7ZKT

Moss spermine/spermidine acetyl transferase (PpSSAT) in complex with CoA and lysine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Biochemical and structural basis of polyamine, lysine and ornithine acetylation catalyzed by spermine/spermidine N-acetyl transferase in moss and maize.

Belicek, J.Luptakova, E.Kopecny, D.Frommel, J.Vigouroux, A.Cavar Zeljkovic, S.Jagic, F.Briozzo, P.Kopecny, D.J.Tarkowski, P.Nisler, J.De Diego, N.Morera, S.Kopecna, M.

(2023) Plant J 114: 482-498

  • DOI: https://doi.org/10.1111/tpj.16148
  • Primary Citation of Related Structures:  
    7ZHC, 7ZKT

  • PubMed Abstract: 

    Polyamines such as spermidine and spermine are essential regulators of cell growth, differentiation, maintenance of ion balance and abiotic stress tolerance. Their levels are controlled by the spermidine/spermine N 1 -acetyltransferase (SSAT) via acetylation to promote either their degradation or export outside the cell as shown in mammals. Plant genomes contain at least one gene coding for SSAT (also named NATA for N-AcetylTransferase Activity). Combining kinetics, HPLC-MS and crystallography, we show that three plant SSATs, one from the lower plant moss Physcomitrium patens and two from the higher plant Zea mays, acetylate various aliphatic polyamines and two amino acids lysine (Lys) and ornithine (Orn). Thus, plant SSATs exhibit a broad substrate specificity, unlike more specific human SSATs (hSSATs) as hSSAT1 targets polyamines, whereas hSSAT2 acetylates Lys and thiaLys. The crystal structures of two PpSSAT ternary complexes, one with Lys and CoA, the other with acetyl-CoA and polyethylene glycol (mimicking spermine), reveal a different binding mode for polyamine versus amino acid substrates accompanied by structural rearrangements of both the coenzyme and the enzyme. Two arginine residues, unique among plant SSATs, hold the carboxyl group of amino acid substrates. The most abundant acetylated compound accumulated in moss was N 6 -acetyl-Lys, whereas N 5 -acetyl-Orn, known to be toxic for aphids, was found in maize. Both plant species contain very low levels of acetylated polyamines. The present study provides a detailed biochemical and structural basis of plant SSAT enzymes that can acetylate a wide range of substrates and likely play various roles in planta.


  • Organizational Affiliation

    Department of Experimental Biology, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, CZ-78371, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-acetyltransferase domain-containing protein
A, B, C, D, E
A, B, C, D, E, F, G, H
234Physcomitrium patensMutation(s): 0 
Gene Names: PHYPA_008003
UniProt
Find proteins for A0A2K1KKM6 (Physcomitrium patens)
Explore A0A2K1KKM6 
Go to UniProtKB:  A0A2K1KKM6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2K1KKM6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COA (Subject of Investigation/LOI)
Query on COA

Download Ideal Coordinates CCD File 
AA [auth D]
EA [auth E]
I [auth A]
IA [auth F]
LA [auth G]
AA [auth D],
EA [auth E],
I [auth A],
IA [auth F],
LA [auth G],
QA [auth H],
R [auth B],
U [auth C]
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
LYS (Subject of Investigation/LOI)
Query on LYS

Download Ideal Coordinates CCD File 
GA [auth E]
HA [auth F]
J [auth A]
L [auth A]
NA [auth G]
GA [auth E],
HA [auth F],
J [auth A],
L [auth A],
NA [auth G],
PA [auth H],
W [auth C],
Z [auth D]
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
SO4
Query on SO4

Download Ideal Coordinates CCD File 
N [auth A]
O [auth A]
OA [auth G]
SA [auth H]
T [auth B]
N [auth A],
O [auth A],
OA [auth G],
SA [auth H],
T [auth B],
Y [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
CA [auth D]
KA [auth F]
M [auth A]
P [auth A]
Q [auth A]
CA [auth D],
KA [auth F],
M [auth A],
P [auth A],
Q [auth A],
TA [auth H],
X [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
BA [auth D]
DA [auth D]
FA [auth E]
JA [auth F]
K [auth A]
BA [auth D],
DA [auth D],
FA [auth E],
JA [auth F],
K [auth A],
MA [auth G],
RA [auth H],
S [auth B],
V [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.01α = 90
b = 138.43β = 94.03
c = 129.78γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Centre National de la Recherche Scientifique (CNRS)France--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-22
    Type: Initial release
  • Version 1.1: 2023-05-10
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description