4WTV | pdb_00004wtv

Crystal structure of the phosphatidylinositol 4-kinase IIbeta

PDB DOI: https://doi.org/10.2210/pdb4WTV/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens, Tequatrovirus T4
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2014-10-30 Released: 2015-07-15
Deposition Author(s): Klima, M., Baumlova, A., Chalupska, D., Boura, E.
Funding Organization(s): MarieCurie

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.240 (Depositor), 0.250 (DCC)
R-Value Work:
0.209 (Depositor)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

The high-resolution crystal structure of phosphatidylinositol 4-kinase II beta and the crystal structure of phosphatidylinositol 4-kinase II alpha containing a nucleoside analogue provide a structural basis for isoform-specific inhibitor design.

Klima, M., Baumlova, A., Chalupska, D., Hrebabecky, H., Dejmek, M., Nencka, R., Boura, E.

(2015) Acta Crystallogr D Biol Crystallogr 71: 1555-1563

PubMed: 26143926 Search on PubMed
DOI: https://doi.org/10.1107/S1399004715009505
Primary Citation Related Structures:
4WTV, 4YC4

PubMed Abstract:
Phosphatidylinositol 4-phosphate (PI4P) is the most abundant monophosphoinositide in eukaryotic cells. Humans have four phosphatidylinositol 4-kinases (PI4Ks) that synthesize PI4P, among which are PI4K IIβ and PI4K IIα. In this study, two crystal structures are presented: the structure of human PI4K IIβ and the structure of PI4K IIα containing a nucleoside analogue. The former, a complex with ATP, is the first high-resolution (1.9 Å) structure of a PI4K. These structures reveal new details such as high conformational heterogeneity of the lateral hydrophobic pocket of the C-lobe and together provide a structural basis for isoform-specific inhibitor design.

Organizational Affiliation

Department of Biochemistry, Institute of Organic Chemistry and Biochemistry, Flemingovo nam. 2, 166 10 Prague, Czech Republic.

Macromolecule Content

Total Structure Weight: 119.75 kDa
Atom Count: 7,414
Modeled Residue Count: 873
Deposited Residue Count: 1,028
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4-kinase type 2-beta,Endolysin,Phosphatidylinositol 4-kinase type 2-beta	A, B	514	Homo sapiens, Tequatrovirus T4	Mutation(s): 0 Gene Names: PI4K2B EC: 2.7.1.67 (PDB Primary Data), 3.2.1.17 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720 Go to UniProtKB: P00720
Find proteins for Q8TCG2 (Homo sapiens) Explore Q8TCG2 Go to UniProtKB: Q8TCG2
PHAROS: Q8TCG2 GTEx: ENSG00000038210
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P00720 Q8TCG2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.240 (Depositor), 0.250 (DCC)
R-Value Work: 0.209 (Depositor)
R-Value Observed: 0.210 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.01	α = 90
b = 106.01	β = 90
c = 214.53	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Coot	model building
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-07-15

Deposition Author(s):

Funding Organization	Location	Grant Number
MarieCurie	Czech Republic	FP7-PEOPLE-2012-CIG, project number 333916

Revision History (Full details and data files)

Version 1.0: 2015-07-15
Type: Initial release
Version 1.1: 2016-07-27
Changes: Database references
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Refinement description