4KVM

The NatA (Naa10p/Naa15p) amino-terminal acetyltransferase complex bound to a bisubstrate analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

Starting Model: experimental
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This is version 2.2 of the entry. See complete history


Literature

Molecular basis for N-terminal acetylation by the heterodimeric NatA complex.

Liszczak, G.Goldberg, J.M.Foyn, H.Petersson, E.J.Arnesen, T.Marmorstein, R.

(2013) Nat Struct Mol Biol 20: 1098-1105

  • DOI: https://doi.org/10.1038/nsmb.2636
  • Primary Citation of Related Structures:  
    4KVM, 4KVO, 4KVX

  • PubMed Abstract: 

    N-terminal acetylation is ubiquitous among eukaryotic proteins and controls a myriad of biological processes. Of the N-terminal acetyltransferases (NATs) that facilitate this cotranslational modification, the heterodimeric NatA complex has the most diversity for substrate selection and modifies the majority of all N-terminally acetylated proteins. Here, we report the X-ray crystal structure of the 100-kDa holo-NatA complex from Schizosaccharomyces pombe, in the absence and presence of a bisubstrate peptide-CoA-conjugate inhibitor, as well as the structure of the uncomplexed Naa10p catalytic subunit. The NatA-Naa15p auxiliary subunit contains 13 tetratricopeptide motifs and adopts a ring-like topology that wraps around the NatA-Naa10p subunit, an interaction that alters the Naa10p active site for substrate-specific acetylation. These studies have implications for understanding the mechanistic details of other NAT complexes and how regulatory subunits modulate the activity of the broader family of protein acetyltransferases.


  • Organizational Affiliation

    1] Program in Gene Expression and Regulation, Wistar Institute, Philadelphia, Pennsylvania, USA. [2] Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-terminal acetyltransferase A complex subunit nat1
A, B, C, D
734Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: nat1SPCC338.07c
UniProt
Find proteins for O74985 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O74985 
Go to UniProtKB:  O74985
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO74985
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
N-terminal acetyltransferase A complex catalytic subunit ard1
E, F, G, H
156Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: ard1SPAC15E1.08
EC: 2.3.1.255
UniProt
Find proteins for Q9UTI3 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9UTI3 
Go to UniProtKB:  Q9UTI3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UTI3
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
bisubstrate analog inhibitor
I, J, K, L
4synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1XE
Query on 1XE

Download Ideal Coordinates CCD File 
AC [auth I],
BC [auth J],
CC [auth K],
DC [auth L]
[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
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth A],
TB [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
AB [auth C]
BA [auth B]
BB [auth C]
CA [auth B]
CB [auth C]
AB [auth C],
BA [auth B],
BB [auth C],
CA [auth B],
CB [auth C],
DA [auth B],
DB [auth C],
EA [auth B],
EB [auth D],
FA [auth B],
FB [auth D],
GA [auth B],
GB [auth D],
HA [auth B],
HB [auth D],
IA [auth B],
IB [auth D],
JA [auth B],
JB [auth D],
KA [auth B],
KB [auth D],
LA [auth B],
LB [auth D],
M [auth A],
MA [auth B],
MB [auth D],
N [auth A],
NA [auth B],
NB [auth D],
O [auth A],
OA [auth B],
OB [auth D],
P [auth A],
PA [auth B],
PB [auth D],
Q [auth A],
QA [auth B],
QB [auth D],
R [auth A],
RA [auth C],
RB [auth D],
S [auth A],
SA [auth C],
SB [auth D],
T [auth A],
TA [auth C],
U [auth A],
UA [auth C],
UB [auth E],
V [auth A],
VA [auth C],
VB [auth E],
W [auth A],
WA [auth C],
WB [auth E],
X [auth A],
XA [auth C],
XB [auth F],
Y [auth A],
YA [auth C],
YB [auth G],
Z [auth A],
ZA [auth C],
ZB [auth H]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.439α = 80.2
b = 119.381β = 76.6
c = 134.063γ = 70.42
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2013-08-28
    Changes: Database references
  • Version 1.2: 2013-10-23
    Changes: Database references
  • Version 2.0: 2021-09-22
    Changes: Advisory, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2023-09-20
    Changes: Data collection, Refinement description
  • Version 2.2: 2024-10-30
    Changes: Structure summary