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(-) Description

Title :  CHANGES IN CONFORMATIONAL EQUILIBRIA REGULATE THE ACTIVITY OF THE DCP2 DECAPPING ENZYME
 
Authors :  I. Holdermann, R. Sprangers
Date :  08 Feb 17  (Deposition) - 24 May 17  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. P. Wurm, I. Holdermann, J. H. Overbeck, P. H. O. Mayer, R. Sprangers
Changes In Conformational Equilibria Regulate The Activity Of The Dcp2 Decapping Enzyme.
Proc. Natl. Acad. Sci. V. 114 6034 2017 U. S. A.
PubMed-ID: 28533364  |  Reference-DOI: 10.1073/PNAS.1704496114

(-) Compounds

Molecule 1 - MRNA-DECAPPING ENZYME SUBUNIT 1
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DCP1, SPBC3B9.21
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 4896
 
Molecule 2 - MRNA DECAPPING COMPLEX SUBUNIT 2
    Chains: B, E
    EC Number: 3.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DCP2, SPAC19A8.12
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 4896
 
Molecule 3 - EDC1
    Chains: C, F
    Engineered: YES
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 4896
    Synthetic: YES

 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  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
18NK2Ligand/Ion7-METHYLGUANOSINE 5'-DIPHOSPHATE
2MG6Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
18NK1Ligand/Ion7-METHYLGUANOSINE 5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
18NK1Ligand/Ion7-METHYLGUANOSINE 5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:143 , GLU B:146 , MG B:302 , 8NK B:304binding site for residue MG B 301
2AC2SOFTWAREGLU B:143 , GLU B:146 , GLU B:147 , GLU B:192 , MG B:301 , 8NK B:304binding site for residue MG B 302
3AC3SOFTWARELYS B:127 , GLU B:147 , GLU B:192 , 8NK B:304binding site for residue MG B 303
4AC4SOFTWARETRP B:43 , ASP B:47 , LYS B:127 , GLY B:128 , LYS B:129 , GLU B:143 , GLU B:147 , ARG B:190 , LYS B:191 , GLU B:192 , MG B:301 , MG B:302 , MG B:303binding site for residue 8NK B 304
5AC5SOFTWARELYS E:127 , GLU E:147 , GLU E:192 , 8NK E:304binding site for residue MG E 301
6AC6SOFTWAREGLU E:143 , GLU E:146 , GLU E:147 , GLU E:192 , MG E:303 , 8NK E:304binding site for residue MG E 302
7AC7SOFTWAREGLU E:143 , GLU E:146 , MG E:302 , 8NK E:304binding site for residue MG E 303
8AC8SOFTWARETRP E:43 , ASP E:47 , LYS E:127 , GLY E:128 , LYS E:129 , GLU E:143 , GLU E:147 , ARG E:190 , LYS E:191 , GLU E:192 , MG E:301 , MG E:302 , MG E:303binding site for residue 8NK E 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5N2V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5N2V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5N2V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5N2V)

(-) Exons   (0, 0)

(no "Exon" information available for 5N2V)

(-) 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 hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeeeee....eee....eeeeeeeee....eeeeeee......eeee..hhh.eeee..eeeeee...eeeeeee.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5n2v A   0 AMEDENILRNAVNLQVLKFHYPEIESIIDIASHVAVYQFDVGSQKWLKTSIEGTFFLVKDQRARVGYVILNRNSPENLYLFINHPSNVHLVDRYLIHRTENQHVVGLWMFDPNDMSRIFNIVKESL 125
                                     9        19        29        39        49        59        69        79        89        99       109       119      


Chain B from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhh...eeeeeeee....eeeeee.......ee..eee.....hhhhhhhhhhhhhhh...........eeeeee..eeeeeeeeeee...............eeeeee.hhh.....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5n2v B   2 SFTNATFSQVLDDLSARFILNLPAEEQSSVERLCFQIEQAHWFYEDFIRAQNDQLPSLGLRVFSAKLFAHCPLLWKWSKVHEEAFDDFLRYKTRIPVRGAIMLDMSMQQCVLVKGWKASSGWGFPKGKIDKDESDVDCAIREVYEETGFDCSSRINPNEFIDMTIRGQNVRLYIIPGISLDTRFESRTRKEISKIEWHNLMDLPTFYMVIPFLAPLKKWIKKR 236
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201    || 223       233   
                                                                                                                                                                                                                                      206|                 
                                                                                                                                                                                                                                       219                 


Chain C from PDB  Type:PROTEIN  Length:23
                                                       
               SCOP domains ----------------------- SCOP domains
               CATH domains ----------------------- CATH domains
               Pfam domains ----------------------- Pfam domains
         Sec.struct. author ............hhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------- SAPs(SNPs)
                    PROSITE ----------------------- PROSITE
                 Transcript ----------------------- Transcript
                 5n2v C 156 ILYAGPTFTHSPAASNLPIPTFL 178
                                   165       175   


Chain D from PDB  Type:PROTEIN  Length:126
                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeeeee....eee....eeeeeeeee....eeeeeee......eeee..hhh.eeee..eeeeee...eeeeeee.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5n2v D   0 AMEDENILRNAVNLQVLKFHYPEIESIIDIASHVAVYQFDVGSQKWLKTSIEGTFFLVKDQRARVGYVILNRNSPENLYLFINHPSNVHLVDRYLIHRTENQHVVGLWMFDPNDMSRIFNIVKESL 125
                                     9        19        29        39        49        59        69        79        89        99       109       119      


Chain E from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhh...eeeeeeee....eeeeee.......ee..eee.....hhhhhhhhhhhhhhh...........eeeeee..eeeeeeeeeee...............eeeeee.hhh.....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5n2v E   2 SFTNATFSQVLDDLSARFILNLPAEEQSSVERLCFQIEQAHWFYEDFIRAQNDQLPSLGLRVFSAKLFAHCPLLWKWSKVHEEAFDDFLRYKTRIPVRGAIMLDMSMQQCVLVKGWKASSGWGFPKGKIDKDESDVDCAIREVYEETGFDCSSRINPNEFIDMTIRGQNVRLYIIPGISLDTRFESRTRKEISKIEWHNLMDLPTFYMVIPFLAPLKKWIKKR 236
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201    || 223       233   
                                                                                                                                                                                                                                      206|                 
                                                                                                                                                                                                                                       219                 


Chain F from PDB  Type:PROTEIN  Length:23
                                                       
               SCOP domains ----------------------- SCOP domains
               CATH domains ----------------------- CATH domains
               Pfam domains ----------------------- Pfam domains
         Sec.struct. author ............hhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------- SAPs(SNPs)
                    PROSITE ----------------------- PROSITE
                 Transcript ----------------------- Transcript
                 5n2v F 156 ILYAGPTFTHSPAASNLPIPTFL 178
                                   165       175
   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 5N2V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5N2V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5N2V)

(-) Gene Ontology  (29, 43)

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  DCP2_SCHPO | O13828
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  YAQ9_SCHPO | Q10108
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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 5j3y 5jp4 5kq1 5kq4
        DCP2_SCHPO | O13828: 2a6t 2qkl 2qkm 4a54 5j3t 5j3y 5kq1 5kq4
        YAQ9_SCHPO | Q10108: 5j3q 5j3t 5jp4

(-) Related Entries Specified in the PDB File

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