5NNR

Structure of Naa15/Naa10 bound to HypK-THB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of HypK regulating N-terminal acetylation by the NatA complex.

Weyer, F.A.Gumiero, A.Lapouge, K.Bange, G.Kopp, J.Sinning, I.

(2017) Nat Commun 8: 15726-15726

  • DOI: https://doi.org/10.1038/ncomms15726
  • Primary Citation of Related Structures:  
    5NNP, 5NNR

  • PubMed Abstract: 

    In eukaryotes, N-terminal acetylation is one of the most common protein modifications involved in a wide range of biological processes. Most N-acetyltransferase complexes (NATs) act co-translationally, with the heterodimeric NatA complex modifying the majority of substrate proteins. Here we show that the Huntingtin yeast two-hybrid protein K (HypK) binds tightly to the NatA complex comprising the auxiliary subunit Naa15 and the catalytic subunit Naa10. The crystal structures of NatA bound to HypK or to a N-terminal deletion variant of HypK were determined without or with a bi-substrate analogue, respectively. The HypK C-terminal region is responsible for high-affinity interaction with the C-terminal part of Naa15. In combination with acetylation assays, the HypK N-terminal region is identified as a negative regulator of the NatA acetylation activity. Our study provides mechanistic insights into the regulation of this pivotal protein modification.


  • Organizational Affiliation

    Heidelberg University Biochemistry Center (BZH), INF328, D-69120 Heidelberg, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-terminal acetyltransferase-like protein
A, D
751Thermochaetoides thermophilaMutation(s): 0 
Gene Names: CTHT_0031530
UniProt
Find proteins for G0S4M4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S4M4 
Go to UniProtKB:  G0S4M4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S4M4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Naa10
B, E
195Thermochaetoides thermophilaMutation(s): 0 
Gene Names: CTHT_0063490
UniProt
Find proteins for G0SEE8 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SEE8 
Go to UniProtKB:  G0SEE8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0SEE8
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HypK
C, F
133Thermochaetoides thermophilaMutation(s): 0 
Gene Names: CTHT_0058830
UniProt
Find proteins for G0SCY6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SCY6 
Go to UniProtKB:  G0SCY6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0SCY6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
B, E
L-PEPTIDE LINKINGC6 H11 N O3 SMET
MSE
Query on MSE
C, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.348α = 90
b = 85.348β = 90
c = 319.626γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyGRK1188
German Research FoundationGermanyLeibniz Program
German Research FoundationGermanyFOR967

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Author supporting evidence, Data collection, Database references, Refinement description