4A54 - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   STRUCTURAL BASIS OF THE DCP1:DCP2 MRNA DECAPPING COMPLEX ACTIVATION BY EDC3 AND SCD6

Authors :   S. A. Fromm, V. Truffault, J. Kamenz, J. E. Braun, N. A. Hoffmann, E. Izau R. Sprangers

Date :   24 Oct 11 (Deposition) - 01 Feb 12 (Release) - 01 Feb 12 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (22x)
NMR Structure *: A,B  (1x)

Keywords :   Rna Binding Protein-Hydrolase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. A. Fromm, V. Truffault, J. Kamenz, J. E. Braun, N. A. Hoffmann, E. Izaurralde, R. Sprangers
The Structural Basis Of Edc3- And Scd6-Mediated Activation Of The Dcp1:Dcp2 Mrna Decapping Complex.
Embo J. V. 31 279 2011
PubMed-ID: 22085934 | Reference-DOI: 10.1038/EMBOJ.2011.408

Molecule 1 - EDC3
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector	:	PET
	Expression System Vector Type	:	PLASMID
	Fragment	:	LSM, RESIDUES 1-94
	Organism Common	:	FISSION YEAST
	Organism Scientific	:	SCHIZOSACCHAROMYCES POMBE
	Organism Taxid	:	4896
	Synonym	:	UNCHARACTERIZED PROTEIN C18E5.11C

Molecule 2 - MRNA DECAPPING COMPLEX SUBUNIT 2
	Chains	:	B
	EC Number	:	3.-.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector	:	PET
	Expression System Vector Type	:	PLASMID
	Fragment	:	HLM1, RESIDUES 242-291
	Organism Common	:	FISSION YEAST
	Organism Scientific	:	SCHIZOSACCHAROMYCES POMBE
	Organism Taxid	:	4896
	Synonym	:	DCP2

		1	2
NMR Structure (22x)	:	A	B
NMR Structure * (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 4A54)

(no "Site" information available for 4A54)

(no "SS Bond" information available for 4A54)

(no "Cis Peptide Bond" information available for 4A54)

(no "SAP(SNP)/Variant" information available for 4A54)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DFDF	PS51512	DFDF domain profile.	EDC3_SCHPO	87-123	1	A:87-94

NMR Structure * (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DFDF	PS51512	DFDF domain profile.	EDC3_SCHPO	87-123	1	A:87-94

(no "Exon" information available for 4A54)

NMR Structure

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
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Chain A from PDB  Type:PROTEIN  Length:96
 aligned with EDC3_SCHPO | O94752 from UniProtKB/Swiss-Prot  Length:454

    Alignment length:96
                              1                                                                                             
                              |      8        18        28        38        48        58        68        78        88      
           EDC3_SCHPO     - --MSVADFYGSNVEVLLNNDSKARGVITNFDSSNSILQLRLANDSTKSIVTKDIKDLRILPKNEIMPKNGTKSPSTNSTKLKSAETYSSKNKWSMD  94
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhh..eeeeee....eeeeeeeeee....eeeeee...eeeeee...eeeeee..................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------DFDF     PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 4a54 A  -1 MGMSVADFYGSNVEVLLNNDSKARGVITNFDSSNSILQLRLANDSTKSIVTKDIKDLRILPKNEIMPKNGTKSPSTNSTKLKSAETYSSKNKWSMD  94
                                     8        18        28        38        48        58        68        78        88

Chain B from PDB  Type:PROTEIN  Length:52
 aligned with DCP2_SCHPO | O13828 from UniProtKB/Swiss-Prot  Length:741

    Alignment length:52
                                   249       259       269       279       289  
           DCP2_SCHPO   240 NNTTKEKNISVDVDADASSQLLSLLKSSTAPSDLATPQPSTFPQPPVESHSS 291
               SCOP domains ---------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------- Transcript
                 4a54 B 240 GATTKEKNISVDVDADASSQLLSLLKSSTAPSDLATPQPSTFPQPPVESHSS 291
                                   249       259       269       279       289

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	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 '\|'

(no "SCOP Domain" information available for 4A54)

(no "CATH Domain" information available for 4A54)

(no "Pfam Domain" information available for 4A54)

NMR Structure(hide GO term definitions)

Chain A (EDC3_SCHPO | O94752)

molecular function
	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:0003674	molecular_function	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
	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:0033962	cytoplasmic mRNA processing body assembly	The aggregation, arrangement and bonding together of proteins and RNA molecules to form a cytoplasmic mRNA processing body.
	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.
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:0010494	cytoplasmic stress granule	A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.

Chain B (DCP2_SCHPO | O13828)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0000340	RNA 7-methylguanosine cap binding	Interacting selectively and non-covalently with the 7-methylguanosine group added cotranscriptionally to the 5' end of RNA molecules transcribed by polymerase II.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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:0050072	m7G(5')pppN diphosphatase activity	Catalysis of the reaction: 7-methylguanosine 5'-triphospho-5'-polynucleotide + H2O = 7-methylguanosine 5'-phosphate + polynucleotide.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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).
	GO:0003727	single-stranded RNA binding	Interacting selectively and non-covalently with single-stranded RNA.
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.
cellular component
	GO:0098745	Dcp1-Dcp2 complex	A protein complex consisting of a Dcp1 regulatory subunit and a Dcp2 catalytic subunit that has mRNA cap binding activity and is involved in decapping of nuclear-transcribed mRNA.
	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:0010494	cytoplasmic stress granule	A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
	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:0005845	mRNA cap binding complex	Any protein complex that binds to an mRNA cap at any time in the lifetime of the mRNA.
	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.

NMR Structure
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	4a54
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	EDC3_SCHPO \| O94752
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	3.-.-.-
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UniProtKB/Swiss-Prot
	DCP2_SCHPO \| O13828	:	2a6t 2qkl 2qkm 5j3t 5j3y 5kq1 5kq4 5n2v
	EDC3_SCHPO \| O94752	:	4a53

2a6t	CRYSTAL STRUCTURE OF S.POMBE MRNA DECAPPING ENZYME DCP2P
4a53	STRUCTURAL BASIS OF THE DCP1:DCP2 MRNA DECAPPING COMPLEX ACTIVATION BY EDC3 AND SCD6

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