Home LiteratureArticle Details
PMID: 14618157 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't

X-ray structure and activity of the yeast Pop2 protein: a nuclease subunit of the mRNA deadenylase complex.

EMBO reports ·Vol. 4 ·No. 12 ·2003-12-00 ·Pages 1150-5

Thore S, Mauxion F, Séraphin B, Suck D

Abstract

In Saccharomyces cerevisiae, a large complex, known as the Ccr4-Not complex, containing two nucleases, is responsible for mRNA deadenylation. One of these nucleases is called Pop2 and has been identified by similarity with PARN, a human poly(A) nuclease. Here, we present the crystal structure of the nuclease domain of Pop2 at 2.3 A resolution. The domain has the fold of the DnaQ family and represents the first structure of an RNase from the DEDD superfamily. Despite the presence of two non-canonical residues in the active site, the domain displays RNase activity on a broad range of RNA substrates. Site-directed mutagenesis of active-site residues demonstrates the intrinsic ability of the Pop2 RNase D domain to digest RNA. This first structure of a nuclease involved in the 3'-5' deadenylation of mRNA in yeast provides information for the understanding of the mechanism by which the Ccr4-Not complex achieves its functions.

MeSH Terms
Amino Acid Sequence Binding Sites Crystallography, X-Ray DNA-Binding Proteins/chemistry Death Domain Receptor Signaling Adaptor Proteins Humans Intracellular Signaling Peptides and Proteins Molecular Sequence Data Mutagenesis, Site-Directed Poly A/genetics Polyribonucleotides/genetics Proteins/chemistry,genetics Ribonucleases/chemistry,metabolism Saccharomyces cerevisiae Saccharomyces cerevisiae Proteins Sequence Alignment Transcription Factors Yeasts/enzymology,genetics
Chemicals
CNOT8 protein, human DEDD protein, human DNA-Binding Proteins Death Domain Receptor Signaling Adaptor Proteins Intracellular Signaling Peptides and Proteins Polyribonucleotides Proteins Saccharomyces cerevisiae Proteins Transcription Factors Poly A CCR4 protein, S cerevisiae Ribonucleases mRNA deadenylase POP2 protein, S cerevisiae
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Thore Stéphane
European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.
Mauxion Fabienne
Séraphin Bertrand
Suck Dietrich
References (32)
32 references, click to expand
  1. Automated MAD and MIR structure solution.
    Acta Crystallogr D Biol Crystallogr. 1999 Apr;55(Pt 4):849-61 PMID: 10089316
  2. The CCR4 and CAF1 proteins of the CCR4-NOT complex are physically and functionally separated from NOT2, NOT4, and NOT5.
    Mol Cell Biol. 1999 Oct;19(10):6642-51 PMID: 10490603
  3. Functionally unrelated signalling proteins contain a fold similar to Mg2+-dependent endonucleases.
    Trends Biochem Sci. 2000 Jun;25(6):272-3 PMID: 10838565
  4. The TATA-binding protein-associated factor yTafII19p functionally interacts with components of the global transcriptional regulator Ccr4-Not complex and physically interacts with the Not5 subunit.
    J Biol Chem. 2000 Sep 1;275(35):26925-34 PMID: 10864925
  5. Functional interaction of CCR4-NOT proteins with TATAA-binding protein (TBP) and its associated factors in yeast.
    Genetics. 2000 Jul;155(3):1045-54 PMID: 10880468
  6. Maximum-likelihood density modification.
    Acta Crystallogr D Biol Crystallogr. 2000 Aug;56(Pt 8):965-72 PMID: 10944333
  7. Structure of Escherichia coli exonuclease I suggests how processivity is achieved.
    Nat Struct Biol. 2000 Dec;7(12):1125-8 PMID: 11101894
  8. Characterization of CAF4 and CAF16 reveals a functional connection between the CCR4-NOT complex and a subset of SRB proteins of the RNA polymerase II holoenzyme.
    J Biol Chem. 2001 Mar 9;276(10):7541-8 PMID: 11113136
  9. Exoribonuclease superfamilies: structural analysis and phylogenetic distribution.
    Nucleic Acids Res. 2001 Mar 1;29(5):1017-26 PMID: 11222749
  10. The transcription factor associated Ccr4 and Caf1 proteins are components of the major cytoplasmic mRNA deadenylase in Saccharomyces cerevisiae.
    Cell. 2001 Feb 9;104(3):377-86 PMID: 11239395
  11. Yak1p, a DYRK family kinase, translocates to the nucleus and phosphorylates yeast Pop2p in response to a glucose signal.
    Genes Dev. 2001 May 15;15(10):1217-28 PMID: 11358866
  12. The yeast POP2 gene encodes a nuclease involved in mRNA deadenylation.
    Nucleic Acids Res. 2001 Jun 15;29(12):2448-55 PMID: 11410650
  13. Purification and characterization of the 1.0 MDa CCR4-NOT complex identifies two novel components of the complex.
    J Mol Biol. 2001 Dec 7;314(4):683-94 PMID: 11733989
  14. CCR4, a 3'-5' poly(A) RNA and ssDNA exonuclease, is the catalytic component of the cytoplasmic deadenylase.
    EMBO J. 2002 Mar 15;21(6):1414-26 PMID: 11889047
  15. Ccr4p is the catalytic subunit of a Ccr4p/Pop2p/Notp mRNA deadenylase complex in Saccharomyces cerevisiae.
    EMBO J. 2002 Mar 15;21(6):1427-36 PMID: 11889048
  16. Structural basis for proofreading during replication of the Escherichia coli chromosome.
    Structure. 2002 Apr;10(4):535-46 PMID: 11937058
  17. Identification of multiple RNA features that influence CCR4 deadenylation activity.
    J Biol Chem. 2003 Apr 25;278(17):14949-55 PMID: 12590136
  18. The CCP4 suite: programs for protein crystallography.
    Acta Crystallogr D Biol Crystallogr. 1994 Sep 1;50(Pt 5):760-3 PMID: 15299374
  19. Improved methods for building protein models in electron density maps and the location of errors in these models.
    Acta Crystallogr A. 1991 Mar 1;47 ( Pt 2):110-9 PMID: 2025413
  20. Processing of X-ray diffraction data collected in oscillation mode.
    Methods Enzymol. 1997;276:307-26 PMID: 27754618
  21. Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP.
    Nature. 1985 Feb 28-Mar 6;313(6005):762-6 PMID: 3883192
  22. Identification of new genes involved in the regulation of yeast alcohol dehydrogenase II.
    Genetics. 1984 Dec;108(4):833-44 PMID: 6392016
  23. Function and structure relationships in DNA polymerases.
    Annu Rev Biochem. 1994;63:777-822 PMID: 7526780
  24. Identification of a mouse protein whose homolog in Saccharomyces cerevisiae is a component of the CCR4 transcriptional regulatory complex.
    Mol Cell Biol. 1995 Jul;15(7):3487-95 PMID: 7791755
  25. CCR4 is a glucose-regulated transcription factor whose leucine-rich repeat binds several proteins important for placing CCR4 in its proper promoter context.
    Mol Cell Biol. 1994 Jul;14(7):4522-31 PMID: 8007957
  26. Mechanisms and control of mRNA turnover in Saccharomyces cerevisiae.
    Microbiol Rev. 1996 Mar;60(1):233-49 PMID: 8852902
  27. Comparative sequence analysis of ribonucleases HII, III, II PH and D.
    Nucleic Acids Res. 1997 Aug 15;25(16):3187-95 PMID: 9241229
  28. DBF2, a cell cycle-regulated protein kinase, is physically and functionally associated with the CCR4 transcriptional regulatory complex.
    EMBO J. 1997 Sep 1;16(17):5289-98 PMID: 9311989
  29. The proofreading domain of Escherichia coli DNA polymerase I and other DNA and/or RNA exonuclease domains.
    Nucleic Acids Res. 1997 Dec 15;25(24):5110-8 PMID: 9396823
  30. The NOT proteins are part of the CCR4 transcriptional complex and affect gene expression both positively and negatively.
    EMBO J. 1998 Feb 16;17(4):1096-106 PMID: 9463387
  31. Crystallography & NMR system: A new software suite for macromolecular structure determination.
    Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):905-21 PMID: 9757107
  32. Association of distinct yeast Not2 functional domains with components of Gcn5 histone acetylase and Ccr4 transcriptional regulatory complexes.
    EMBO J. 1998 Nov 16;17(22):6714-22 PMID: 9822614
Article Info
Journal
EMBO reports
Abbr.
EMBO Rep
ISSN
1469-221X
DOI
10.1038/sj.embor.7400020
Published
2003-12-00
Epub
2003-00-14
Pages
1150-5
Language
English
Region
England
NLM ID
100963049
PMCID
PMC1326415
Subset
IM
Databases
PDB
1UOC
External Links
PubMed source DOI: 10.1038/sj.embor.7400020 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2