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(-) Description

Title :  CRYSTAL STRUCTURE OF DCP1P
 
Authors :  M. She, C. J. Decker, Y. Liu, N. Chen, R. Parker, H. Song
Date :  12 Aug 03  (Deposition) - 02 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta Sandwich, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. She, C. J. Decker, K. Sundramurthy, Y. Liu, N. Chen, R. Parker, H. Song
Crystal Structure Of Dcp1P And Its Functional Implications In Mrna Decapping
Nat. Struct. Mol. Biol. V. 11 249 2004
PubMed-ID: 14758354  |  Reference-DOI: 10.1038/NSMB730
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DECAPPING PROTEIN INVOLVED IN MRNA DEGRADATION- DCP1P
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneDCP1
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1Q67)

(-) Sites  (0, 0)

(no "Site" information available for 1Q67)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q67)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Q67)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q67)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q67)

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YOL149W1YOL149W.1XV:44937-45632696DCP1_YEAST1-2312312A:22-228 (gaps)
B:17-231 (gaps)
207
215

(-) 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:146
 aligned with DCP1_YEAST | Q12517 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:207
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       
           DCP1_YEAST    22 LNFNVIGRYDPKIKQLLFHTPHASLYKWDFKKDEWNKLEYQGVLAIYLRDVSQNTNLLPVSPQEVDIFDSQNGSNNIQVNNGSDNSNRNSSGNGNSYKSNDSLTYNCGKTLSGKDIYNYGLIILNRINPDNFSMGIVPNSVVNKRKVFNAEEDTLNPLECMGVEVKDELVIIKNLKHEVYGIWIHTVSDRQNIYELIKYLLENEPKD 228
               SCOP domains d1q67a_ A: Dcp1                                                                                                                                                                                                 SCOP domains
               CATH domains --1q67A01 A:24-224 Pleckstrin-homology domain (PH do                                                             main)/Phosphotyrosine-binding domain (PTB)                                                ---- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh..eeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeee...-------------------------------------------------------------.....eeeeeee.....eeeeee.hhhhhhhhhhhhhhhhhhh.....eeeee..eeeee.....eeeeee.hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:22-228 (gaps) UniProt: 1-231 [INCOMPLETE]                                                                                                                                                      Transcript 1
                 1q67 A  22 LNFNVIGRYDPKIKQLLFHTPHASLYKWDFKKDEWNKLEYQGVLAIYLRDVS-------------------------------------------------------------KDIYNYGLIILNRINPDNFSMGIVPNSVVNKRKVFNAEEDTLNPLECMGVEVKDELVIIKNLKHEVYGIWIHTVSDRQNIYELIKYLLENEPKD 228
                                    31        41        51        61        71 |       -         -         -         -         -         -   |   141       151       161       171       181       191       201       211       221       
                                                                              73                                                           135                                                                                             

Chain B from PDB  Type:PROTEIN  Length:161
 aligned with DCP1_YEAST | Q12517 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:215
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226     
           DCP1_YEAST    17 FYRKALNFNVIGRYDPKIKQLLFHTPHASLYKWDFKKDEWNKLEYQGVLAIYLRDVSQNTNLLPVSPQEVDIFDSQNGSNNIQVNNGSDNSNRNSSGNGNSYKSNDSLTYNCGKTLSGKDIYNYGLIILNRINPDNFSMGIVPNSVVNKRKVFNAEEDTLNPLECMGVEVKDELVIIKNLKHEVYGIWIHTVSDRQNIYELIKYLLENEPKDSFA 231
               SCOP domains d1q67b_ B: Dcp1                                                                                                                                                                                                         SCOP domains
               CATH domains -------1q67B01 B:24-224 Pleckstrin-homology domain (PH domain)/P                                                      hosphotyrosine-binding domain (PTB)                                                       ------- CATH domains
           Pfam domains (1) DCP1-1q67B01 B:17-80                                            ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) DCP1-1q67B02 B:17-80                                            ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .........hhhhh...eeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeee..........------------------------------------------------------.....eeeeeee.....eeeeee.hhhhhhhhhhhhhhhhhhh.....eeeee..eeeee.....eeeeee.hhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:17-231 (gaps) UniProt: 1-231 [INCOMPLETE]                                                                                                                                                              Transcript 1
                 1q67 B  17 FYRKALNFNVIGRYDPKIKQLLFHTPHASLYKWDFKKDEWNKLEYQGVLAIYLRDVSQNTNLLP------------------------------------------------------KDIYNYGLIILNRINPDNFSMGIVPNSVVNKRKVFNAEEDTLNPLECMGVEVKDELVIIKNLKHEVYGIWIHTVSDRQNIYELIKYLLENEPKDSFA 231
                                    26        36        46        56        66        76   |     -         -         -         -         -       136       146       156       166       176       186       196       206       216       226     
                                                                                          80                                                    135                                                                                                

   Legend:   → Mismatch (orange background)
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    → 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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PH (111)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DCP1_YEAST | Q12517)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008047    enzyme activator activity    Binds to and increases the activity of an enzyme.
    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:0000290    deadenylation-dependent decapping of nuclear-transcribed mRNA    Cleavage of the 5'-cap of a nuclear mRNA triggered by shortening of the poly(A) tail to below a minimum functional length.
    GO:0031087    deadenylation-independent decapping of nuclear-transcribed mRNA    Cleavage of the 5'-cap of a nuclear-transcribed mRNA that is independent of poly(A) tail shortening.
    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:0000184    nuclear-transcribed mRNA catabolic process, nonsense-mediated decay    The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
    GO:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
cellular component
    GO:0000932    P-body    A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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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