7K0A | pdb_00007k0a

Puromycin N-acetyltransferase in complex with acetylated puromycin and CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.240 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.207 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7K0A

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Structure-guided selection of puromycin N-acetyltransferase mutants with enhanced selection stringency for deriving mammalian cell lines expressing recombinant proteins.

Caputo, A.T.Eder, O.M.Bereznakova, H.Pothuis, H.Ardevol, A.Newman, J.Nuttall, S.Peat, T.S.Adams, T.E.

(2021) Sci Rep 11: 5247-5247

  • DOI: https://doi.org/10.1038/s41598-021-84551-9
  • Primary Citation Related Structures: 
    7K09, 7K0A

  • PubMed Abstract: 

    Puromycin and the Streptomyces alboniger-derived puromycin N-acetyltransferase (PAC) enzyme form a commonly used system for selecting stably transfected cultured cells. The crystal structure of PAC has been solved using X-ray crystallography, revealing it to be a member of the GCN5-related N-acetyltransferase (GNAT) family of acetyltransferases. Based on structures in complex with acetyl-CoA or the reaction products CoA and acetylated puromycin, four classes of mutations in and around the catalytic site were designed and tested for activity. Single-residue mutations were identified that displayed a range of enzymatic activities, from complete ablation to enhanced activity relative to wild-type (WT) PAC. Cell pools of stably transfected HEK293 cells derived using two PAC mutants with attenuated activity, Y30F and A142D, were found to secrete up to three-fold higher levels of a soluble, recombinant target protein than corresponding pools derived with the WT enzyme. A third mutant, Y171F, appeared to stabilise the intracellular turnover of PAC, resulting in an apparent loss of selection stringency. Our results indicate that the structure-guided manipulation of PAC function can be utilised to enhance selection stringency for the derivation of mammalian cell lines secreting elevated levels of recombinant proteins.


  • Organizational Affiliation
    • Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation, 343 Royal Parade, Parkville, Victoria, 3052, Australia. alex.caputo@csiro.au.

Macromolecule Content 

  • Total Structure Weight: 48.7 kDa 
  • Atom Count: 3,493 
  • Modeled Residue Count: 392 
  • Deposited Residue Count: 416 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Puromycin N-acetyltransferase
A, B
208Streptomyces albonigerMutation(s): 0 
Gene Names: pac
EC: 2.3
UniProt
Find proteins for P13249 (Streptomyces alboniger)
Explore P13249 
Go to UniProtKB:  P13249
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13249
Sequence Annotations
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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
D [auth A],
O [auth B]
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
VQ1
(Subject of Investigation/LOI)

Query on VQ1



Download:Ideal Coordinates CCD File
C [auth A],
K [auth B]
N-Acetylpuromycin
C24 H31 N7 O6
LADKVYSQIGJMFP-IYRMOJGWSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth A]
P [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
P [auth B],
Q [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
L [auth B],
M [auth B],
N [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.240 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.207 (Depositor) 
Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.596α = 90
b = 141.509β = 100.341
c = 98.985γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
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: 2021-03-17
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description