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(-) Description

Title :  ASYMMETRIC TRIMER OF THE DROSOPHILA MELANOGASTER DCP1 C-TERMINAL DOMAIN
 
Authors :  F. Tritschler, O. Weichenrieder
Date :  01 Nov 09  (Deposition) - 01 Dec 09  (Release) - 26 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Asymmetric Assembly, Trimerization Module, Mrna Decapping, P-Body Component, Structural Protein (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 - DECAPPING PROTEIN 1
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSFDUET-1
    Expression System Strain: K-12
    Expression System Taxid: 83333
    Fragment: TRIMERIZATION DOMAIN, RESIDUES 328-366
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Other Details: EC6.1.1.- IN UNIPROT DISPUTED BY AUTHOR
    Synonym: DCP1

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO C:322 , HIS C:323 , MET C:324 , HOH C:2008 , HOH C:2009 , ASN E:350BINDING SITE FOR RESIDUE SO4 C1364
2AC2SOFTWAREILE D:342 , GLN D:343 , ASP D:345 , LYS D:346 , PHE D:348 , ALA D:349 , CYS F:360BINDING SITE FOR RESIDUE SO4 D1366
3AC3SOFTWAREPRO F:322 , HIS F:323 , MET F:324 , HOH F:2012BINDING SITE FOR RESIDUE SO4 F1367
4AC4SOFTWAREHIS D:323 , MET D:324 , HOH D:2012BINDING SITE FOR RESIDUE SO4 D1367
5AC5SOFTWAREGLN A:336 , TYR A:340 , ASN E:358BINDING SITE FOR RESIDUE SO4 A1359

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WX4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WX4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WX4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WX4)

(-) Exons   (0, 0)

(no "Exon" information available for 2WX4)

(-) 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:38
 aligned with Q9W1H5_DROME | Q9W1H5 from UniProtKB/TrEMBL  Length:372

    Alignment length:60
                                   308       318       328       338       348       358
         Q9W1H5_DROME   299 GPALMPPTMFDAPNNGNPEPQQPQQPQQPLLNSTQFVQAFTYLIQNDKEFANKLHKAYLN 358
               SCOP domains ------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author .-----......-----------------....hhhhhhhhhhhhh...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                 2wx4 A 321 G-----PHMADL-----------------LLNSTQFVQAFTYLIQNDKEFANKLHKAYLN 358
                            |     |325 |       -       328       338       348       358
                            |   322  327               328                              
                          321                                                           


Chain B from PDB  Type:PROTEIN  Length:41
 aligned with Q9W1H5_DROME | Q9W1H5 from UniProtKB/TrEMBL  Length:372

    Alignment length:41
                                   335       345       355       365 
         Q9W1H5_DROME   326 QPLLNSTQFVQAFTYLIQNDKEFANKLHKAYLNGCSNLLLD 366
               SCOP domains ----------------------------------------- SCOP domains
               CATH domains ----------------------------------------- CATH domains
               Pfam domains ----------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------- PROSITE
                 Transcript ----------------------------------------- Transcript
                 2wx4 B 326 DLLLNSTQFVQAFTYLIQNDKEFANKLHKAYLNGCSNLLLD 366
                                   335       345       355       365 


Chain C from PDB  Type:PROTEIN  Length:43
 aligned with Q9W1H5_DROME | Q9W1H5 from UniProtKB/TrEMBL  Length:372

    Alignment length:65
                                   308       318       328       338       348       358     
         Q9W1H5_DROME   299 GPALMPPTMFDAPNNGNPEPQQPQQPQQPLLNSTQFVQAFTYLIQNDKEFANKLHKAYLNGCSNL 363
               SCOP domains ----------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .-----......-----------------...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                 2wx4 C 321 G-----PHMADL-----------------LLNSTQFVQAFTYLIQNDKEFANKLHKAYLNGCSNL 363
                            |     |325 |       -       328       338       348       358     
                          321   322  327               328                                   


Chain D from PDB  Type:PROTEIN  Length:45
 aligned with Q9W1H5_DROME | Q9W1H5 from UniProtKB/TrEMBL  Length:372

    Alignment length:67
                                   308       318       328       338       348       358       
         Q9W1H5_DROME   299 GPALMPPTMFDAPNNGNPEPQQPQQPQQPLLNSTQFVQAFTYLIQNDKEFANKLHKAYLNGCSNLLL 365
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author .-----......-----------------....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                 2wx4 D 321 G-----PHMADL-----------------LLNSTQFVQAFTYLIQNDKEFANKLHKAYLNGCSNLLL 365
                            |     |325 |       -       328       338       348       358       
                          321   322  327               328                                     


Chain E from PDB  Type:PROTEIN  Length:43
 aligned with Q9W1H5_DROME | Q9W1H5 from UniProtKB/TrEMBL  Length:372

    Alignment length:60
                                   315       325       335       345       355       365
         Q9W1H5_DROME   306 TMFDAPNNGNPEPQQPQQPQQPLLNSTQFVQAFTYLIQNDKEFANKLHKAYLNGCSNLLL 365
               SCOP domains ------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author .....-----------------...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                 2wx4 E 323 HMADL-----------------LLNSTQFVQAFTYLIQNDKEFANKLHKAYLNGCSNLLL 365
                                |    -         -  |    335       345       355       365
                              327               328                                     


Chain F from PDB  Type:PROTEIN  Length:45
 aligned with Q9W1H5_DROME | Q9W1H5 from UniProtKB/TrEMBL  Length:372

    Alignment length:62
                                   314       324       334       344       354       364  
         Q9W1H5_DROME   305 PTMFDAPNNGNPEPQQPQQPQQPLLNSTQFVQAFTYLIQNDKEFANKLHKAYLNGCSNLLLD 366
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author ......-----------------...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                 2wx4 F 322 PHMADL-----------------LLNSTQFVQAFTYLIQNDKEFANKLHKAYLNGCSNLLLD 366
                                 |   -         -   |   334       344       354       364  
                               327               328
   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 2WX4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WX4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2WX4)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (Q9W1H5_DROME | Q9W1H5)
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:0050072    m7G(5')pppN diphosphatase activity    Catalysis of the reaction: 7-methylguanosine 5'-triphospho-5'-polynucleotide + H2O = 7-methylguanosine 5'-phosphate + polynucleotide.
    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:0035195    gene silencing by miRNA    Downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: endolytic cleavage of mRNA cleavage or translational repression, usually accompanied by poly-A tail shortening and subsequent degradation of the mRNA.
    GO:0000956    nuclear-transcribed mRNA catabolic process    The chemical reactions and pathways resulting in the breakdown of nuclear-transcribed mRNAs in eukaryotic cells.
    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:0045451    pole plasm oskar mRNA localization    Any process in which oskar mRNA is transported to, or maintained in, the oocyte pole plasm.
    GO:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
    GO:2000637    positive regulation of gene silencing by miRNA    Any process that activates or increases the frequency, rate or extent of gene silencing by miRNA.
    GO:0010603    regulation of cytoplasmic mRNA processing body assembly    Any process that modulates the rate, frequency, or extent of the aggregation, arrangement and bonding together of proteins and RNA molecules to form a cytoplasmic mRNA processing body.
    GO:0019233    sensory perception of pain    The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process.
cellular component
    GO:0043186    P granule    A small cytoplasmic, non-membranous RNA/protein complex aggregates in the primordial germ cells of many higher eukaryotes.
    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.

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        Q9W1H5_DROME | Q9W1H5: 2lyd

(-) Related Entries Specified in the PDB File

2wx3 ASYMMETRIC TRIMER OF THE HUMAN DCP1A C- TERMINAL DOMAIN