PDBsum entry 2bf0

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protein metals links
Transcription PDB id
Protein chain
131 a.a. *
Waters ×56
* Residue conservation analysis
PDB id:
Name: Transcription
Title: Crystal structure of the rpr of pcf11
Structure: Pcf11. Chain: x. Fragment: cid, residues 1-138. Engineered: yes
Source: Saccharomyces cerevisiae. Bakers yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 469008.
2.3Å     R-factor:   0.260     R-free:   0.282
Authors: C.G.Noble,D.Hollingworth,S.R.Martin,V.E.Adeniran, S.J.Smerdon,G.Kelly,I.A.Taylor,A.Ramos
Key ref:
C.G.Noble et al. (2005). Key features of the interaction between Pcf11 CID and RNA polymerase II CTD. Nat Struct Mol Biol, 12, 144-151. PubMed id: 15665873 DOI: 10.1038/nsmb887
02-Dec-04     Release date:   18-Jan-05    
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Protein chain
Pfam   ArchSchema ?
P39081  (PCF11_YEAST) -  Protein PCF11
626 a.a.
131 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain


DOI no: 10.1038/nsmb887 Nat Struct Mol Biol 12:144-151 (2005)
PubMed id: 15665873  
Key features of the interaction between Pcf11 CID and RNA polymerase II CTD.
C.G.Noble, D.Hollingworth, S.R.Martin, V.Ennis-Adeniran, S.J.Smerdon, G.Kelly, I.A.Taylor, A.Ramos.
The C-terminal domain (CTD) of the large subunit of RNA polymerase II is a platform for mRNA processing factors and links gene transcription to mRNA capping, splicing and polyadenylation. Pcf11, an essential component of the mRNA cleavage factor IA, contains a CTD-interaction domain that binds in a phospho-dependent manner to the heptad repeats within the RNA polymerase II CTD. We show here that the phosphorylated CTD exists as a dynamic disordered ensemble in solution and, by induced fit, it assumes a structured conformation when bound to Pcf11. In addition, we detected cis-trans populations for the CTD prolines, and found that only the all-trans form is selected for binding. These data suggest that the recognition of the CTD is regulated by independent site-specific modifications (phosphorylation and proline cis-trans isomerization) and, probably, by the local concentration of suitable binding sites.
  Selected figure(s)  
Figure 1.
Figure 1. Peptides used in this study. In the table (bottom) the first amino acid of each peptide has been aligned to the corresponding position within the first repeat (repeat a). The nomenclature used in the manuscript identifies (i) the amino acid type (ii) its number within the repeat, and (iii) the repeat it belongs to. Phosphorylated residues are indicated in red. A graphical representation of one heptad repeat is shown.
Figure 6.
Figure 6. Binding of Pcf11 CID to CTD-derived peptides. (a) 1H-decoupled 1D 31P NMR spectra of YSpPTSPS (top); (YSpPTSPS)[2] (middle); and (YSpPTSPS)[3] (bottom). The downfield peak in the spectrum can be assigned to the 31P resonance of Ser[2a] (S[2a]) as this peak does not change substantially in the three spectra. (b) 1H-decoupled 1D 31P NMR spectra recorded on (YSpPTSPS)[3], alone and with increasing concentration of Pcf11(1 -142) (ratios of 1:0, 1:1 and 1:3, top to bottom). The 31P resonances of Ser[2b] and Ser[2c] (S[2b] and S[2c]) broaden and shift upon protein binding, whereas Ser[2a] (S[2a]) is essentially identical in the free and bound form. (c) Chemical shift perturbation of Pcf11 CID upon binding to (YSpPTSPS)[2] (top) and (YSpPTSPS)[3] (bottom). The weighted chemical shift changes are plotted against the CID sequence. Well-dispersed resonances in the free protein spectrum that could not be assigned in the bound protein spectrum were given a weighted chemical shift change value of 0.5 as default.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2005, 12, 144-151) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20818393 B.M.Lunde, S.L.Reichow, M.Kim, H.Suh, T.C.Leeper, F.Yang, H.Mutschler, S.Buratowski, A.Meinhart, and G.Varani (2010).
Cooperative interaction of transcription termination factors with the RNA polymerase II C-terminal domain.
  Nat Struct Mol Biol, 17, 1195-1201.
PDB codes: 2km4 2l0i
21129186 N.Jouvet, J.Poschmann, J.Douville, L.Bulet, and D.Ramotar (2010).
Rrd1 isomerizes RNA polymerase II in response to rapamycin.
  BMC Mol Biol, 11, 92.  
19706593 D.A.Gell, L.Feng, S.Zhou, P.D.Jeffrey, K.Bendak, A.Gow, M.J.Weiss, Y.Shi, and J.P.Mackay (2009).
A cis-proline in alpha-hemoglobin stabilizing protein directs the structural reorganization of alpha-hemoglobin.
  J Biol Chem, 284, 29462-29469.
PDB code: 3ia3
19679665 M.Kim, H.Suh, E.J.Cho, and S.Buratowski (2009).
Phosphorylation of the yeast Rpb1 C-terminal domain at serines 2, 5, and 7.
  J Biol Chem, 284, 26421-26426.  
19332564 S.Krishnamurthy, M.A.Ghazy, C.Moore, and M.Hampsey (2009).
Functional interaction of the Ess1 prolyl isomerase with components of the RNA polymerase II initiation and termination machineries.
  Mol Cell Biol, 29, 2925-2934.  
18782776 A.K.Sharma, G.P.Zhou, J.Kupferman, H.K.Surks, E.N.Christensen, J.J.Chou, M.E.Mendelsohn, and A.C.Rigby (2008).
Probing the Interaction between the Coiled Coil Leucine Zipper of cGMP-dependent Protein Kinase I{alpha} and the C Terminus of the Myosin Binding Subunit of the Myosin Light Chain Phosphatase.
  J Biol Chem, 283, 32860-32869.  
18158581 C.R.Mandel, Y.Bai, and L.Tong (2008).
Protein factors in pre-mRNA 3'-end processing.
  Cell Mol Life Sci, 65, 1099-1122.  
18660819 L.Vasiljeva, M.Kim, H.Mutschler, S.Buratowski, and A.Meinhart (2008).
The Nrd1-Nab3-Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain.
  Nat Struct Mol Biol, 15, 795-804.
PDB code: 3clj
18550522 R.Becker, B.Loll, and A.Meinhart (2008).
Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the carboxyl-terminal domain of RNA polymerase II.
  J Biol Chem, 283, 22659-22669.
PDB codes: 3d9i 3d9j 3d9k 3d9l 3d9m 3d9n 3d9o 3d9p
17151076 C.G.Noble, B.Beuth, and I.A.Taylor (2007).
Structure of a nucleotide-bound Clp1-Pcf11 polyadenylation factor.
  Nucleic Acids Res, 35, 87-99.
PDB code: 2npi
17355257 I.Karbat, R.Kahn, L.Cohen, N.Ilan, N.Gilles, G.Corzo, O.Froy, M.Gur, G.Albrecht, S.H.Heinemann, D.Gordon, and M.Gurevitz (2007).
The unique pharmacology of the scorpion alpha-like toxin Lqh3 is associated with its flexible C-tail.
  FEBS J, 274, 1918-1931.  
17339332 M.Gullerova, A.Barta, and Z.J.Lorkovic (2007).
Rct1, a nuclear RNA recognition motif-containing cyclophilin, regulates phosphorylation of the RNA polymerase II C-terminal domain.
  Mol Cell Biol, 27, 3601-3611.  
17584787 P.Legrand, N.Pinaud, L.Minvielle-Sébastia, and S.Fribourg (2007).
The structure of the CstF-77 homodimer provides insights into CstF assembly.
  Nucleic Acids Res, 35, 4515-4522.
PDB code: 2uy1
16253993 A.Gasch, S.Wiesner, P.Martin-Malpartida, X.Ramirez-Espain, L.Ruiz, and M.J.Macias (2006).
The structure of Prp40 FF1 domain and its interaction with the crn-TPR1 motif of Clf1 gives a new insight into the binding mode of FF domains.
  J Biol Chem, 281, 356-364.
PDB code: 2b7e
16497660 D.Hollingworth, C.G.Noble, I.A.Taylor, and A.Ramos (2006).
RNA polymerase II CTD phosphopeptides compete with RNA for the interaction with Pcf11.
  RNA, 12, 555-560.  
15702066 C.D.Lima (2005).
Inducing interactions with the CTD.
  Nat Struct Mol Biol, 12, 102-103.  
15901493 D.L.Bentley (2005).
Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors.
  Curr Opin Cell Biol, 17, 251-256.  
16012166 D.P.Morris, G.A.Michelotti, and D.A.Schwinn (2005).
Evidence that phosphorylation of the RNA polymerase II carboxyl-terminal repeats is similar in yeast and humans.
  J Biol Chem, 280, 31368-31377.  
16314571 M.Li, H.P.Phatnani, Z.Guan, H.Sage, A.L.Greenleaf, and P.Zhou (2005).
Solution structure of the Set2-Rpb1 interacting domain of human Set2 and its interaction with the hyperphosphorylated C-terminal domain of Rpb1.
  Proc Natl Acad Sci U S A, 102, 17636-17641.
PDB code: 2a7o
16209948 S.Kaneko, and J.L.Manley (2005).
The mammalian RNA polymerase II C-terminal domain interacts with RNA to suppress transcription-coupled 3' end formation.
  Mol Cell, 20, 91.  
15998810 Z.Zhang, J.Fu, and D.S.Gilmour (2005).
CTD-dependent dismantling of the RNA polymerase II elongation complex by the pre-mRNA 3'-end processing factor, Pcf11.
  Genes Dev, 19, 1572-1580.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.