4UA3

Crystal structure of selenomethionine labeled SpNatD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Molecular Basis for Histone H4- and H2A-Specific Amino-Terminal Acetylation by NatD.

Magin, R.S.Liszczak, G.P.Marmorstein, R.

(2015) Structure 23: 332-341

  • DOI: 10.1016/j.str.2014.10.025
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • N-terminal acetylation is among the most common protein modifications in eukaryotes and is mediated by evolutionarily conserved N-terminal acetyltransferases (NATs). NatD is among the most selective NATs; its only known substrates are histones H4 and ...

    N-terminal acetylation is among the most common protein modifications in eukaryotes and is mediated by evolutionarily conserved N-terminal acetyltransferases (NATs). NatD is among the most selective NATs; its only known substrates are histones H4 and H2A, containing the N-terminal sequence SGRGK in humans. Here we characterize the molecular basis for substrate-specific acetylation by NatD by reporting its crystal structure bound to cognate substrates and performing related biochemical studies. A novel N-terminal segment wraps around the catalytic core domain to make stabilizing interactions, and the α1-α2 and β6-β7 loops adopt novel conformations to properly orient the histone N termini in the binding site. Ser1 and Arg3 of the histone make extensive contacts to highly conserved NatD residues in the substrate binding pocket, and flanking glycine residues also appear to contribute to substrate-specific binding by NatD, together defining a Ser-Gly-Arg-Gly recognition sequence. These studies have implications for understanding substrate-specific acetylation by NAT enzymes.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized N-acetyltransferase C825.04c
A, B
194Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: naa40
EC: 2.3.1.257
Find proteins for Q9USH6 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9USH6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
COA
Query on COA

Download SDF File 
Download CCD File 
A, B
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
ACE
Query on ACE
A, B
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.179 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 114.701α = 90.00
b = 42.629β = 98.68
c = 85.417γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-3000data scaling
HKL-3000data collection

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 Sciences (NIH/NIGMS)United StatesGM060293

Revision History 

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2015-02-11
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.3: 2019-12-04
    Type: Author supporting evidence