4IAN | pdb_00004ian

Crystal Structure of apo Human PRPF4B kinase domain

• PDB DOI: https://doi.org/10.2210/pdb4IAN/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2012-12-06 Released: 2013-08-28 
• Deposition Author(s): Mechin, I., Haas, K., Chen, X., Zhang, Y., McLean, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 
  0.288 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.234 (DCC) 

Literature

Evaluation of Cancer Dependence and Druggability of PRP4 Kinase Using Cellular, Biochemical, and Structural Approaches.

Gao, Q., Mechin, I., Kothari, N., Guo, Z., Deng, G., Haas, K., McManus, J., Hoffmann, D., Wang, A., Wiederschain, D., Rocnik, J., Czechtizky, W., Chen, X., McLean, L., Arlt, H., Harper, D., Liu, F., Majid, T., Patel, V., Lengauer, C., Garcia-Echeverria, C., Zhang, B., Cheng, H., Dorsch, M., Huang, S.M.

(2013) J Biological Chem 288: 30125-30138

• PubMed: 24003220 
• DOI: https://doi.org/10.1074/jbc.M113.473348
• Primary Citation Related Structures: 
  4IAN, 4IFC, 4IIR, 4IJP


• PubMed Abstract: 
  

  PRP4 kinase is known for its roles in regulating pre-mRNA splicing and beyond. Therefore, a wider spectrum of PRP4 kinase substrates could be expected. The role of PRP4 kinase in cancer is also yet to be fully elucidated. Attaining specific and potent PRP4 inhibitors would greatly facilitate the study of PRP4 biological function and its validation as a credible cancer target. In this report, we verified the requirement of enzymatic activity of PRP4 in regulating cancer cell growth and identified an array of potential novel substrates through orthogonal proteomics approaches. The ensuing effort in structural biology unveiled for the first time unique features of PRP4 kinase domain and its potential mode of interaction with a low molecular weight inhibitor. These results provide new and important information for further exploration of PRP4 kinase function in cancer.

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Organizational Affiliation: 
• From Discovery and Early Development, Sanofi Oncology, Cambridge, Massachusetts 02139 and 94400 Vitry-sur-Seine Cedex, France.
Tucson Research Center, Sanofi, Tucson, Arizona 85755.
Lead Generation and Candidate Realization, Sanofi, Bridgewater, New Jersey 08807, and.
Lead Generation and Candidate Realization, Sanofi, Industriepark Höchst, 65926 Frankfurt, Germany.
Lead Generation and Candidate Realization, Sanofi, Waltham, Massachusetts 02451.
From Discovery and Early Development, Sanofi Oncology, Cambridge, Massachusetts 02139 and 94400 Vitry-sur-Seine Cedex, France,. Electronic address: [e-mail].

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)

Macromolecule Content 

• Total Structure Weight: 84.44 kDa 
• Atom Count: 5,333 
• Modeled Residue Count: 642 
• Deposited Residue Count: 716 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PRP4 homolog	A, B	358	Homo sapiens	Mutation(s): 0  Gene Names: KIAA0536, PRP4, PRP4H, PRP4K, PRPF4B EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13523 (Homo sapiens) Explore Q13523  Go to UniProtKB:  Q13523
PHAROS:  Q13523 GTEx:  ENSG00000112739

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A, B	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free:  0.288 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.234 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.266	α = 90
b = 75.286	β = 97.21
c = 148.003	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-28 
Deposition Author(s): Mechin, I., Haas, K., Chen, X., Zhang, Y., McLean, L.

Revision History  

• Version 1.0: 2013-08-28
  Type: Initial release
  
• Version 1.1: 2013-09-04
  Changes: Data collection
• Version 1.2: 2013-09-18
  Changes: Database references
• Version 1.3: 2013-11-06
  Changes: Database references
• Version 1.4: 2017-11-15
  Changes: Refinement description
• Version 1.5: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary