5ICV

Crystal structure of human NatF (hNaa60) bound to a bisubstrate analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of the Golgi-Associated Human N alpha-Acetyltransferase 60 Reveals the Molecular Determinants for Substrate-Specific Acetylation.

Stve, S.I.Magin, R.S.Foyn, H.Haug, B.E.Marmorstein, R.Arnesen, T.

(2016) Structure 24: 1044-1056

  • DOI: 10.1016/j.str.2016.04.020
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • N-Terminal acetylation is a common and important protein modification catalyzed by N-terminal acetyltransferases (NATs). Six human NATs (NatA-NatF) contain one catalytic subunit each, Naa10 to Naa60, respectively. In contrast to the ribosome-associat ...

    N-Terminal acetylation is a common and important protein modification catalyzed by N-terminal acetyltransferases (NATs). Six human NATs (NatA-NatF) contain one catalytic subunit each, Naa10 to Naa60, respectively. In contrast to the ribosome-associated NatA to NatE, NatF/Naa60 specifically associates with Golgi membranes and acetylates transmembrane proteins. To gain insight into the molecular basis for the function of Naa60, we developed an Naa60 bisubstrate CoA-peptide conjugate inhibitor, determined its X-ray structure when bound to CoA and inhibitor, and carried out biochemical experiments. We show that Naa60 adapts an overall fold similar to that of the catalytic subunits of ribosome-associated NATs, but with the addition of two novel elongated loops that play important roles in substrate-specific binding. One of these loops mediates a dimer to monomer transition upon substrate-specific binding. Naa60 employs a catalytic mechanism most similar to Naa50. Collectively, these data reveal the molecular basis for Naa60-specific acetyltransferase activity with implications for its Golgi-specific functions.


    Organizational Affiliation

    Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, 5021 Bergen, Norway.,Department of Chemistry, University of Bergen, 5020 Bergen, Norway.,Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway.,Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Program in Gene Expression and Regulation, Wistar Institute, Philadelphia, PA 19104, USA.,Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, 5021 Bergen, Norway. Electronic address: thomas.arnesen@uib.no.,Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Program in Gene Expression and Regulation, Wistar Institute, Philadelphia, PA 19104, USA. Electronic address: marmor@mail.med.upenn.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-alpha-acetyltransferase 60
A, B
180Homo sapiensMutation(s): 0 
Gene Names: NAA60 (HAT4, NAT15)
EC: 2.3.1.259
Find proteins for Q9H7X0 (Homo sapiens)
Go to Gene View: NAA60
Go to UniProtKB:  Q9H7X0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MET-LYS-ALA-VAL-LIG
C, D
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1XE
Query on 1XE

Download SDF File 
Download CCD File 
C, D
[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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.191 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 48.448α = 90.00
b = 48.448β = 90.00
c = 148.368γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Norwegian Cancer SocietyNorway--
The Bergen Research Foundation BFSNorway--
Research Council of NorwayNorway--
National Institutes of HealthUnited StatesGM060293
National Institutes of HealthUnited StatesGM071339

Revision History 

  • Version 1.0: 2016-06-22
    Type: Initial release
  • Version 1.1: 2016-07-06
    Type: Database references
  • Version 1.2: 2016-07-20
    Type: Database references