2npi

From Proteopedia

(Difference between revisions)

Revision as of 18:13, 24 December 2014

Clp1-ATP-Pcf11 complex

Structural highlights

2npi is a 4 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
NonStd Res:
Gene:	CLP1 (Saccharomyces cerevisiae), PCF11 (Saccharomyces cerevisiae)
Resources:	FirstGlance, OCA, RCSB, PDBsum

Function

[CLP1_YEAST] Component of the cleavage factor IA (CFIA) complex, which is involved in the endonucleolytic cleavage during polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with the cleavage factor NAB4/CFIB and the cleavage and polyadenylation factor (CPF) complex.^[1] [PCF11_YEAST] Component of the cleavage factor IA (CFIA) complex, which is involved in the endonucleolytic cleavage during polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with cleavage factor NAB4/CFIB and the cleavage and polyadenylation factor (CPF) complex. Independently involved in RNA polymerase II transcript termination. Binds RNA. Seems to bridge RNA polymerase II and the native transcript and may be involved in dismantling the RNA polymerase II elongation complex.^[2] ^[3]

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

Pcf11 and Clp1 are subunits of cleavage factor IA (CFIA), an essential polyadenylation factor in Saccahromyces cerevisiae. We have determined the structure of a ternary complex of Clp1 together with ATP and the Clp1-binding region of Pcf11. Clp1 contains three domains, a small N-terminal beta sandwich domain, a C-terminal domain containing a novel alpha/beta-fold and a central domain that binds ATP. The arrangement of the nucleotide binding site is similar to that observed in SIMIBI-class ATPase subunits found in other multisubunit macromolecular complexes. However, despite this similarity, nucleotide hydrolysis does not occur. The Pcf11 binding site is also located in the central domain where three highly conserved residues in Pcf11 mediate many of the protein-protein interactions. We propose that this conserved Clp1-Pcf11 interaction is responsible for maintaining a tight coupling between the Clp1 nucleotide binding subunit and the other components of the polyadenylation machinery. Moreover, we suggest that this complex represents a stabilized ATP bound form of Clp1 that requires the participation of other non-CFIA processing factors in order to initiate timely ATP hydrolysis during 3' end processing.

Structure of a nucleotide-bound Clp1-Pcf11 polyadenylation factor.,Noble CG, Beuth B, Taylor IA Nucleic Acids Res. 2007;35(1):87-99. Epub 2006 Dec 6. PMID:17151076^[4]

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

References

↑ Gross S, Moore C. Five subunits are required for reconstitution of the cleavage and polyadenylation activities of Saccharomyces cerevisiae cleavage factor I. Proc Natl Acad Sci U S A. 2001 May 22;98(11):6080-5. Epub 2001 May 8. PMID:11344258 doi:http://dx.doi.org/10.1073/pnas.101046598
↑ Gross S, Moore C. Five subunits are required for reconstitution of the cleavage and polyadenylation activities of Saccharomyces cerevisiae cleavage factor I. Proc Natl Acad Sci U S A. 2001 May 22;98(11):6080-5. Epub 2001 May 8. PMID:11344258 doi:http://dx.doi.org/10.1073/pnas.101046598
↑ Zhang Z, Fu J, Gilmour DS. CTD-dependent dismantling of the RNA polymerase II elongation complex by the pre-mRNA 3'-end processing factor, Pcf11. Genes Dev. 2005 Jul 1;19(13):1572-80. PMID:15998810 doi:http://dx.doi.org/19/13/1572
↑ Noble CG, Beuth B, Taylor IA. Structure of a nucleotide-bound Clp1-Pcf11 polyadenylation factor. Nucleic Acids Res. 2007;35(1):87-99. Epub 2006 Dec 6. PMID:17151076 doi:10.1093/nar/gkl1010

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/2npi"

@@ Line 3: / Line 3: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[2npi]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NPI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NPI FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CLP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), PCF11 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CLP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), PCF11 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2npi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2npi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2npi RCSB], [http://www.ebi.ac.uk/pdbsum/2npi 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=2npi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2npi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2npi RCSB], [http://www.ebi.ac.uk/pdbsum/2npi PDBsum]</span></td></tr>
-<table>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/CLP1_YEAST CLP1_YEAST]] Component of the cleavage factor IA (CFIA) complex, which is involved in the endonucleolytic cleavage during polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with the cleavage factor NAB4/CFIB and the cleavage and polyadenylation factor (CPF) complex.<ref>PMID:11344258</ref>  [[http://www.uniprot.org/uniprot/PCF11_YEAST PCF11_YEAST]] Component of the cleavage factor IA (CFIA) complex, which is involved in the endonucleolytic cleavage during polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with cleavage factor NAB4/CFIB and the cleavage and polyadenylation factor (CPF) complex. Independently involved in RNA polymerase II transcript termination. Binds RNA. Seems to bridge RNA polymerase II and the native transcript and may be involved in dismantling the RNA polymerase II elongation complex.<ref>PMID:11344258</ref> <ref>PMID:15998810</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 31: / Line 33: @@
 </StructureSection>
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Beuth, B.]]
+[[Category: Beuth, B]]
-[[Category: Noble, C G.]]
+[[Category: Noble, C G]]
-[[Category: Taylor, I A.]]
+[[Category: Taylor, I A]]
 [[Category: Atp binding]]
 [[Category: Clp1-pcf11 complex]]
 [[Category: Ternary complex]]
 [[Category: Transcription]]

2npi

From Proteopedia

Revision as of 18:13, 24 December 2014

Clp1-ATP-Pcf11 complex

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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