4B6H - JenaLib

Molecule 1 - MRNA-DECAPPING ENZYME 1A
	Chains	:	A, B
	EC Number	:	3.-.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Variant	:	ROSETTA
	Expression System Vector	:	PET-DUET
	Expression System Vector Type	:	PLASMID
	Fragment	:	EVH1 DOMAIN, RESIDUES 1-130
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HDCP1A, SMAD4-INTERACTING TRANSCRIPTIONAL CO-ACTIVATOR, TRANSCRIPTION FACTOR SMIF

Molecule 2 - PROLINE-RICH NUCLEAR RECEPTOR COACTIVATOR 2
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Variant	:	ROSETTA
	Expression System Vector	:	PET-DUET
	Expression System Vector Type	:	PLASMID
	Fragment	:	PROLINE RICH SEQUENCE, RESIDUES 1-121
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PNRC2

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:129
 aligned with DCP1A_HUMAN | Q9NPI6 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:130
                             1                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129
          DCP1A_HUMAN     - -MEALSRAGQEMSLAALKQHDPYITSIADLTGQVALYTFCPKANQWEKTDIEGTLFVYRRSASPYHGFTIVNRLNMHNLVEPVNKDLEFQLHEPFLLYRNASLSIYSIWFYDKNDCHRIAKLMADVVEEE 129
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeee.....eeeeeee.-....eeee.....eeeee..eeeee.....eeeeee.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b6h A   0 LMEALSRAGQEMSLAALKQHDPYITSIADLTGQVALYTFCPKANQWEKTDIEGTLFVYRRSASPYHGFTIVNR-NMHNLVEPVNKDLEFQLHEPFLLYRNASLSIYSIWFYDKNDCHRIAKLMADVVEEE 129
                                     9        19        29        39        49        59        69  | |   79        89        99       109       119       129
                                                                                                   72 |                                                       
                                                                                                     74

Chain B from PDB  Type:PROTEIN  Length:101
 aligned with DCP1A_HUMAN | Q9NPI6 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:107
                                    30        40        50        60        70        80        90       100       110       120       
          DCP1A_HUMAN    21 PYITSIADLTGQVALYTFCPKANQWEKTDIEGTLFVYRRSASPYHGFTIVNRLNMHNLVEPVNKDLEFQLHEPFLLYRNASLSIYSIWFYDKNDCHRIAKLMADVVE 127
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeeeee.--.-.eeeeeeeeeeeeee......eeeeee.--..-.eeee.....eeeee..eeeee.....eeeeee.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 4b6h B  21 PYITSIADLTGQVALYTFC--A-QWEKTDIEGTLFVYRRSASPYHGFTIVN--NM-NLVEPVNKDLEFQLHEPFLLYRNASLSIYSIWFYDKNDCHRIAKLMADVVE 127
                                    30        |- | |    50        60        70|  || | 80        90       100       110       120       
                                             39 42 |                         71 74| |                                                  
                                                  44                             75 |                                                  
                                                                                   77

Chain C from PDB  Type:PROTEIN  Length:15
 aligned with PNRC2_HUMAN | Q9NPJ4 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:15
                                   111     
          PNRC2_HUMAN   102 PSPSVLPKPPSHWVP 116
               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
                 4b6h C 102 PSPSVLPKPPSHWVP 116
                                   111

Chain D from PDB  Type:PROTEIN  Length:14
 aligned with PNRC2_HUMAN | Q9NPJ4 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:15
                                   111     
          PNRC2_HUMAN   102 PSPSVLPKPPSHWVP 116
               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
                 4b6h D 102 PS-SVLPKPPSHWVP 116
                             | |   111     
                           103 |           
                             105

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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (21, 27)

Asymmetric Unit(hide GO term definitions)

Chain A,B (DCP1A_HUMAN | Q9NPI6)

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: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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0043928	exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that occurs when the ends are not protected by the 3'-poly(A) tail.
	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.
	GO:1903608	protein localization to cytoplasmic stress granule	A process in which a protein is transported to, or maintained in, a location within a cytoplasmic stress granule.
	GO:0043488	regulation of mRNA stability	Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.
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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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 C,D (PNRC2_HUMAN | Q9NPJ4)

molecular function
	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: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: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:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
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: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.

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	4b6h
		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
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		Structure Classification	:	CATH \| Dali \| SCOP
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	DCP1A_HUMAN \| Q9NPI6
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	PNRC2_HUMAN \| Q9NPJ4
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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	3.-.-.-
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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Description

Compounds