8PUU

Giardia intestinales deoxyadenosine kinase forms a functional tetramer

• PDB DOI: https://doi.org/10.2210/pdb8PUU/pdb

• Classification: TRANSFERASE
• Organism(s): Giardia intestinalis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-07-17 Released: 2024-10-30 
• Deposition Author(s): Ranjbarian, F., Rafie, K., Shankar, K., Krakovka, S., Svaerd, S., Carlson, L.-A., Hofer, A.
• Funding Organization(s): Swedish Research Council, Knut and Alice Wallenberg Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.225 
• R-Value Work: 0.200 

Starting Model: in silico

Literature

Giardia intestinalis deoxyadenosine kinase has a unique tetrameric structure that enables high substrate affinity and makes the parasite sensitive to deoxyadenosine analogues

Ranjbarian, F., Rafie, K., Shankar, K., Krakovka, S., Svaerd, S., Carlson, L.-A., Hofer, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy, assay for oligomerization

Macromolecule Content

• Total Structure Weight: 55.57 kDa 
• Atom Count: 3,825 
• Modelled Residue Count: 442 
• Deposited Residue Count: 471 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxynucleoside kinase	A	242	Giardia intestinalis	Mutation(s): 0  Gene Names: GL50803_0017451, GL50803_17451
UniProt
Find proteins for A8B9V6 (Giardia intestinalis (strain ATCC 50803 / WB clone C6)) Explore A8B9V6  Go to UniProtKB:  A8B9V6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxynucleoside kinase	B	221	Giardia intestinalis	Mutation(s): 0  Gene Names: GL50803_0017451, GL50803_17451
UniProt
Find proteins for A8B9V6 (Giardia intestinalis (strain ATCC 50803 / WB clone C6)) Explore A8B9V6  Go to UniProtKB:  A8B9V6

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Giardia intestinales dAK	C	8	Giardia intestinalis	Mutation(s): 0  EC: 2.7.1.76

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DAT (Subject of Investigation/LOI)	D [auth A]	2'-DEOXYADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O9 P2 DAEAPNUQQAICNR-RRKCRQDMSA-N
D5M (Subject of Investigation/LOI)	E [auth B]	2'-DEOXYADENOSINE-5'-MONOPHOSPHATE C10 H14 N5 O6 P KHWCHTKSEGGWEX-RRKCRQDMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.225 
• R-Value Work: 0.200 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.13	α = 90
b = 103.13	β = 90
c = 147.109	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MxCuBE	data collection
Coot	model building
PHASER	phasing
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-30 
Deposition Author(s): Ranjbarian, F., Rafie, K., Shankar, K., Krakovka, S., Svaerd, S., Carlson, L.-A., Hofer, A.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2018-05851
Swedish Research Council	Sweden	2021-01145
Knut and Alice Wallenberg Foundation	Sweden	--
Swedish Research Council	Sweden	2022-00593

Revision History  

• Version 1.0: 2024-10-30
  Type: Initial release