Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 108887.37 
• Atom Count: 7302 
• Residue Count: 926 
• Unique protein chains: 1

4W7S

Crystal structure of the yeast DEAD-box splicing factor Prp28 at 2.54 Angstroms resolution

• DOI: 10.2210/pdb4W7S/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
• Expression System: Escherichia coli


• Deposited: 2014-08-22 Released: 2014-10-29 
• Deposition Author(s): Jacewicz, A., Smith, P., Schwer, B., Shuman, S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences 

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.542 Å
• R-Value Free: 0.219 
• R-Value Work: 0.166 

Literature

Crystal structure, mutational analysis and RNA-dependent ATPase activity of the yeast DEAD-box pre-mRNA splicing factor Prp28.

Jacewicz, A., Schwer, B., Smith, P., Shuman, S.

(2014) Nucleic Acids Res. 42: 12885-12898

• PubMed: 25303995 
• DOI: 10.1093/nar/gku930


• PubMed Abstract: 
  

Yeast Prp28 is a DEAD-box pre-mRNA splicing factor implicated in displacing U1 snRNP from the 5' splice site. Here we report that the 588-aa Prp28 protein consists of a trypsin-sensitive 126-aa N-terminal segment (of which aa 1-89 are dispensable for Prp28 function in vivo) fused to a trypsin-resistant C-terminal catalytic domain. Purified recombinant Prp28 and Prp28-(127-588) have an intrinsic RNA-dependent ATPase activity, albeit with a low turnover number. The crystal structure of Prp28-(127-588) comprises two RecA-like domains splayed widely apart. AMPPNP•Mg2+ is engaged by the proximal domain, with proper and specific contacts from Phe194 and Gln201 (Q motif) to the adenine nucleobase. The triphosphate moiety of AMPPNP•Mg2+ is not poised for catalysis in the open domain conformation. Guided by the Prp28•AMPPNP structure, and that of the Drosophila Vasa•AMPPNP•Mg2+•RNA complex, we targeted 20 positions in Prp28 for alanine scanning. ATP-site components Asp341 and Glu342 (motif II) and Arg527 and Arg530 (motif VI) and RNA-site constituent Arg476 (motif Va) are essential for Prp28 activity in vivo. Synthetic lethality of double-alanine mutations highlighted functionally redundant contacts in the ATP-binding (Phe194-Gln201, Gln201-Asp502) and RNA-binding (Arg264-Arg320) sites. Overexpression of defective ATP-site mutants, but not defective RNA-site mutants, elicited severe dominant-negative growth defects.

---

Organizational Affiliation: 

Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Pre-mRNA-splicing ATP-dependent RNA helicase PRP28	A, B	463	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: PRP28 EC: 3.6.4.13
Find proteins for P23394 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P23394

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ANP	B	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG	B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
P6G	A, B	HEXAETHYLENE GLYCOL POLYETHYLENE GLYCOL PEG400 C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.542 Å
• R-Value Free: 0.219 
• R-Value Work: 0.166 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 114.719	α = 90.00
b = 114.719	β = 90.00
c = 156.186	γ = 120.00

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2014-08-22 
• Released Date: 2014-10-29 
• Deposition Author(s): Jacewicz, A., Smith, P., Schwer, B., Shuman, S.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences	United States	GM52470
National Institutes of Health/National Institute of General Medical Sciences	United States	GM102961

Revision History 

• Version 1.0: 2014-10-29
  Type: Initial release
• Version 1.1: 2014-11-26
  Type: Database references
• Version 1.2: 2017-09-06
  Type: Advisory, Data collection, Database references, Derived calculations, Other, Source and taxonomy
• Version 1.3: 2017-09-20
  Type: Author supporting evidence