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(-) Description

Title :  EXTENDED INTERFACE BETWEEN PCF11P AND CLP1P AND STRUCTURAL BASIS FOR ATP LOSS IN GLY135ARG POINT MUTANT
 
Authors :  A. F. Dupin, S. Fribourg
Date :  02 Aug 13  (Deposition) - 19 Feb 14  (Release) - 30 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  B,D  (1x)
Biol. Unit 2:  A,C  (1x)
Keywords :  Transcription, 3' End Mrna Processing, Mutant (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. F. Dupin, S. Fribourg
Structural Basis For Atp Loss By Clp1P In A G135R Mutant Protein.
Biochmie V. 101 203 2014
PubMed-ID: 24508575  |  Reference-DOI: 10.1016/J.BIOCHI.2014.01.017

(-) Compounds

Molecule 1 - MRNA CLEAVAGE AND POLYADENYLATION FACTOR CLP1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: CLP1P
 
Molecule 2 - PCF11P
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: RESIDUES 454-563
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x):  B D
Biological Unit 2 (1x): A C 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4C0H)

(-) Sites  (0, 0)

(no "Site" information available for 4C0H)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C0H)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn C:465 -Ser C:466

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C0H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C0H)

(-) Exons   (2, 4)

Asymmetric Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR228C1YDR228C.1IV:923803-9219231881PCF11_YEAST1-6266262C:464-499 (gaps)
D:462-499 (gaps)		36
38
2.1YOR250C1YOR250C.1XV:802308-8009711338CLP1_YEAST1-4454452A:19-445 (gaps)
B:19-445		427
427

(-) Sequences/Alignments

Asymmetric 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:422
 aligned with CLP1_YEAST | Q08685 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:427
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       
           CLP1_YEAST    19 GDNEWHKLVIPKGSDWQIDLKAEGKLIVKVNSGIVEIFGTELAVDDEYTFQNWKFPIYAVEETELLWKCPDLTTNTITVKPNHTMKYIYNLHFMLEKIRMSNFEGPRVVIVGGSQTGKTSLSRTLCSYALKFNAYQPLYINLDPQQPIFTVPGCISATPISDILDAQLPTWGQSLTSGATLLHNKQPMVKNFGLERINENKDLYLECISQLGQVVGQRLHLDPQVRRSGCIVDTPSISQLDENLAELHHIIEKLNVNIMLVLCSETDPLWEKVKKTFGPELGNNNIFFIPKLDGVSAVDDVYKRSLQRTSIREYFYGSLDTALSPYAIGVDYEDLTIWKPSNVFDNEVGRVELFPVTITPSNLQHAIIAITFAERRADQATVIKSPILGFALITEVNEKRRKLRVLLPVPGRLPSKAMILTSYRYLE 445
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...eeeeee.....eeeeeeee..eee..ee.....eeeee..eeeeee...eeeeee.........eeee..hhhhhhhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhhh.....eeee............eeeeee............................eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeee..hhhhh...hhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh...eeee...-----.hhhhhhhhhhhhhhhhhhee..ee...eeeeee.hhh.eeee............eee...hhhhhh.eeeeee......hhhhhhhh.eeeeeeeeeee....eeeeee..........eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: A:19-445 (gaps) UniProt: 1-445 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                  Transcript 2
                 4c0h A  19 GDNEWHKLVIPKGSDWQIDLKAEGKLIVKVNSGIVEIFGTELAVDDEYTFQNWKFPIYAVEETELLWKCPDLTTNTITVKPNHTMKYIYNLHFMLEKIRMSNFEGPRVVIVGGSQTRKTSLSRTLCSYALKFNAYQPLYINLDPQQPIFTVPGCISATPISDILDAQLPTWGQSLTSGATLLHNKQPMVKNFGLERINENKDLYLECISQLGQVVGQRLHLDPQVRRSGCIVDTPSISQLDENLAELHHIIEKLNVNIMLVLCSETDPLWEKVKKTFGPELGNNNIFFIPKL-----VDDVYKRSLQRTSIREYFYGSLDTALSPYAIGVDYEDLTIWKPSNVFDNEVGRVELFPVTITPSNLQHAIIAITFAERRADQATVIKSPILGFALITEVNEKRRKLRVLLPVPGRLPSKAMILTSYRYLE 445
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308 |     318       328       338       348       358       368       378       388       398       408       418       428       438       
                                                                                                                                                                                                                                                                                                                             310   316                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:427
 aligned with CLP1_YEAST | Q08685 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:427
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       
           CLP1_YEAST    19 GDNEWHKLVIPKGSDWQIDLKAEGKLIVKVNSGIVEIFGTELAVDDEYTFQNWKFPIYAVEETELLWKCPDLTTNTITVKPNHTMKYIYNLHFMLEKIRMSNFEGPRVVIVGGSQTGKTSLSRTLCSYALKFNAYQPLYINLDPQQPIFTVPGCISATPISDILDAQLPTWGQSLTSGATLLHNKQPMVKNFGLERINENKDLYLECISQLGQVVGQRLHLDPQVRRSGCIVDTPSISQLDENLAELHHIIEKLNVNIMLVLCSETDPLWEKVKKTFGPELGNNNIFFIPKLDGVSAVDDVYKRSLQRTSIREYFYGSLDTALSPYAIGVDYEDLTIWKPSNVFDNEVGRVELFPVTITPSNLQHAIIAITFAERRADQATVIKSPILGFALITEVNEKRRKLRVLLPVPGRLPSKAMILTSYRYLE 445
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...eeeeee.....eeeeeeee..eee..ee.....eeeee..eeeeee...eeeeee.........eeee..hhhhhhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhh...eeee............eeeeee............................eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhh...hhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhhhhee..ee...eeeeee.hhh.eeee.hhhhhh.....eee...hhhhhh.eeeeee......hhhhhhhh.eeeeeeeeeee....eeeeee..........eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: B:19-445 UniProt: 1-445 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                         Transcript 2
                 4c0h B  19 GDNEWHKLVIPKGSDWQIDLKAEGKLIVKVNSGIVEIFGTELAVDDEYTFQNWKFPIYAVEETELLWKCPDLTTNTITVKPNHTMKYIYNLHFMLEKIRMSNFEGPRVVIVGGSQTRKTSLSRTLCSYALKFNAYQPLYINLDPQQPIFTVPGCISATPISDILDAQLPTWGQSLTSGATLLHNKQPMVKNFGLERINENKDLYLECISQLGQVVGQRLHLDPQVRRSGCIVDTPSISQLDENLAELHHIIEKLNVNIMLVLCSETDPLWEKVKKTFGPELGNNNIFFIPKLDGVSAVDDVYKRSLQRTSIREYFYGSLDTALSPYAIGVDYEDLTIWKPSNVFDNEVGRVELFPVTITPSNLQHAIIAITFAERRADQATVIKSPILGFALITEVNEKRRKLRVLLPVPGRLPSKAMILTSYRYLE 445
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       


Chain C from PDB  Type:PROTEIN  Length:28
 aligned with N1P6M1_YEASC | N1P6M1 from UniProtKB/TrEMBL  Length:626

    Alignment length:36
                                   473       483       493      
         N1P6M1_YEASC   464 SNSNLNTTTTRKNIQSRNWYLSDSQWAAFKDDEITS 499
               SCOP domains ------------------------------------ SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author ....--------.........hhhhhhh.hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
                 Transcript ------------------------------------ Transcript
                 4c0h C 464 SNSN--------NIQSRNWYLSDSQWAAFKDDEITS 499
                               |     -  |    483       493      
                             467      476                       


Chain C from PDB  Type:PROTEIN  Length:28
 aligned with PCF11_YEAST | P39081 from UniProtKB/Swiss-Prot  Length:626

    Alignment length:36
                                   473       483       493      
          PCF11_YEAST   464 SNSNLNTTTTRKNIQSRNWYLSDSQWAAFKDDEITS 499
               SCOP domains ------------------------------------ SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author ....--------.........hhhhhhh.hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: C:464-499 (gaps)      Transcript 1
                 4c0h C 464 SNSN--------NIQSRNWYLSDSQWAAFKDDEITS 499
                               |     -  |    483       493      
                             467      476                       


Chain D from PDB  Type:PROTEIN  Length:33
 aligned with N1P6M1_YEASC | N1P6M1 from UniProtKB/TrEMBL  Length:626

    Alignment length:38
                                   471       481       491        
         N1P6M1_YEASC   462 GISNSNLNTTTTRKNIQSRNWYLSDSQWAAFKDDEITS 499
               SCOP domains -------------------------------------- SCOP domains
               CATH domains -------------------------------------- CATH domains
               Pfam domains -------------------------------------- Pfam domains
         Sec.struct. author ....ee..-----..........hhhhhhh.hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------- PROSITE
                 Transcript -------------------------------------- Transcript
                 4c0h D 462 GISNSNLN-----KNIQSRNWYLSDSQWAAFKDDEITS 499
                                   | -   |   481       491        
                                 469   475                        


Chain D from PDB  Type:PROTEIN  Length:33
 aligned with PCF11_YEAST | P39081 from UniProtKB/Swiss-Prot  Length:626

    Alignment length:38
                                   471       481       491        
          PCF11_YEAST   462 GISNSNLNTTTTRKNIQSRNWYLSDSQWAAFKDDEITS 499
               SCOP domains -------------------------------------- SCOP domains
               CATH domains -------------------------------------- CATH domains
               Pfam domains -------------------------------------- Pfam domains
         Sec.struct. author ....ee..-----..........hhhhhhh.hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:462-499 (gaps)        Transcript 1
                 4c0h D 462 GISNSNLN-----KNIQSRNWYLSDSQWAAFKDDEITS 499
                                   | -   |   481       491        
                                 469   475
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (0, 0)

(no "SCOP Domain" information available for 4C0H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C0H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C0H)

(-) Gene Ontology  (22, 33)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CLP1_YEAST | Q08685)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0051731    polynucleotide 5'-hydroxyl-kinase activity    Catalysis of the reaction: NTP + 5'-dephosphopolynucleotide = NDP + 5'-phosphopolynucleotide. The polynucleotide may be DNA or RNA.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0090202    gene looping    The formation and maintenance of DNA loops that juxtapose sequentially separated regions of RNA polymerase II-transcribed genes.
    GO:0031124    mRNA 3'-end processing    Any process involved in forming the mature 3' end of an mRNA molecule.
    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:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    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.
    GO:0006388    tRNA splicing, via endonucleolytic cleavage and ligation    Splicing of tRNA substrates via recognition of the folded RNA structure that brings the 5' and 3' splice sites into proximity and cleavage of the RNA at both the 3' and 5' splice sites by an endonucleolytic mechanism, followed by ligation of the exons.
cellular component
    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.

Chain C,D   (PCF11_YEAST | P39081)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0000993    RNA polymerase II core binding    Interacting selectively and non-covalently with RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits.
    GO:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006353    DNA-templated transcription, termination    The cellular process that completes DNA-templated transcription; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA.
    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.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006369    termination of RNA polymerase II transcription    The process in which the synthesis of an RNA molecule by RNA polymerase II using a DNA template is completed.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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.

Chain C,D   (N1P6M1_YEASC | N1P6M1)
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:0006369    termination of RNA polymerase II transcription    The process in which the synthesis of an RNA molecule by RNA polymerase II using a DNA template is completed.
cellular component
    GO:0005849    mRNA cleavage factor complex    Any macromolecular complex involved in cleavage or polyadenylation of mRNA molecules.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CLP1_YEAST | Q08685: 2npi 4c0b 4oi4
        N1P6M1_YEASC | N1P6M1: 4c0b
        PCF11_YEAST | P39081: 1sz9 1sza 2bf0 2nax 2npi 4c0b 4oi4

(-) Related Entries Specified in the PDB File

4c0b STRUCTURE OF WILD-TYPE CLP1P-PCF11P (454-563) COMPLEX