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 
  • R-Value Observed: 0.191 

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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:  
    5ICV, 5ICW

  • 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-associated NatA to NatE, NatF/Naa60 specifically associates with Golgi membranes and acetylates transmembrane proteins ...

    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. Electronic address: thomas.arnesen@uib.no.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 60A, B180Homo sapiensMutation(s): 0 
Gene Names: NAA60HAT4NAT15UNQ2771/PRO7155
EC: 2.3.1.48 (PDB Primary Data), 2.3.1.88 (PDB Primary Data), 2.3.1.259 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H7X0 (Homo sapiens)
Explore Q9H7X0 
Go to UniProtKB:  Q9H7X0
PHAROS:  Q9H7X0
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MET-LYS-ALA-VAL-LIGC, D4Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1XE (Subject of Investigation/LOI)
Query on 1XE

Download Ideal Coordinates CCD File 
E [auth C], F [auth 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 
  • R-Value Observed: 0.191 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.448α = 90
b = 48.448β = 90
c = 148.368γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction

Structure Validation

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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  (Full details and data files)

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