4KVM

The NatA (Naa10p/Naa15p) amino-terminal acetyltransferase complex bound to a bisubstrate analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.597 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular basis for N-terminal acetylation by the heterodimeric NatA complex.

Liszczak, G.Goldberg, J.M.Foyn, H.Petersson, E.J.Arnesen, T.Marmorstein, R.

(2013) Nat.Struct.Mol.Biol. 20: 1098-1105

  • DOI: 10.1038/nsmb.2636
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • N-terminal acetylation is ubiquitous among eukaryotic proteins and controls a myriad of biological processes. Of the N-terminal acetyltransferases (NATs) that facilitate this cotranslational modification, the heterodimeric NatA complex has the most d ...

    N-terminal acetylation is ubiquitous among eukaryotic proteins and controls a myriad of biological processes. Of the N-terminal acetyltransferases (NATs) that facilitate this cotranslational modification, the heterodimeric NatA complex has the most diversity for substrate selection and modifies the majority of all N-terminally acetylated proteins. Here, we report the X-ray crystal structure of the 100-kDa holo-NatA complex from Schizosaccharomyces pombe, in the absence and presence of a bisubstrate peptide-CoA-conjugate inhibitor, as well as the structure of the uncomplexed Naa10p catalytic subunit. The NatA-Naa15p auxiliary subunit contains 13 tetratricopeptide motifs and adopts a ring-like topology that wraps around the NatA-Naa10p subunit, an interaction that alters the Naa10p active site for substrate-specific acetylation. These studies have implications for understanding the mechanistic details of other NAT complexes and how regulatory subunits modulate the activity of the broader family of protein acetyltransferases.


    Organizational Affiliation

    1] Program in Gene Expression and Regulation, Wistar Institute, Philadelphia, Pennsylvania, USA. [2] Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-terminal acetyltransferase A complex subunit nat1
A, B, C, D
734Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: nat1
Find proteins for O74985 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O74985
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
N-terminal acetyltransferase A complex catalytic subunit ard1
E, F, G, H
156Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: ard1
EC: 2.3.1.255
Find proteins for Q9UTI3 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9UTI3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
bisubstrate analog inhibitor
I, J, K, L
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1XE
Query on 1XE

Download SDF File 
Download CCD File 
I, J, K, L
[5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)furan-2-yl]methyl (3R)-4-{[3-({(E)-2-[(2,2-dihydroxyethyl)sulfanyl]ethenyl}amino)-3-oxopropyl]amino}-3-hydroxy-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate
C23 H34 N7 O18 P3 S
IWZWXZGRAJOFTE-QWNKOJSDSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B, C, D, E, F, G, H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LIG
Query on LIG
I, J, K, L
NON-POLYMERC15 H11 N3

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.597 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.222 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 81.439α = 80.20
b = 119.381β = 76.60
c = 134.063γ = 70.42
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXrefinement
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2013-08-28
    Type: Database references
  • Version 1.2: 2013-10-23
    Type: Database references