5K18

The NatB Acetyltransferase Complex Bound To bisubstrate inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

Molecular Basis of Substrate Specific Acetylation by N-Terminal Acetyltransferase NatB

Hong, H.Cai, Y.Zhang, S.Ding, H.Wang, H.Han, A.

(2017) Structure 25: 641-649.e3

  • DOI: https://doi.org/10.1016/j.str.2017.03.003
  • Primary Citation of Related Structures:  
    5K04, 5K18

  • PubMed Abstract: 

    The NatB N-terminal acetyltransferase specifically acetylates the N-terminal group of substrate protein peptides starting with Met-Asp/Glu/Asn/Gln. How NatB recognizes and acetylates these substrates remains unknown. Here, we report crystal structures of a NatB holoenzyme from Candida albicans in the presence of its co-factor CoA and substrate peptides. The auxiliary subunit Naa25 of NatB forms a horseshoe-like deck to hold specifically its catalytic subunit Naa20. The first two amino acids Met and Asp of a substrate peptide mediate the major interactions with the active site in the Naa20 subunit. The hydrogen bonds between the substrate Asp and pocket residues of Naa20 are essential to determine the NatB substrate specificity. Moreover, a hydrogen bond between the amino group of the substrate Met and a carbonyl group in the Naa20 active site directly anchors the substrate toward acetyl-CoA. Together, these structures define a unique molecular mechanism of specific N-terminal acetylation acted by NatB.


  • Organizational Affiliation

    State Key Laboratory for Cellular Stress Biology, Department of Biomedical Sciences, School of Life Sciences, Xiamen University, Xiang'an, Xiamen 361102, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein
A, C
766Candida albicans WO-1Mutation(s): 0 
Gene Names: CAWG_01335
UniProt
Find proteins for C4YFL7 (Candida albicans (strain WO-1))
Explore C4YFL7 
Go to UniProtKB:  C4YFL7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4YFL7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
N-terminal acetyltransferase B complex subunit NAT3
B, D
188Candida albicans WO-1Mutation(s): 0 
Gene Names: CAWG_00748
UniProt
Find proteins for C4YDZ9 (Candida albicans (strain WO-1))
Explore C4YDZ9 
Go to UniProtKB:  C4YDZ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4YDZ9
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Bisubstrate inhibitorE [auth F],
F [auth E]
12synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.054α = 70.12
b = 91.087β = 88.91
c = 101.74γ = 84.05
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-19
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Advisory, Derived calculations
  • Version 2.0: 2023-04-05
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2023-11-29
    Changes: Data collection, Refinement description