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(-) Description

Title :  ASYMMETRIC TRIMER OF THE HUMAN DCP1A C-TERMINAL DOMAIN
 
Authors :  F. Tritschler, C. Motz, O. Weichenrieder
Date :  01 Nov 09  (Deposition) - 01 Dec 09  (Release) - 26 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Structural Protein, Trimerization Module, Mrna Decapping, P-Body Component, Asymmetric Assembly (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Tritschler, J. E. Braun, C. Motz, C. Igreja, G. Haas, V. Truffault, E. Izaurralde, O. Weichenrieder
Dcp1 Forms Asymmetric Trimers To Assemble Into Active Mrna Decapping Complexes In Metazoa.
Proc. Natl. Acad. Sci. Usa V. 106 21591 2009
PubMed-ID: 19966221  |  Reference-DOI: 10.1073/PNAS.0909871106

(-) Compounds

Molecule 1 - MRNA-DECAPPING ENZYME 1A
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPRSFDUET-1
    Expression System StrainK-12
    Expression System Taxid83333
    FragmentTRIMERIZATION DOMAIN, RESIDUES 539-582
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsEC3.-.-.- IN UNIPROT DISPUTED BY DEPOSITOR

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2WX3)

(-) Sites  (0, 0)

(no "Site" information available for 2WX3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WX3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WX3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WX3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WX3)

(-) Exons   (0, 0)

(no "Exon" information available for 2WX3)

(-) 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:43
 aligned with DCP1A_HUMAN | Q9NPI6 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:72
                                   512       522       532       542       552       562       572  
          DCP1A_HUMAN   503 APSVFQQTVTRSSDLERKASSPSPLTIGTPESQRKPSIILSKSQLQDTLIHLIKNDSSFLSTLHEVYLQVLT 574
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..--------...hh---------------------hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 2wx3 A 532 GP--------HMADL---------------------SIILSKSQLQDTLIHLIKNDSSFLSTLHEVYLQVLT 574
                             |       -|   |    -         -      |542       552       562       572  
                             |      534 538                   539                                   
                           533                                                                      

Chain B from PDB  Type:PROTEIN  Length:42
 aligned with DCP1A_HUMAN | Q9NPI6 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:63
                                   523       533       543       553       563       573   
          DCP1A_HUMAN   514 SSDLERKASSPSPLTIGTPESQRKPSIILSKSQLQDTLIHLIKNDSSFLSTLHEVYLQVLTKN 576
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author ....---------------------.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 2wx3 B 535 MADL---------------------SIILSKSQLQDTLIHLIKNDSSFLSTLHEVYLQVLTKN 576
                               |     -         -     | 543       553       563       573   
                             538                   539                                     

Chain C from PDB  Type:PROTEIN  Length:47
 aligned with DCP1A_HUMAN | Q9NPI6 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:68
                                   524       534       544       554       564       574        
          DCP1A_HUMAN   515 SDLERKASSPSPLTIGTPESQRKPSIILSKSQLQDTLIHLIKNDSSFLSTLHEVYLQVLTKNKDNHNL 582
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....---------------------....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 2wx3 C 536 ADLS---------------------IILSKSQLQDTLIHLIKNDSSFLSTLHEVYLQVLTKNKDNHNL 582
                               |     -         -     | 544       554       564       574        
                             539                   540                                          

   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 2WX3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WX3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2WX3)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (DCP1A_HUMAN | Q9NPI6)
molecular function
    GO:0008047    enzyme activator activity    Binds to and increases the activity of an enzyme.
    GO:0030234    enzyme regulator activity    Binds to and modulates the activity of an enzyme.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0043928    exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay    The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that occurs when the ends are not protected by the 3'-poly(A) tail.
    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.
    GO:1903608    protein localization to cytoplasmic stress granule    A process in which a protein is transported to, or maintained in, a location within a cytoplasmic stress granule.
    GO:0043488    regulation of mRNA stability    Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.
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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        DCP1A_HUMAN | Q9NPI64b6h

(-) Related Entries Specified in the PDB File

2wx4 ASYMMETRIC TRIMER OF THE DROSOPHILA MELANOGASTER DCP1 C-TERMINAL DOMAIN