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(-) Description

Title :  CRYSTAL STRUCTURE OF S. POMBE DCP2:DCP1 MRNA DECAPPING COMPLEX
 
Authors :  E. Valkov, S. Muthukumar, C. T. Chang, S. Jonas, O. Weichenrieder, E. Iz
Date :  31 Mar 16  (Deposition) - 18 May 16  (Release) - 15 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.29
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Hydrolase, Decapping, Mrna Decay, Evh1, Nudix (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Valkov, S. Muthukumar, C. T. Chang, S. Jonas, O. Weichenrieder, E. Izaurralde
Structure Of The Dcp2-Dcp1 Mrna-Decapping Complex In The Activated Conformation.
Nat. Struct. Mol. Biol. V. 23 574 2016
PubMed-ID: 27183195  |  Reference-DOI: 10.1038/NSMB.3232

(-) Compounds

Molecule 1 - MRNA-DECAPPING ENZYME SUBUNIT 1
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PNEAPG
    Expression System Taxid: 469008
    Expression System Variant: STAR
    Expression System Vector Type: PLASMID
    Gene: DCP1, SPBC3B9.21
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE (STRAIN 972 / ATCC 24843)
    Organism Taxid: 284812
    Strain: 972 / ATCC 24843
 
Molecule 2 - MRNA DECAPPING COMPLEX SUBUNIT 2
    Chains: B, D
    EC Number: 3.6.1.62
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PNYC
    Expression System Taxid: 469008
    Expression System Variant: STAR
    Expression System Vector Type: PLASMID
    Gene: DCP2, SPAC19A8.12
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE (STRAIN 972 / ATCC 24843)
    Organism Taxid: 284812
    Strain: 972 / ATCC 24843

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5J3Y)

(-) Sites  (0, 0)

(no "Site" information available for 5J3Y)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5J3Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5J3Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5J3Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5J3Y)

(-) Exons   (0, 0)

(no "Exon" information available for 5J3Y)

(-) 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:126
                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh...eeeeeeeeeeeeeeee......eeeeeeeeeeeeeee....eeeeeee......eeee......eeee..eeeee.....eeeeee..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5j3y A  -1 PHMEDENILRNAVNLQVLKFHYPEIESIIDIASHVAVYQFDVGSQKWLKTSIEGTFFLVKDQRARVGYVILNRNSPENLYLFINHPSNVHLVDRYLIHRTENQHVVGLWMFDPNDMSRIFNIVKES 124
                                     8        18        28        38        48        58        68        78        88        98       108       118      


Chain B from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhh.....hhhh..hhhhhhhhhhhhhhhhh.hhhh........hhhhhhhhhhh....hhhhhh.hhhhhhhhhh...eeeeeeee......eeeeeee..........eee......hhhhhhhhhhhhh............eeeeee..eeeeeeee................eeeeeeee.........................hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j3y B   1 MSFTNATFSQVLDDLSARFILNLPAEEQSSVERLCFQIEQAHWFYEDFIRAQNDQLPSLGLRVFSAKLFAHCPLLWKWSKVHEEAFDDFLRYKTRIPVRGAIMLDMSMQQCVLVKGWKASSGWGFPKGKIDKDESDVDCAIREVYEETGFDCSSRINPNEFIDMTIRGQNVRLYIIPGISLDTRFESRTRKEISKIEWHNLMDLPTFKKNKPQTMKNKFYMVIPFLAPLKKWIKKRNIANNT 242
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240  


Chain C from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh...eeeeeeeeeeeeeeee......eeeeeeeeeeeeeee....eeeeeee......eeee......eeee..eeeee.....eeeeee..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j3y C   1 MEDENILRNAVNLQVLKFHYPEIESIIDIASHVAVYQFDVGSQKWLKTSIEGTFFLVKDQRARVGYVILNRNSPENLYLFINHPSNVHLVDRYLIHRTENQHVVGLWMFDPNDMSRIFNIVKES 124
                                    10        20        30        40        50        60        70        80        90       100       110       120    


Chain D from PDB  Type:PROTEIN  Length:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhh.....hhhh..hhhhhhhhhhhhhhhhh.hhhh........hhhhhhhhhhh........hhhhhhhhh...eeeeeeee......eeeeee...........eee......hhhhhhhhhhhhh............eeeeee..eeeeeeee..................eeeeee.........................hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j3y D   1 MSFTNATFSQVLDDLSARFILNLPAEEQSSVERLCFQIEQAHWFYEDFIRAQNDQLPSLGLRVFSAKLFAHCPLSKVHEEAFDDFLRYKTRIPVRGAIMLDMSMQQCVLVKGWKASSGWGFPKGKIDKDESDVDCAIREVYEETGFDCSSRINPNEFIDMTIRGQNVRLYIIPGISLDTRFESRTRKEISKIEWHNLMDLPTFKKNKPQTMKNKFYMVIPFLAPLKKWIKKRNIANN 241
                                    10        20        30        40        50        60        70   ||   84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       
                                                                                                    74|                                                                                                                                                                  
                                                                                                     79
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  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 5J3Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J3Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J3Y)

(-) Gene Ontology  (27, 39)

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  DCP2_SCHPO | O13828
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 Related Entries

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

UniProtKB/Swiss-Prot
        DCP1_SCHPO | Q9P805: 2qkl 2qkm 5j3q 5j3t 5jp4 5kq1 5kq4 5n2v
        DCP2_SCHPO | O13828: 2a6t 2qkl 2qkm 4a54 5j3t 5kq1 5kq4 5n2v

(-) Related Entries Specified in the PDB File

5j3q CRYSTAL STRUCTURE OF S. POMBE DCP1:EDC1 MRNA DECAPPING COMPLEX
5j3t CRYSTAL STRUCTURE OF S. POMBE DCP2:DCP1:EDC1 MRNA DECAPPING COMPLEX