6JBC | pdb_00006jbc

Phosphotransferase related to CoA biosynthesis pathway

• PDB DOI: https://doi.org/10.2210/pdb6JBC/pdb

• Classification: TRANSFERASE
• Organism(s): Thermococcus kodakarensis KOD1
• Expression System: Thermococcus kodakarensis
• Mutation(s): No 


• Deposited: 2019-01-25 Released: 2020-01-29 
• Deposition Author(s): Kita, A., Kishimoto, A., Shimosaka, T., Tomita, H., Yokooji, Y., Imanaka, T., Atomi, H., Miki, K.
• Funding Organization(s): Japan Society for the Promotion of Science, Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.278 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.235 (DCC) 

Starting Model: experimental

Literature

Crystal structure of pantoate kinase from Thermococcus kodakarensis.

Kita, A., Kishimoto, A., Shimosaka, T., Tomita, H., Yokooji, Y., Imanaka, T., Atomi, H., Miki, K.

(2020) Proteins 88: 718-724

• PubMed: 31697438 
• DOI: https://doi.org/10.1002/prot.25852
• Primary Citation Related Structures: 
  6JBC, 6JBD


• PubMed Abstract: 
  

  The coenzyme A biosynthesis pathways in most archaea involve two unique enzymes, pantoate kinase and phosphopantothenate synthetase, to convert pantoate to 4'-phosphopantothenate. Here, we report the first crystal structure of pantoate kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis and its complex with ATP and a magnesium ion. The electron density for the adenosine moiety of ATP was very weak, which most likely relates to its broad nucleotide specificity. Based on the structure of the active site that contains a glycerol molecule, the pantoate binding site and the roles of the highly conserved residues are suggested.

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Organizational Affiliation: 
• Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka, Japan.
Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan.
Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan.
Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan.
JST, CREST, Tokyo, Japan.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.67 kDa 
• Atom Count: 2,299 
• Modeled Residue Count: 295 
• Deposited Residue Count: 300 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pantoate kinase	A	300	Thermococcus kodakarensis KOD1	Mutation(s): 0  Gene Names: TK2141 EC: 2.7.1.169
UniProt
Find proteins for Q5JHF1 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JHF1  Go to UniProtKB:  Q5JHF1

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	B [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PPV	G [auth A]	PYROPHOSPHATE H4 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-N
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	H [auth A], I [auth A], J [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	K [auth A], L [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.278 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.235 (DCC) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.803	α = 90
b = 94.803	β = 90
c = 60.04	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-01-29 
Deposition Author(s): Kita, A., Kishimoto, A., Shimosaka, T., Tomita, H., Yokooji, Y., Imanaka, T., Atomi, H., Miki, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	24.2716
Japan Society for the Promotion of Science	Japan	JP17J08246
Japan Society for the Promotion of Science	Japan	JP18H03934
Other private	Japan	--

Revision History  

• Version 1.0: 2020-01-29
  Type: Initial release
  
• Version 1.1: 2020-08-19
  Changes: Database references, Derived calculations
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description