6FND

Crystal structure of Toxoplasma gondii AKMT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure of a Novel Dimeric SET Domain Methyltransferase that Regulates Cell Motility.

Pivovarova, Y.Liu, J.Lesigang, J.Koldyka, O.Rauschmeier, R.Hu, K.Dong, G.

(2018) J Mol Biol 430: 4209-4229

  • DOI: https://doi.org/10.1016/j.jmb.2018.08.017
  • Primary Citation of Related Structures:  
    6FND

  • PubMed Abstract: 

    Lysine methyltransferases (KMTs) were initially associated with transcriptional control through their methylation of histones and other nuclear proteins, but have since been found to regulate many other cellular activities. The apical complex lysine (K) methyltransferase (AKMT) of the human parasite Toxoplasma gondii was recently shown to play a critical role in regulating cellular motility. Here we report a 2.1-Å resolution crystal structure of the conserved and functional C-terminal portion (aa289-709) of T. gondii AKMT. AKMT dimerizes via a unique intermolecular interface mediated by the C-terminal tetratricopeptide repeat-like domain together with a specific zinc-binding motif that is absent from all other KMTs. Disruption of AKMT dimerization impaired both its enzyme activity and parasite egress from infected host cells in vivo. Structural comparisons reveal that AKMT is related to the KMTs in the SMYD family, with, however, a number of distinct structural features in addition to the unusual dimerization interface. These features are conserved among the apicomplexan parasites and their free-living relatives, but not found in any known KMTs in animals. AKMT therefore is the founding member of a new subclass of KMT that has important implications for the evolution of the apicomplexans.


  • Organizational Affiliation

    Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria. Electronic address: gang.dong@meduniwien.ac.at.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apical complex lysine methyltransferase423Toxoplasma gondiiMutation(s): 0 
Gene Names: TGPRC2_216080B
UniProt
Find proteins for B9Q0K5 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore B9Q0K5 
Go to UniProtKB:  B9Q0K5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9Q0K5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Apical complex lysine methyltransferase418Toxoplasma gondii TgCatPRC2Mutation(s): 0 
Gene Names: TGPRC2_216080B
UniProt
Find proteins for B9Q0K5 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore B9Q0K5 
Go to UniProtKB:  B9Q0K5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9Q0K5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Apical complex lysine methyltransferase424Toxoplasma gondii TgCatPRC2Mutation(s): 0 
Gene Names: TGPRC2_216080B
UniProt
Find proteins for B9Q0K5 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore B9Q0K5 
Go to UniProtKB:  B9Q0K5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9Q0K5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Apical complex lysine methyltransferase425Toxoplasma gondii TgCatPRC2Mutation(s): 0 
Gene Names: TGPRC2_216080B
UniProt
Find proteins for B9Q0K5 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore B9Q0K5 
Go to UniProtKB:  B9Q0K5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9Q0K5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AA [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
DA [auth C],
G [auth A],
PA [auth D],
R [auth B],
S [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
EA [auth C]
FA [auth C]
H [auth A]
I [auth A]
J [auth A]
EA [auth C],
FA [auth C],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
QA [auth D],
RA [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth C]
CA [auth C]
E [auth A]
F [auth A]
NA [auth D]
BA [auth C],
CA [auth C],
E [auth A],
F [auth A],
NA [auth D],
OA [auth D],
P [auth B],
Q [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
GA [auth C]
HA [auth C]
IA [auth C]
JA [auth C]
KA [auth C]
GA [auth C],
HA [auth C],
IA [auth C],
JA [auth C],
KA [auth C],
L [auth A],
LA [auth C],
M [auth A],
MA [auth C],
N [auth A],
O [auth A],
SA [auth D],
T [auth B],
TA [auth D],
U [auth B],
UA [auth D],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
MLY
Query on MLY
A
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
MLZ
Query on MLZ
A
L-PEPTIDE LINKINGC7 H16 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.935α = 108.69
b = 89.371β = 101.31
c = 91.72γ = 103.41
Software Package:
Software NamePurpose
XDSdata reduction
xia2data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
AutoSolphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustriaW 1258

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-14
    Type: Initial release