6WUG | pdb_00006wug

Crystal Structure of S. pombe Rai1 in complex with 3'-FADP

• PDB DOI: https://doi.org/10.2210/pdb6WUG/pdb

• Classification: HYDROLASE
• Organism(s): Schizosaccharomyces pombe
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-05-04 Released: 2020-05-20 
• Deposition Author(s): Doamekpor, S.K., Tong, L.
• Funding Organization(s): National Institutes of Health/National Library of Medicine (NIH/NLM)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.229 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

DXO/Rai1 enzymes remove 5'-end FAD and dephospho-CoA caps on RNAs.

Doamekpor, S.K., Grudzien-Nogalska, E., Mlynarska-Cieslak, A., Kowalska, J., Kiledjian, M., Tong, L.

(2020) Nucleic Acids Res 48: 6136-6148

• PubMed: 32374864 
• DOI: https://doi.org/10.1093/nar/gkaa297
• Primary Citation Related Structures: 
  6WUF, 6WUG, 6WUI, 6WUK


• PubMed Abstract: 
  

  In eukaryotes, the DXO/Rai1 enzymes can eliminate most of the incomplete and non-canonical NAD caps through their decapping, deNADding and pyrophosphohydrolase activities. Here, we report that these enzymes can also remove FAD and dephospho-CoA (dpCoA) non-canonical caps from RNA, and we have named these activities deFADding and deCoAping. The crystal structures of mammalian DXO with 3'-FADP or CoA and fission yeast Rai1 with 3'-FADP provide elegant insight to these activities. FAD and CoA are accommodated in the DXO/Rai1 active site by adopting folded conformations. The flavin of FAD and the pantetheine group of CoA contact the same region at the bottom of the active site tunnel, which undergoes conformational changes to accommodate the different cap moieties. We have developed FAD-capQ to detect and quantify FAD-capped RNAs and determined that FAD caps are present on short RNAs (with less than ∼200 nucleotides) in human cells and that these RNAs are stabilized in the absence of DXO.

---

Organizational Affiliation: 
• Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
Dept. Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA.
Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 43.95 kDa 
• Atom Count: 2,800 
• Modeled Residue Count: 313 
• Deposited Residue Count: 373 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Decapping nuclease din1	A	372	Schizosaccharomyces pombe	Mutation(s): 0  Gene Names: din1, SPAC19D5.06c EC: 3.6.1
UniProt
Find proteins for O13836 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore O13836  Go to UniProtKB:  O13836

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UBG	D [auth A]	[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) C27 H34 N9 O18 P3 QOJVPCDYXUQNMD-UYBVJOGSSA-N
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS	A	L-PEPTIDE LINKING	C3 H7 N O2 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.229 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.594	α = 90
b = 59.978	β = 104.67
c = 72.545	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-05-20 
Deposition Author(s): Doamekpor, S.K., Tong, L.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Library of Medicine (NIH/NLM)	United States	R35GM118093

Revision History  

• Version 1.0: 2020-05-20
  Type: Initial release
  
• Version 1.1: 2020-06-24
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-11-06
  Changes: Structure summary