Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.59 kDa 
• Atom Count: 941 
• Modelled Residue Count: 95 
• Deposited Residue Count: 103 
• Unique protein chains: 1

1XMT

X-ray structure of gene product from arabidopsis thaliana at1g77540

• PDB DOI: 10.2210/pdb1XMT/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-10-04 Released: 2004-10-12 
• Deposition Author(s): Wesenberg, G.E., Smith, D.W., Phillips Jr., G.N., Bitto, E., Bingman, C.A., Allard, S.T.M., Center for Eukaryotic Structural Genomics (CESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.170 
• R-Value Work: 0.148 
• R-Value Observed: 0.149 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 2Q44

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 Jr., G.N., Markley, J.L.

(2006) Biochemistry 45: 14325-14336

• PubMed: 17128971 
• DOI: 10.1021/bi0612059
• Primary Citation of Related Structures:  
  1XMT, 2EVN, 2IL4


• 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 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative acetyltransferase	A	103	Arabidopsis thaliana	Mutation(s): 0  Gene Names: At1g77540, T5M16.13 EC: 2.3.1
UniProt
Find proteins for Q9CAQ2 (Arabidopsis thaliana) Explore Q9CAQ2  Go to UniProtKB:  Q9CAQ2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BR	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.170 
• R-Value Work: 0.148 
• R-Value Observed: 0.149 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.349	α = 90
b = 60.601	β = 91.5
c = 29.424	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing
CNS	refinement
REFMAC	refinement
PHENIX	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-10-04 
• Released Date: 2004-10-12 
Deposition Author(s): Wesenberg, G.E., Smith, D.W., Phillips Jr., G.N., Bitto, E., Bingman, C.A., Allard, S.T.M., Center for Eukaryotic Structural Genomics (CESG)

Revision History  

• Version 1.0: 2004-10-12
  Type: Initial release
  
• Version 1.1: 2008-04-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description