4KVX

Crystal structure of Naa10 (Ard1) bound to AcCoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

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This is version 1.4 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: https://doi.org/10.1038/nsmb.2636
  • Primary Citation of Related Structures:  
    4KVM, 4KVO, 4KVX

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-terminal acetyltransferase A complex catalytic subunit ard1
A, B
156Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: ard1SPAC15E1.08
EC: 2.3.1.88
UniProt
Find proteins for Q9UTI3 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9UTI3 
Go to UniProtKB:  Q9UTI3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UTI3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.974α = 90
b = 64.833β = 97.55
c = 60.723γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2013-08-28
    Changes: Database references
  • Version 1.2: 2013-10-09
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-12-06
    Changes: Data collection