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1ifw

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Revision as of 08:54, 10 January 2018

SOLUTION STRUCTURE OF C-TERMINAL DOMAIN OF POLY(A) BINDING PROTEIN FROM SACCHAROMYCES CEREVISIAE

Structural highlights

1ifw is a 1 chain structure with sequence from Atcc 18824. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:	PAB1 (ATCC 18824)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[PABP_YEAST] Binds the poly(A) tail of mRNA. Appears to be an important mediator of the multiple roles of the poly(A) tail in mRNA biogenesis, stability and translation. In the nucleus, interacts with the nuclear cleavage factor IA (CFIA), which is required for both mRNA cleavage and polyadenylation. Is also required for efficient mRNA export to the cytoplasm. Acts in concert with a poly(A)-specific nuclease (PAN) to affect poly(A) tail shortening, which may occur concomitantly with either nucleocytoplasmic mRNA transport or translational initiation. Regulates PAN activity via interaction with the stimulator PAN3 or the inhibitor PBP1. In the cytoplasm, affects both translation and mRNA decay. Stimulates translation by interaction with translation initiation factor eIF4G, a subunit of the cap-binding complex eIF4F, bringing the 5'- and 3'-ends of the mRNA in proximity. The formation of this circular mRNP structure appears to be critical for the synergistic effects of the cap and the poly(A) tail in facilitating translation initiation, recycling of ribosomes, and mRNA stability. Also regulates translation termination by recruiting eukaryotic release factor 3 (eRF3). Interaction with eRF3 is also required for regulation of normal mRNA decay through translation termination-coupled poly(A) shortening, probably mediated by PAN. Loss of PAB1 from the mRNP after deadenylation triggers mRNA degradation. Inhibits the major cytoplasmic mRNA deadenylase CCR4-NOT complex. Is also associated peripherally with COPI vesicles through its interaction with ARF1, and this is required for correct localization of the asymmetrically distributed ASH1 mRNA.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13] ^[14]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

We have determined the solution structure of the PABC domain from Saccharomyces cerevisiae Pab1p and mapped its peptide-binding site. PABC domains are peptide binding domains found in poly(A)-binding proteins (PABP) and are a subset of HECT-family E3 ubiquitin ligases (also known as hyperplastic discs proteins (HYDs)). In mammals, the PABC domain of PABP functions to recruit several different translation factors to the mRNA poly(A) tail. PABC domains are highly conserved, with high specificity for peptide sequences of roughly 12 residues with conserved alanine, phenylalanine, and proline residues at positions 7, 10, and 12. Compared with human PABP, the yeast PABC domain is missing the first alpha helix, contains two extra amino acids between helices 2 and 3, and has a strongly bent C-terminal helix. These give rise to unique peptide binding specificity wherein yeast PABC binds peptides from Paip2 and RF3 but not Paip1. Mapping of the peptide-binding site reveals that the bend in the C-terminal helix disrupts binding interactions with the N terminus of peptide ligands and leads to greatly reduced binding affinity for the peptides tested. No high affinity or natural binding partners from S. cerevisiae could be identified by sequence analysis of known PABC ligands. Comparison of the three known PABC structures shows that the features responsible for peptide binding are highly conserved and responsible for the distinct but overlapping binding specificities.

Solution structure of the orphan PABC domain from Saccharomyces cerevisiae poly(A)-binding protein.,Kozlov G, Siddiqui N, Coillet-Matillon S, Trempe JF, Ekiel I, Sprules T, Gehring K J Biol Chem. 2002 Jun 21;277(25):22822-8. Epub 2002 Apr 8. PMID:11940585^[15]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Sachs AB, Davis RW. The poly(A) binding protein is required for poly(A) shortening and 60S ribosomal subunit-dependent translation initiation. Cell. 1989 Sep 8;58(5):857-67. PMID:2673535
↑ Bernstein P, Peltz SW, Ross J. The poly(A)-poly(A)-binding protein complex is a major determinant of mRNA stability in vitro. Mol Cell Biol. 1989 Feb;9(2):659-70. PMID:2565532
↑ Caponigro G, Parker R. Multiple functions for the poly(A)-binding protein in mRNA decapping and deadenylation in yeast. Genes Dev. 1995 Oct 1;9(19):2421-32. PMID:7557393
↑ Amrani N, Minet M, Le Gouar M, Lacroute F, Wyers F. Yeast Pab1 interacts with Rna15 and participates in the control of the poly(A) tail length in vitro. Mol Cell Biol. 1997 Jul;17(7):3694-701. PMID:9199303
↑ Minvielle-Sebastia L, Preker PJ, Wiederkehr T, Strahm Y, Keller W. The major yeast poly(A)-binding protein is associated with cleavage factor IA and functions in premessenger RNA 3'-end formation. Proc Natl Acad Sci U S A. 1997 Jul 22;94(15):7897-902. PMID:9223284
↑ Coller JM, Gray NK, Wickens MP. mRNA stabilization by poly(A) binding protein is independent of poly(A) and requires translation. Genes Dev. 1998 Oct 15;12(20):3226-35. PMID:9784497
↑ Otero LJ, Ashe MP, Sachs AB. The yeast poly(A)-binding protein Pab1p stimulates in vitro poly(A)-dependent and cap-dependent translation by distinct mechanisms. EMBO J. 1999 Jun 1;18(11):3153-63. PMID:10357826 doi:http://dx.doi.org/10.1093/emboj/18.11.3153
↑ Tharun S, Parker R. Targeting an mRNA for decapping: displacement of translation factors and association of the Lsm1p-7p complex on deadenylated yeast mRNAs. Mol Cell. 2001 Nov;8(5):1075-83. PMID:11741542
↑ Tucker M, Staples RR, Valencia-Sanchez MA, Muhlrad D, Parker R. 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 doi:http://dx.doi.org/10.1093/emboj/21.6.1427
↑ Hosoda N, Kobayashi T, Uchida N, Funakoshi Y, Kikuchi Y, Hoshino S, Katada T. Translation termination factor eRF3 mediates mRNA decay through the regulation of deadenylation. J Biol Chem. 2003 Oct 3;278(40):38287-91. Epub 2003 Aug 15. PMID:12923185 doi:http://dx.doi.org/10.1074/jbc.C300300200
↑ Trautwein M, Dengjel J, Schirle M, Spang A. Arf1p provides an unexpected link between COPI vesicles and mRNA in Saccharomyces cerevisiae. Mol Biol Cell. 2004 Nov;15(11):5021-37. Epub 2004 Sep 8. PMID:15356266 doi:http://dx.doi.org/10.1091/mbc.E04-05-0411
↑ Mangus DA, Evans MC, Agrin NS, Smith M, Gongidi P, Jacobson A. Positive and negative regulation of poly(A) nuclease. Mol Cell Biol. 2004 Jun;24(12):5521-33. PMID:15169912 doi:http://dx.doi.org/10.1128/MCB.24.12.5521-5533.2004
↑ Dunn EF, Hammell CM, Hodge CA, Cole CN. Yeast poly(A)-binding protein, Pab1, and PAN, a poly(A) nuclease complex recruited by Pab1, connect mRNA biogenesis to export. Genes Dev. 2005 Jan 1;19(1):90-103. PMID:15630021 doi:http://dx.doi.org/19/1/90
↑ Brune C, Munchel SE, Fischer N, Podtelejnikov AV, Weis K. Yeast poly(A)-binding protein Pab1 shuttles between the nucleus and the cytoplasm and functions in mRNA export. RNA. 2005 Apr;11(4):517-31. PMID:15769879 doi:http://dx.doi.org/11/4/517
↑ Kozlov G, Siddiqui N, Coillet-Matillon S, Trempe JF, Ekiel I, Sprules T, Gehring K. Solution structure of the orphan PABC domain from Saccharomyces cerevisiae poly(A)-binding protein. J Biol Chem. 2002 Jun 21;277(25):22822-8. Epub 2002 Apr 8. PMID:11940585 doi:10.1074/jbc.M201230200

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1ifw"

@@ Line 1: / Line 1: @@
 ==SOLUTION STRUCTURE OF C-TERMINAL DOMAIN OF POLY(A) BINDING PROTEIN FROM SACCHAROMYCES CEREVISIAE==
 <StructureSection load='1ifw' size='340' side='right' caption='[[1ifw]], [[NMR_Ensembles_of_Models | 30 NMR models]]' scene=''>
@@ Line 4: / Line 5: @@
 <table><tr><td colspan='2'>[[1ifw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IFW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IFW FirstGlance]. <br>
 </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PAB1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ifw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ifw OCA], [http://pdbe.org/1ifw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ifw RCSB], [http://www.ebi.ac.uk/pdbsum/1ifw PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ifw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ifw OCA], [http://pdbe.org/1ifw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ifw RCSB], [http://www.ebi.ac.uk/pdbsum/1ifw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ifw ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 12: / Line 13: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/if/1ifw_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/if/1ifw_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

1ifw

From Proteopedia

Revision as of 08:54, 10 January 2018

SOLUTION STRUCTURE OF C-TERMINAL DOMAIN OF POLY(A) BINDING PROTEIN FROM SACCHAROMYCES CEREVISIAE

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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