...

    We describe X-ray crystal and NMR solution structures of the protein coded for by Arabidopsis thaliana gene At1g77540.1 (At1g77540). The crystal structure was determined to 1.15 A with an R factor of 14.9% (Rfree = 17.0%) by multiple-wavelength anomalous diffraction using sodium bromide derivatized crystals. The ensemble of NMR conformers was determined with protein samples labeled with 15N and 13C + 15N. The X-ray structure and NMR ensemble were closely similar with rmsd 1.4 A for residues 8-93. At1g77540 was found to adopt a fold similar to that of GCN5-related N-acetyltransferases. Enzymatic activity assays established that At1g77540 possesses weak acetyltransferase activity against histones H3 and H4. Chemical shift perturbations observed in 15N-HSQC spectra upon the addition of CoA indicated that the cofactor binds and identified its binding site. The molecular details of this interaction were further elucidated by solving the X-ray structure of the At1g77540-CoA complex. This work establishes that the domain family COG2388 represents a novel class of acetyltransferase and provides insight into possible mechanistic roles of the conserved Cys76 and His41 residues of this family.


    Organizational Affiliation

    Center for Eukaryotic Structural Genomics, Biochemistry Department, College of Agricultural and Life Sciences, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706-1544, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein At1g77540
A
103Arabidopsis thalianaMutation(s): 0 
EC: 2.3.1.-
Find proteins for Q9CAQ2 (Arabidopsis thaliana)
Go to UniProtKB:  Q9CAQ2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download SDF File 
Download CCD File 
A
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.054 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 27.905α = 90.00
b = 63.941β = 90.86
c = 29.525γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description