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PDBsum entry 2i7t

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protein ligands metals links
Hydrolase, RNA binding protein PDB id
2i7t
Jmol
Contents
Protein chain
404 a.a. *
Ligands
SO4
Metals
_ZN ×2
Waters ×161
* Residue conservation analysis
PDB id:
2i7t
Name: Hydrolase, RNA binding protein
Title: Structure of human cpsf-73
Structure: Cleavage and polyadenylation specificity factor 73 kda subunit. Chain: a. Synonym: cpsf 73 kda subunit. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: cpsf3, cpsf73. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.10Å     R-factor:   0.231     R-free:   0.276
Authors: C.R.Mandel,H.Zhang,L.Tong
Key ref:
C.R.Mandel et al. (2006). Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease. Nature, 444, 953-956. PubMed id: 17128255 DOI: 10.1038/nature05363
Date:
31-Aug-06     Release date:   30-Jan-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9UKF6  (CPSF3_HUMAN) -  Cleavage and polyadenylation specificity factor subunit 3
Seq:
Struc:
 
Seq:
Struc:
684 a.a.
404 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1038/nature05363 Nature 444:953-956 (2006)
PubMed id: 17128255  
 
 
Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease.
C.R.Mandel, S.Kaneko, H.Zhang, D.Gebauer, V.Vethantham, J.L.Manley, L.Tong.
 
  ABSTRACT  
 
Most eukaryotic messenger RNA precursors (pre-mRNAs) undergo extensive maturational processing, including cleavage and polyadenylation at the 3'-end. Despite the characterization of many proteins that are required for the cleavage reaction, the identity of the endonuclease is not known. Recent analyses indicated that the 73-kDa subunit of cleavage and polyadenylation specificity factor (CPSF-73) might be the endonuclease for this and related reactions, although no direct data confirmed this. Here we report the crystal structures of human CPSF-73 at 2.1 A resolution, complexed with zinc ions and a sulphate that might mimic the phosphate group of the substrate, and the related yeast protein CPSF-100 (Ydh1) at 2.5 A resolution. Both CPSF-73 and CPSF-100 contain two domains, a metallo-beta-lactamase domain and a novel beta-CASP (named for metallo-beta-lactamase, CPSF, Artemis, Snm1, Pso2) domain. The active site of CPSF-73, with two zinc ions, is located at the interface of the two domains. Purified recombinant CPSF-73 possesses RNA endonuclease activity, and mutations that disrupt zinc binding in the active site abolish this activity. Our studies provide the first direct experimental evidence that CPSF-73 is the pre-mRNA 3'-end-processing endonuclease.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: Structures of human CPSF-73 and yeast CPSF-100 (Ydh1). a, Schematic representation of the structure of human CPSF-73. The -strands and -helices are labelled, and the two zinc atoms in the active site are shown as grey spheres. The sulphate ion is shown as a stick model. b, Schematic representation of the structure of yeast CPSF-100. The zinc atoms in the CPSF-73 structure are shown for reference. See Supplementary Fig. 2 For Schematic drawings of the metallo- -lactamase domains of the two proteins.
Figure 2.
Figure 2: The beta--CASP domain of CPSF-73 and CPSF-100. Schematic drawings of the -CASP domains of human CPSF-73 (a) and yeast CPSF-100 (b).
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2006, 444, 953-956) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22781900 C.Adrain, and M.Freeman (2012).
New lives for old: evolution of pseudoenzyme function illustrated by iRhoms.
  Nat Rev Mol Cell Biol, 13, 489-498.  
21397179 B.R.Graveley (2011).
Getting in the loop: new insights into the mechanism of poly(A) site recognition.
  Structure, 19, 279-281.  
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
20007330 J.E.Wilusz, and D.L.Spector (2010).
An unexpected ending: noncanonical 3' end processing mechanisms.
  RNA, 16, 259-266.  
21102410 R.S.Laishram, and R.A.Anderson (2010).
The poly A polymerase Star-PAP controls 3'-end cleavage by promoting CPSF interaction and specificity toward the pre-mRNA.
  EMBO J, 29, 4132-4145.  
20675404 R.Tomecki, and A.Dziembowski (2010).
Novel endoribonucleases as central players in various pathways of eukaryotic RNA metabolism.
  RNA, 16, 1692-1724.  
20695905 S.Kim, J.Yamamoto, Y.Chen, M.Aida, T.Wada, H.Handa, and Y.Yamaguchi (2010).
Evidence that cleavage factor Im is a heterotetrameric protein complex controlling alternative polyadenylation.
  Genes Cells, 15, 1003-1013.  
20044349 S.Millevoi, and S.Vagner (2010).
Molecular mechanisms of eukaryotic pre-mRNA 3' end processing regulation.
  Nucleic Acids Res, 38, 2757-2774.  
21157480 W.F.Marzluff (2010).
More than one way to make a tail.
  EMBO J, 29, 4066-4067.  
20544974 Y.Nishida, H.Ishikawa, S.Baba, N.Nakagawa, S.Kuramitsu, and R.Masui (2010).
Crystal structure of an archaeal cleavage and polyadenylation specificity factor subunit from Pyrococcus horikoshii.
  Proteins, 78, 2395-2398.
PDB codes: 3af5 3af6
19636588 D.Xing, S.Ni, M.A.Kennedy, and Q.Q.Li (2009).
Identification of a plant-specific Zn2+-sensitive ribonuclease activity.
  Planta, 230, 819-825.  
19224921 H.Kiefer, A.Mizutani, S.Iemura, T.Natsume, H.Ando, Y.Kuroda, and K.Mikoshiba (2009).
Inositol 1,4,5-Triphosphate Receptor-binding Protein Released with Inositol 1,4,5-Triphosphate (IRBIT) Associates with Components of the mRNA 3' Processing Machinery in a Phosphorylation-dependent Manner and Inhibits Polyadenylation.
  J Biol Chem, 284, 10694-10705.  
19450530 K.D.Sullivan, M.Steiniger, and W.F.Marzluff (2009).
A core complex of CPSF73, CPSF100, and Symplekin may form two different cleavage factors for processing of poly(A) and histone mRNAs.
  Mol Cell, 34, 322-332.  
19155323 K.Ryan, A.Khleborodova, J.Pan, and X.P.Ryan (2009).
Small molecule activators of pre-mRNA 3' cleavage.
  RNA, 15, 483-492.  
19351879 L.Levinger, A.Hopkinson, R.Desetty, and C.Wilson (2009).
Effect of changes in the flexible arm on tRNase Z processing kinetics.
  J Biol Chem, 284, 15685-15691.  
19223444 M.A.Ditzler, J.Sponer, and N.G.Walter (2009).
Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme.
  RNA, 15, 560-575.  
19188448 M.A.Ghazy, X.He, B.N.Singh, M.Hampsey, and C.Moore (2009).
The essential N terminus of the Pta1 scaffold protein is required for snoRNA transcription termination and Ssu72 function but is dispensable for pre-mRNA 3'-end processing.
  Mol Cell Biol, 29, 2296-2307.  
19239889 M.J.Moore, and N.J.Proudfoot (2009).
Pre-mRNA processing reaches back to transcription and ahead to translation.
  Cell, 136, 688-700.  
19136632 O.Rozenblatt-Rosen, T.Nagaike, J.M.Francis, S.Kaneko, K.A.Glatt, C.M.Hughes, T.Laframboise, J.L.Manley, and M.Meyerson (2009).
The tumor suppressor Cdc73 functionally associates with CPSF and CstF 3' mRNA processing factors.
  Proc Natl Acad Sci U S A, 106, 755-760.  
19487567 P.Richard, and J.L.Manley (2009).
Transcription termination by nuclear RNA polymerases.
  Genes Dev, 23, 1247-1269.  
19273129 R.Jia, and Z.M.Zheng (2009).
Regulation of bovine papillomavirus type 1 gene expression by RNA processing.
  Front Biosci, 14, 1270-1282.  
19576221 S.A.Kennedy, M.L.Frazier, M.Steiniger, A.M.Mast, W.F.Marzluff, and M.R.Redinbo (2009).
Crystal structure of the HEAT domain from the Pre-mRNA processing factor Symplekin.
  J Mol Biol, 392, 115-128.
PDB code: 3gs3
19509282 U.Kühn, M.Gündel, A.Knoth, Y.Kerwitz, S.Rüdel, and E.Wahle (2009).
Poly(A) tail length is controlled by the nuclear poly(A)-binding protein regulating the interaction between poly(A) polymerase and the cleavage and polyadenylation specificity factor.
  J Biol Chem, 284, 22803-22814.  
19854135 X.C.Yang, B.D.Burch, Y.Yan, W.F.Marzluff, and Z.Dominski (2009).
FLASH, a proapoptotic protein involved in activation of caspase-8, is essential for 3' end processing of histone pre-mRNAs.
  Mol Cell, 36, 267-278.  
18955505 X.C.Yang, K.D.Sullivan, W.F.Marzluff, and Z.Dominski (2009).
Studies of the 5' exonuclease and endonuclease activities of CPSF-73 in histone pre-mRNA processing.
  Mol Cell Biol, 29, 31-42.  
19470752 X.C.Yang, M.P.Torres, W.F.Marzluff, and Z.Dominski (2009).
Three proteins of the U7-specific Sm ring function as the molecular ruler to determine the site of 3'-end processing in mammalian histone pre-mRNA.
  Mol Cell Biol, 29, 4045-4056.  
19217410 Y.Shi, D.C.Di Giammartino, D.Taylor, A.Sarkeshik, W.J.Rice, J.R.Yates, J.Frank, and J.L.Manley (2009).
Molecular architecture of the human pre-mRNA 3' processing complex.
  Mol Cell, 33, 365-376.  
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.  
18288197 D.L.Mellman, M.L.Gonzales, C.Song, C.A.Barlow, P.Wang, C.Kendziorski, and R.A.Anderson (2008).
A PtdIns4,5P2-regulated nuclear poly(A) polymerase controls expression of select mRNAs.
  Nature, 451, 1013-1017.  
18537269 G.Meinke, C.Ezeokonkwo, P.Balbo, W.Stafford, C.Moore, and A.Bohm (2008).
Structure of yeast poly(A) polymerase in complex with a peptide from Fip1, an intrinsically disordered protein.
  Biochemistry, 47, 6859-6869.
PDB code: 3c66
18316045 H.E.Radford, H.A.Meijer, and C.H.de Moor (2008).
Translational control by cytoplasmic polyadenylation in Xenopus oocytes.
  Biochim Biophys Acta, 1779, 217-229.  
18204464 I.L.de la Sierra-Gallay, L.Zig, A.Jamalli, and H.Putzer (2008).
Structural insights into the dual activity of RNase J.
  Nat Struct Mol Biol, 15, 206-212.
PDB codes: 3bk1 3bk2
18545667 J.Zhang, B.Addepalli, K.Y.Yun, A.G.Hunt, R.Xu, S.Rao, Q.Q.Li, and D.L.Falcone (2008).
A polyadenylation factor subunit implicated in regulating oxidative signaling in Arabidopsis thaliana.
  PLoS ONE, 3, e2410.  
18157150 K.Glover-Cutter, S.Kim, J.Espinosa, and D.L.Bentley (2008).
RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes.
  Nat Struct Mol Biol, 15, 71-78.  
18468939 K.Ryan, and D.L.Bauer (2008).
Finishing touches: post-translational modification of protein factors involved in mammalian pre-mRNA 3' end formation.
  Int J Biochem Cell Biol, 40, 2384-2396.  
18767156 L.Trésaugues, P.Stenmark, H.Schüler, S.Flodin, M.Welin, T.Nyman, M.Hammarström, M.Moche, S.Gräslund, and P.Nordlund (2008).
The crystal structure of human cleavage and polyadenylation specific factor-5 reveals a dimeric Nudix protein with a conserved catalytic site.
  Proteins, 73, 1047-1052.
PDB codes: 2cl3 2j8q
18971324 M.Garas, B.Dichtl, and W.Keller (2008).
The role of the putative 3' end processing endonuclease Ysh1p in mRNA and snoRNA synthesis.
  RNA, 14, 2671-2684.  
18753150 N.G.Kolev, E.I.Hartland, and P.W.Huber (2008).
A manganese-dependent ribozyme in the 3'-untranslated region of Xenopus Vg1 mRNA.
  Nucleic Acids Res, 36, 5530-5539.  
18688255 N.G.Kolev, T.A.Yario, E.Benson, and J.A.Steitz (2008).
Conserved motifs in both CPSF73 and CPSF100 are required to assemble the active endonuclease for histone mRNA 3'-end maturation.
  EMBO Rep, 9, 1013-1018.  
18304944 N.Viphakone, F.Voisinet-Hakil, and L.Minvielle-Sebastia (2008).
Molecular dissection of mRNA poly(A) tail length control in yeast.
  Nucleic Acids Res, 36, 2418-2433.  
18563245 P.Nicholson, and B.Müller (2008).
Post-transcriptional control of animal histone gene expression--not so different after all...
  Mol Biosyst, 4, 721-725.  
18256699 S.Danckwardt, M.W.Hentze, and A.E.Kulozik (2008).
3' end mRNA processing: molecular mechanisms and implications for health and disease.
  EMBO J, 27, 482-498.  
18378697 T.Pavelitz, A.D.Bailey, C.P.Elco, and A.M.Weiner (2008).
Human U2 snRNA genes exhibit a persistently open transcriptional state and promoter disassembly at metaphase.
  Mol Cell Biol, 28, 3573-3588.  
18927579 W.F.Marzluff, E.J.Wagner, and R.J.Duronio (2008).
Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail.
  Nat Rev Genet, 9, 843-854.  
17572685 A.Nag, K.Narsinh, and H.G.Martinson (2007).
The poly(A)-dependent transcriptional pause is mediated by CPSF acting on the body of the polymerase.
  Nat Struct Mol Biol, 14, 662-669.  
17576667 B.Addepalli, and A.G.Hunt (2007).
A novel endonuclease activity associated with the Arabidopsis ortholog of the 30-kDa subunit of cleavage and polyadenylation specificity factor.
  Nucleic Acids Res, 35, 4453-4463.  
17481902 J.D.Richter (2007).
CPEB: a life in translation.
  Trends Biochem Sci, 32, 279-285.  
17964263 K.Friend, A.F.Lovejoy, and J.A.Steitz (2007).
U2 snRNP binds intronless histone pre-mRNAs to facilitate U7-snRNP-dependent 3' end formation.
  Mol Cell, 28, 240-252.  
18158891 N.G.Walter (2007).
Ribozyme catalysis revisited: is water involved?
  Mol Cell, 28, 923-929.  
17850751 P.B.Balbo, and A.Bohm (2007).
Mechanism of poly(A) polymerase: structure of the enzyme-MgATP-RNA ternary complex and kinetic analysis.
  Structure, 15, 1117-1131.
PDB code: 2q66
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
18066091 P.Soulas-Sprauel, P.Rivera-Munoz, L.Malivert, G.Le Guyader, V.Abramowski, P.Revy, and J.P.de Villartay (2007).
V(D)J and immunoglobulin class switch recombinations: a paradigm to study the regulation of DNA end-joining.
  Oncogene, 26, 7780-7791.  
17570845 R.Keall, S.Whitelaw, J.Pettitt, and B.Müller (2007).
Histone gene expression and histone mRNA 3' end structure in Caenorhabditis elegans.
  BMC Mol Biol, 8, 51.  
17464285 S.Danckwardt, I.Kaufmann, M.Gentzel, K.U.Foerstner, A.S.Gantzert, N.H.Gehring, G.Neu-Yilik, P.Bork, W.Keller, M.Wilm, M.W.Hentze, and A.E.Kulozik (2007).
Splicing factors stimulate polyadenylation via USEs at non-canonical 3' end formation signals.
  EMBO J, 26, 2658-2669.  
17655328 S.Karkashon, A.Hopkinson, and L.Levinger (2007).
tRNase Z catalysis and conserved residues on the carboxy side of the His cluster.
  Biochemistry, 46, 9380-9387.  
17923699 V.Vethantham, N.Rao, and J.L.Manley (2007).
Sumoylation modulates the assembly and activity of the pre-mRNA 3' processing complex.
  Mol Cell Biol, 27, 8848-8858.  
17996698 W.F.Marzluff (2007).
U2 snRNP: not just for poly(A) mRNAs.
  Mol Cell, 28, 353-354.  
17386263 Y.Bai, T.C.Auperin, C.Y.Chou, G.G.Chang, J.L.Manley, and L.Tong (2007).
Crystal structure of murine CstF-77: dimeric association and implications for polyadenylation of mRNA precursors.
  Mol Cell, 25, 863-875.
PDB codes: 2ond 2ooe
  17277459 Y.Bai, T.C.Auperin, and L.Tong (2007).
The use of in situ proteolysis in the crystallization of murine CstF-77.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 135-138.  
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.