5J0A | pdb_00005j0a

Crystal structure of PDZ-binding kinase

PDB DOI: https://doi.org/10.2210/pdb5J0A/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2016-03-28 Released: 2016-09-07
Deposition Author(s): Zou, Q.W., Zhou, H., Yang, X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.74 Å
R-Value Free:
0.271 (Depositor), 0.273 (DCC)
R-Value Work:
0.222 (Depositor), 0.226 (DCC)
R-Value Observed:
0.222 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The crystal structure of an inactive dimer of PDZ-binding kinase

Dong, C., Tang, X., Xie, Y., Zou, Q., Yang, X., Zhou, H.

(2016) Biochem Biophys Res Commun 476: 586-593

PubMed: 27262437 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2016.05.166
Primary Citation Related Structures:
5J0A

PubMed Abstract:
The overexpression of PDZ-binding kinase/T-LAK cell-originated protein kinase (PBK/TOPK) has been associated with hematologic tumors, breast cancer and various other cancers. However, the three-dimensional structure of PBK has not been solved. In this study, we determined the crystal structure of human PBK, which has two phospho-mimicking mutations T9E and T198E. The structural data indicated that PBK may assemble into an inactive dimer in alkaline conditions. Analytical size-exclusion chromatography and analytical ultracentrifugation confirmed that PBK exists in a conformational transition between dimers and monomers at different pH conditions. Co-IP and kinase assays suggested that the active state of PBK is a monomer and does not form a dimer even under alkaline conditions. These results showed that the conformational transition of PBK is important for its kinase activity regulation. Collectively, our observations may provide a novel starting point for structure-based functional studies.

Organizational Affiliation

College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China.

Macromolecule Content

Total Structure Weight: 69.25 kDa
Atom Count: 4,975
Modeled Residue Count: 602
Deposited Residue Count: 604
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lymphokine-activated killer T-cell-originated protein kinase	A	300	Homo sapiens	Mutation(s): 1 Gene Names: PBK, TOPK EC: 2.7.12.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q96KB5 (Homo sapiens) Explore Q96KB5 Go to UniProtKB: Q96KB5
PHAROS: Q96KB5 GTEx: ENSG00000168078
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96KB5
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lymphokine-activated killer T-cell-originated protein kinase	B	304	Homo sapiens	Mutation(s): 1 Gene Names: PBK, TOPK EC: 2.7.12.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q96KB5 (Homo sapiens) Explore Q96KB5 Go to UniProtKB: Q96KB5
PHAROS: Q96KB5 GTEx: ENSG00000168078
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96KB5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HC4 Query on HC4 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain J [auth A]	H [auth A], I [auth A], J [auth A], P [auth B]	4'-HYDROXYCINNAMIC ACID C₉ H₈ O₃ NGSWKAQJJWESNS-ZZXKWVIFSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain K [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]