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(-) Description

Title :  STRUCTURE OF YEAST CPSF-100 (YDH1P)
 
Authors :  C. R. Mandel, H. Zhang, D. Gebauer, L. Tong
Date :  31 Aug 06  (Deposition) - 30 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Polyadenylation, Metallo-B-Lactamase, Pre-Mrna Processing, Artemis, V(D)J Recombination, Double-Strand Break Repair, Rna Binding Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. R. Mandel, S. Kaneko, H. Zhang, D. Gebauer, V. Vethantham, J. L. Manley, L. Tong
Polyadenylation Factor Cpsf-73 Is The Pre-Mrna 3'-End-Processing Endonuclease.
Nature V. 444 953 2006
PubMed-ID: 17128255  |  Reference-DOI: 10.1038/NATURE05363
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN CFT2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CFT2, YDH1
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: CLEAVAGE FACTOR TWO PROTEIN 2, 105 KDA PROTEIN ASSOCIATED WITH POLYADENYLATION FACTOR I

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2I7X)

(-) Sites  (0, 0)

(no "Site" information available for 2I7X)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2I7X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2I7X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2I7X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2I7X)

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YLR115W1YLR115W.1XII:377986-3805652580CFT2_YEAST1-8598591A:1-717 (gaps)717

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:499
 aligned with CFT2_YEAST | Q12102 from UniProtKB/Swiss-Prot  Length:859

    Alignment length:717
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       
           CFT2_YEAST     1 MTYKYNCCDDGSGTTVGSVVRFDNVTLLIDPGWNPSKVSYEQCIKYWEKVIPEIDVIILSQPTIECLGAHSLLYYNFTSHFISRIQVYATLPVINLGRVSTIDSYASAGVIGPYDTNKLDLEDIEISFDHIVPLKYSQLVDLRSRYDGLTLLAYNAGVCPGGSIWCISTYSEKLVYAKRWNHTRDNILNAASILDATGKPLSTLMRPSAIITTLDRFGSSQPFKKRSKIFKDTLKKGLSSDGSVIIPVDMSGKFLDLFTQVHELLFESTKINAHTQVPVLILSYARGRTLTYAKSMLEWLSPSLLKTWENRNNTSPFEIGSRIKIIAPNELSKYPGSKICFVSEVGALINEVIIKVGNSEKTTLILTKPSFECASSLDKILEIVEQDERNWKTFPEDGKSFLCDNYISIDTIKEEPLSKEETEAFKVQLKEKKRDRNKKILLVKRESKKLANGNAIIDDTNGERAMRNQDILVENVNGVPPIDHIMGGDEDDDEEEENDNLLNLLKDNSEKSAAKKNTEVPVDIIIQPSAASKHKMFPFNPAKIKKDDYGTVVDFTMFLPDDSDNVNQNSRKRPLKDGAKTTSPVNEEDNKNEEEDGYNMSDPISKRSKHRASRYSGFSGTGEAENFDNLDYLKIDKTLSKRTISTVNVQLKCSVVILNLQSLVDQRSASIIWPSLKSRKIVLSAPKQIQNEEITAKLIKKNIEVVNMPLNKIVEFS 717
               SCOP domains d2i7xa1 A:1-422,A:626-717 Cleavage factor two protein 2, CFT2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    d2i7xa1 A:1-422,A:626-717 Cleavage factor two protein 2, CFT2                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..........eeeee..eeeee.........hhhhhhhhhhhhhhhh.eee....hhhhhhhhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh.eee.....eee......eeeeeee.......eeeeee....eeeee...............................eeee.........hhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhhhhhh..-------...eeee....hhhhhhhhhhhhhhhhhhhhhhhh............eee.hhhhhhhh...eeeeee.hhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhh..--------....ee..eeeeeeeeeeee......-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------....hhhhh.....eeeeeeeeeeee..eeee.......hhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhh..eeee......eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-717 (gaps) UniProt: 1-859 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Transcript 1
                 2i7x A   1 MTYKYNCCDDGSGTTVGSVVRFDNVTLLIDPGWNPSKVSYEQCIKYWEKVIPEIDVIILSQPTIECLGAHSLLYYNFTSHFISRIQVYATLPVINLGRVSTIDSYASAGVIGPYDTNKLDLEDIEISFDHIVPLKYSQLVDLRSRYDGLTLLAYNAGVCPGGSIWCISTYSEKLVYAKRWNHTRDNILNAASILDATGKPLSTLMRPSAIITTLDRFGSSQPFKKRSKIFKDTLKKGLSSDGSVIIPVDMSGKFLDLFTQVHELLFES-------QVPVLILSYARGRTLTYAKSMLEWLSPSLLKTWENRNNTSPFEIGSRIKIIAPNELSKYPGSKICFVSEVGALINEVIIKVGNSEKTTLILTKPSFECASSLDKILEIVEQDE--------DGKSFLCDNYISIDTIKEEPLSKEET-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NFDNLDYLKIDKTLSKRTISTVNVQLKCSVVILNLQSLVDQRSASIIWPSLKSRKIVLSAPKQIQNEEITAKLIKKNIEVVNMPLNKIVEFS 717
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       | -     | 280       290       300       310       320       330       340       350       360       370       380       | -      |400       410       420 |       -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -     | 630       640       650       660       670       680       690       700       710       
                                                                                                                                                                                                                                                                                                     268     276                                                                                                             388      397                      422                                                                                                                                                                                                         626
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2I7X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I7X)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CFT2_YEAST | Q12102)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
biological process
    GO:0006379    mRNA cleavage    Any process in which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner.
    GO:0006378    mRNA polyadenylation    The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0098789    pre-mRNA cleavage required for polyadenylation    The targeted, endonucleolytic cleavage of a pre-mRNA, required for polyadenylation of the 3' end. This cleavage is directed by binding sites near the 3' end of the mRNA and leaves a 3' hydoxyl end which then becomes a target for adenylation.
cellular component
    GO:0005847    mRNA cleavage and polyadenylation specificity factor complex    A multisubunit complex that binds to the canonical AAUAAA hexamer and to U-rich upstream sequence elements on the pre-mRNA, thereby stimulating the otherwise weakly active and nonspecific polymerase to elongate efficiently RNAs containing a poly(A) signal.
    GO:0005849    mRNA cleavage factor complex    Any macromolecular complex involved in cleavage or polyadenylation of mRNA molecules.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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2i7t 2i7v