6OWU

THE PRP8 INTEIN OF CRYPTOCOCCUS NEOFORMANS in complex with Zn2+

  • Classification: HYDROLASE
  • Organism(s): Cryptococcus neoformans var. grubii
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2019-05-11 Released: 2019-10-23 
  • Deposition Author(s): Li, Z., Li, H.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Spliceosomal Prp8 intein at the crossroads of protein and RNA splicing.

Green, C.M.Li, Z.Smith, A.D.Novikova, O.Bacot-Davis, V.R.Gao, F.Hu, S.Banavali, N.K.Thiele, D.J.Li, H.Belfort, M.

(2019) PLoS Biol 17: e3000104-e3000104

  • DOI: 10.1371/journal.pbio.3000104
  • Primary Citation of Related Structures:  
    6MX6, 6OWU

  • PubMed Abstract: 
  • The spliceosome is a large ribonucleoprotein complex that removes introns from pre-mRNAs. At its functional core lies the essential pre-mRNA processing factor 8 (Prp8) protein. Across diverse eukaryotes, this protein cofactor of RNA catalysis harbors a self-splicing element called an intein ...

    The spliceosome is a large ribonucleoprotein complex that removes introns from pre-mRNAs. At its functional core lies the essential pre-mRNA processing factor 8 (Prp8) protein. Across diverse eukaryotes, this protein cofactor of RNA catalysis harbors a self-splicing element called an intein. Inteins in Prp8 are extremely pervasive and are found at 7 different sites in various species. Here, we focus on the Prp8 intein from Cryptococcus neoformans (Cne), a human fungal pathogen. We solved the crystal structure of this intein, revealing structural homology among protein splicing sequences in eukaryotes, including the Hedgehog C terminus. Working with the Cne Prp8 intein in a reporter assay, we find that the biologically relevant divalent metals copper and zinc inhibit intein splicing, albeit by 2 different mechanisms. Copper likely stimulates reversible modifications on a catalytically important cysteine, whereas zinc binds at the terminal asparagine and the same critical cysteine. Importantly, we also show that copper treatment inhibits Prp8 protein splicing in Cne. Lastly, an intein-containing Prp8 precursor model is presented, suggesting that metal-induced protein splicing inhibition would disturb function of both Prp8 and the spliceosome. These results indicate that Prp8 protein splicing can be modulated, with potential functional implications for the spliceosome.


    Organizational Affiliation

    Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, United States of America.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PRP8 protein
A, B, C, D, E, F
A, B, C, D, E, F
184Cryptococcus neoformans var. grubiiMutation(s): 0 
Gene Names: PRP8
UniProt
Find proteins for Q6TER0 (Cryptococcus neoformans var. grubii)
Explore Q6TER0 
Go to UniProtKB:  Q6TER0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6TER0
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.093α = 94.86
b = 63.039β = 103.13
c = 78.636γ = 117.44
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-05-11 
  • Released Date: 2019-10-23 
  • Deposition Author(s): Li, Z., Li, H.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI140726
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI141178
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM39422
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM44844

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-23
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence