6YGA

Crystal structure of the apo NatC complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

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Literature

Divergent architecture of the heterotrimeric NatC complex explains N-terminal acetylation of cognate substrates.

Grunwald, S.Hopf, L.V.M.Bock-Bierbaum, T.Lally, C.C.M.Spahn, C.M.T.Daumke, O.

(2020) Nat Commun 11: 5506-5506

  • DOI: 10.1038/s41467-020-19321-8
  • Primary Citation of Related Structures:  
    6YGA, 6YGC, 6YGB, 6YGD

  • PubMed Abstract: 
  • The heterotrimeric NatC complex, comprising the catalytic Naa30 and the two auxiliary subunits Naa35 and Naa38, co-translationally acetylates the N-termini of numerous eukaryotic target proteins. Despite its unique subunit composition, its essential role for many aspects of cellular function and its suggested involvement in disease, structure and mechanism of NatC have remained unknown ...

    The heterotrimeric NatC complex, comprising the catalytic Naa30 and the two auxiliary subunits Naa35 and Naa38, co-translationally acetylates the N-termini of numerous eukaryotic target proteins. Despite its unique subunit composition, its essential role for many aspects of cellular function and its suggested involvement in disease, structure and mechanism of NatC have remained unknown. Here, we present the crystal structure of the Saccharomyces cerevisiae NatC complex, which exhibits a strikingly different architecture compared to previously described N-terminal acetyltransferase (NAT) complexes. Cofactor and ligand-bound structures reveal how the first four amino acids of cognate substrates are recognized at the Naa30-Naa35 interface. A sequence-specific, ligand-induced conformational change in Naa30 enables efficient acetylation. Based on detailed structure-function studies, we suggest a catalytic mechanism and identify a ribosome-binding patch in an elongated tip region of NatC. Our study reveals how NAT machineries have divergently evolved to N-terminally acetylate specific subsets of target proteins.


    Organizational Affiliation

    Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany. oliver.daumke@mdc-berlin.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 30 A159Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MAK3NAA30YPR051WYP9499.08
EC: 2.3.1.256
Find proteins for Q03503 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03503 
Go to UniProtKB:  Q03503
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 35, NatC auxiliary subunit B735Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MAK10NAA35YEL053C
Find proteins for Q02197 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02197 
Go to UniProtKB:  Q02197
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 38, NatC auxiliary subunit C77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MAK31NAA38YCR020C-AYCR20C-A
Find proteins for P23059 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P23059 
Go to UniProtKB:  P23059
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download Ideal Coordinates CCD File 
A, B, C
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.124α = 90
b = 140.421β = 90
c = 166.409γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL2Mapphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB958-A12

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-28
    Type: Initial release
  • Version 1.1: 2020-11-18
    Changes: Database references