6JBD | pdb_00006jbd

Phosphotransferase-ATP complex related to CoA biosynthesis pathway

PDB DOI: https://doi.org/10.2210/pdb6JBD/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.259 (Depositor), 0.261 (DCC)
R-Value Work:
0.219 (Depositor), 0.224 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka, Japan.

Macromolecule Content

Total Structure Weight: 33.98 kDa
Atom Count: 2,370
Modeled Residue Count: 295
Deposited Residue Count: 300
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JHF1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	I [auth A], J [auth A], K [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	L [auth A], M [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain L [auth A] Focus chain M [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.259 (Depositor), 0.261 (DCC)
R-Value Work: 0.219 (Depositor), 0.224 (DCC)

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.323	α = 90
b = 95.323	β = 90
c = 60.691	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-01-29

Deposition Author(s):

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	--