5HGZ

Crystal structure of human Naa60 in complex with acetyl-CoA

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): 

  • Deposited: 2016-01-09 Released: 2016-09-14 
  • Deposition Author(s): Chen, J.Y., Liu, L., Yun, C.H.
  • Funding Organization(s): National Basic Research Program of China; National Science Foundation of China; Ministry of Science and Technology of China 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.383 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure and function of human Naa60 (NatF), a Golgi-localized bi-functional acetyltransferase

Chen, J.Y.Liu, L.Cao, C.L.Li, M.J.Tan, K.Yang, X.Yun, C.H.

(2016) Sci Rep 6: 31425-31425

  • DOI: 10.1038/srep31425
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • N-terminal acetylation (Nt-acetylation), carried out by N-terminal acetyltransferases (NATs), is a conserved and primary modification of nascent peptide chains. Naa60 (also named NatF) is a recently identified NAT found only in multicellular eukaryot ...

    N-terminal acetylation (Nt-acetylation), carried out by N-terminal acetyltransferases (NATs), is a conserved and primary modification of nascent peptide chains. Naa60 (also named NatF) is a recently identified NAT found only in multicellular eukaryotes. This protein was shown to locate on the Golgi apparatus and mainly catalyze the Nt-acetylation of transmembrane proteins, and it also harbors lysine N(ε)-acetyltransferase (KAT) activity to catalyze the acetylation of lysine ε-amine. Here, we report the crystal structures of human Naa60 (hNaa60) in complex with Acetyl-Coenzyme A (Ac-CoA) or Coenzyme A (CoA). The hNaa60 protein contains an amphipathic helix following its GNAT domain that may contribute to Golgi localization of hNaa60, and the β7-β8 hairpin adopted different conformations in the hNaa60(1-242) and hNaa60(1-199) crystal structures. Remarkably, we found that the side-chain of Phe 34 can influence the position of the coenzyme, indicating a new regulatory mechanism involving enzyme, co-factor and substrates interactions. Moreover, structural comparison and biochemical studies indicated that Tyr 97 and His 138 are key residues for catalytic reaction and that a non-conserved β3-β4 long loop participates in the regulation of hNaa60 activity.


    Organizational Affiliation

    Institute of Systems Biomedicine and Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, P. R. China.,Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China.,Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, P. R. China.,Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-alpha-acetyltransferase 60
A
243Homo sapiensMutation(s): 3 
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
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACO
Query on ACO

Download SDF File 
Download CCD File 
A
ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
 Ligand Interaction
MLA
Query on MLA

Download SDF File 
Download CCD File 
A
MALONIC ACID
DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; METHANEDICARBOXYLIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.383 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.287α = 90.00
b = 57.365β = 90.00
c = 68.818γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data processing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Basic Research Program of ChinaChina2012CB917202
National Science Foundation of ChinaChina31270769
Ministry of Science and Technology of ChinaChinaNCET-12-0013

Revision History 

  • Version 1.0: 2016-09-14
    Type: Initial release