2QKL - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF FISSION YEAST MRNA DECAPPING ENZYME DCP1-DCP2 COMPLEX

Authors :   M. She, N. Chen, H. Song

Date :   11 Jul 07 (Deposition) - 25 Mar 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.33

Chains :   Asym./Biol. Unit : A,B

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

Reference :   M. She, C. J. Decker, D. I. Svergun, A. Round, N. Chen, D. Muhlrad, R. Parker, H. Song
Structural Basis Of Dcp2 Recognition And Activation By Dcp1
Mol. Cell V. 29 337 2008
PubMed-ID: 18280239 | Reference-DOI: 10.1016/J.MOLCEL.2008.01.002

Molecule 1 - SPBC3B9.21 PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Strain	:	BL21 STAR
	Expression System Taxid	:	562
	Gene	:	DCP1
	Organism Common	:	FISSION YEAST
	Organism Scientific	:	SCHIZOSACCHAROMYCES POMBE
	Organism Taxid	:	4896
	Synonym	:	DCP1 PROTEIN

Molecule 2 - SPAC19A8.12 PROTEIN
	Chains	:	B
	EC Number	:	3.6.1.30
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Strain	:	BL21 STAR
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 1-95
	Gene	:	SPAC19A8.12
	Organism Common	:	FISSION YEAST
	Organism Scientific	:	SCHIZOSACCHAROMYCES POMBE
	Organism Taxid	:	4896

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	PB	1	Ligand/Ion	LEAD (II) ION

(no "Site" information available for 2QKL)

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

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

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

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

(no "Exon" information available for 2QKL)

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:121
 aligned with DCP1_SCHPO | Q9P805 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:127
                                    10        20        30        40        50        60        70        80        90       100       110       120       
           DCP1_SCHPO     1 MEDENILRNAVNLQVLKFHYPEIESIIDIASHVAVYQFDVGSQKWLKTSIEGTFFLVKDQRARVGYVILNRNSPENLYLFINHPSNVHLVDRYLIHRTENQHVVGLWMFDPNDMSRIFNIVKESLLR 127
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---DCP1-2qklA01 A:4-125                                                                                                      -- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee..------..eeeeeeeeeeeee....eeeeeee......eeeee.hhh.eeee..eeeeee...eeeeeee..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qkl A   1 MEDENILRNAVNLQVLKFHYPEIESIIDIASHVAVYQF------WLKTSIEGTFFLVKDQRARVGYVILNRNSPENLYLFINHPSNVHLVDRYLIHRTENQHVVGLWMFDPNDMSRIFNIVKESLLR 127
                                    10        20        30       | -    |   50        60        70        80        90       100       110       120       
                                                                38     45

Chain B from PDB  Type:PROTEIN  Length:90
 aligned with DCP2_SCHPO | O13828 from UniProtKB/Swiss-Prot  Length:741

    Alignment length:90
                                    11        21        31        41        51        61        71        81        91
           DCP2_SCHPO     2 SFTNATFSQVLDDLSARFILNLPAEEQSSVERLCFQIEQAHWFYEDFIRAQNDQLPSLGLRVFSAKLFAHCPLLWKWSKVHEEAFDDFLR  91
               SCOP domains d2qklb_ B: mRNA decapping enzyme Dcp2p, N-terminal domain                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -------DCP2-2qklB01 B:9-91                                                                 Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 2qkl B   2 SFTNATFSQVLDDLSARFILNLPAEEQSSVERLCFQIEQAHWFYEDFIRAQNDQLPSLGLRVFSAKLFAHCPLLWKWSKVHEEAFDDFLR  91
                                    11        21        31        41        51        61        71        81        91

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Dcp2 domain-like (3)

Superfamily: Dcp2 domain-like (3)

Family: Dcp2 box A domain (3)

Protein domain: mRNA decapping enzyme Dcp2p, N-terminal domain (3)

Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] (3)

d2qklb_

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (DCP1_SCHPO | Q9P805)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0008047	enzyme activator activity	Binds to and increases the activity of an enzyme.
	GO:1990521	m7G(5')pppN diphosphatase activator activity	Binds to and increases the activity of m7G(5')pppN diphosphatase.
	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: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.
	GO:0034428	nuclear-transcribed mRNA catabolic process, exonucleolytic, 5'-3'	The chemical reactions and pathways resulting in the breakdown of the mRNA transcript body that occurs when the 5' end is not protected by a 5'-cap; degradation proceeds in the 5' to 3' direction.
	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.
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.

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.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		PB	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 2qkl)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2qkl)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2qkl
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	DCP1_SCHPO \| Q9P805
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	DCP2_SCHPO \| O13828
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.6.1.30
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	DCP1_SCHPO \| Q9P805
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	DCP2_SCHPO \| O13828
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Related Entries Specified in the PDB File" available for 2QKL)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (2, 2)

Gene Ontology (27, 39)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File