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Title :   SOLUTION STRUCTURE OF THE DSRM DOMAIN OF PROTEIN ACTIVATOR OF THE INTERFERON-INDUCED PROTEIN KINASE

Authors :   W. Dang, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   30 Mar 06 (Deposition) - 30 Sep 06 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Nmr, Structure Genomics, Dsrm Domain, Hypothetical Protein Prkra, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Dang, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama
Solution Structure Of The Dsrm Domain Of Protein Activator Of The Interferon-Induced Protein Kinase
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - INTERFERON-INDUCIBLE DOUBLE STRANDED RNA- DEPENDENT PROTEIN KINASE ACTIVATOR A
	Chains	:	A
	Engineered	:	YES
	Expression System	:	CELL FREE SYNTHESIS
	Expression System Plasmid	:	P050912-05
	Expression System Vector Type	:	PLASMID
	Fragment	:	DSRM DOMAIN
	Gene	:	PRKRA, DKFZP564I0123, PACT
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL FREE PROTEIN SYNTHESIS
	Synonym	:	PROTEIN ACTIVATOR OF THE INTERFERON-INDUCED PROTEIN KINASE, PROTEIN KINASE, INTERFERON-INDUCIBLE DOUBLE STRANDED RNA DEPENDENT ACTIVATOR, PKR-ASSOCIATED PROTEIN X, HYPOTHETICAL PROTEIN DKFZP564I0123


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2DIX)

(no "Site" information available for 2DIX)

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

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

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

NMR Structure (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DS_RBD	PS50137	Double stranded RNA-binding domain (dsRBD) profile.	PRKRA_HUMAN	34-101 126-194 240-308	2	A:9-76 A:84-84 -

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2a	ENST00000325748	2a	ENSE00001657361	chr2:179315958-179315693	266	PRKRA_HUMAN	1-22	22	1	A:1-5	5
1.2k	ENST00000325748	2k	ENSE00001621396	chr2:179315138-179314969	170	PRKRA_HUMAN	22-79	58	1	A:6-54	49
1.3a	ENST00000325748	3a	ENSE00002130594	chr2:179312313-179312232	82	PRKRA_HUMAN	79-106	28	1	A:54-79	26
1.5	ENST00000325748	5	ENSE00002098950	chr2:179309227-179309149	79	PRKRA_HUMAN	106-132	27	1	A:80-84 (gaps)	14
1.6d	ENST00000325748	6d	ENSE00002100222	chr2:179308111-179307994	118	PRKRA_HUMAN	133-172	40	0	-	-
1.7	ENST00000325748	7	ENSE00002096970	chr2:179306431-179306337	95	PRKRA_HUMAN	172-203	32	0	-	-
1.8b	ENST00000325748	8b	ENSE00002109738	chr2:179301046-179300872	175	PRKRA_HUMAN	204-262	59	0	-	-
1.9f	ENST00000325748	9f	ENSE00001248246	chr2:179296981-179296141	841	PRKRA_HUMAN	262-313	52	0	-	-

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

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Chain A from PDB  Type:PROTEIN  Length:84
 aligned with PRKRA_HUMAN | O75569 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:114
                                    25        35        45        55        65        75        85        95       105       115       125    
          PRKRA_HUMAN    16 EDSGTFSLGKMITAKPGKTPIQVLHEYGMKTKNIPVYECERSDVQIHVPTFTFRVTVGDITCTGEGTSKKLAKHRAAEAAINILKANASICFAVPDPLMPDPSKQPKNQLNPIG 129
               SCOP domains ----------------d2dixa1 A:7-79                                                           ------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....----------....hhhhhhhhhhh.....eeeeeeee......eeeeeeee..eeeee......hhhhhhhhhhhhhhhh...-----------....---------. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------DS_RBD  PDB: A:9-76 UniProt: 34-101                                 ------------------------DS_R PROSITE
           Transcript 1 (1) 1.2a   --------------------------------------------------------Exon 1.3a  PDB: A:54-79     ----------------------- Transcript 1 (1)
           Transcript 1 (2) ------Exon 1.2k  PDB: A:6-54 UniProt: 22-79 [INCOMPLETE]        --------------------------Exon 1.5 [INCOMPLETE]    Transcript 1 (2)
                 2dix A   1 GSSGS----------SGKTPIQVLHEYGMKTKNIPVYECERSDVQIHVPTFTFRVTVGDITCTGEGTSKKLAKHRAAEAAINILKANAS-----------GPSS---------G  84
                                |    -     |  10        20        30        40        50        60        70        |-         -|  |     -   |
                                5          6                                                                       79          80 83        84

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 '\|'

NMR Structure

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

)

Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: dsRBD-like (111)

Superfamily: dsRNA-binding domain-like (98)

Family: Double-stranded RNA-binding domain (dsRBD) (34)

Protein domain: Interferon-inducible double stranded RNA-dependent protein kinase activator A (1)

Human (Homo sapiens) [TaxId: 9606] (1)

d2dixa1

A:7-79

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

(no "Pfam Domain" information available for 2DIX)

NMR Structure(hide GO term definitions)

Chain A (PRKRA_HUMAN | O75569)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003725	double-stranded RNA binding	Interacting selectively and non-covalently with double-stranded RNA.
	GO:0008047	enzyme activator activity	Binds to and increases the activity of an enzyme.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0034599	cellular response to oxidative stress	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	GO:0031047	gene silencing by RNA	Any process in which RNA molecules inactivate expression of target genes.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0042474	middle ear morphogenesis	The process in which the anatomical structures of the middle ear are generated and organized. The middle ear is the air-filled cavity within the skull of vertebrates that lies between the outer ear and the inner ear. It is linked to the pharynx (and therefore to outside air) via the Eustachian tube and in mammals contains the three ear ossicles, which transmit auditory vibrations from the outer ear (via the tympanum) to the inner ear (via the oval window).
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0042473	outer ear morphogenesis	The process in which the anatomical structures of the outer ear are generated and organized. The outer ear is the part of the ear external to the tympanum (eardrum). It consists of a tube (the external auditory meatus) that directs sound waves on to the tympanum, and may also include the external pinna, which extends beyond the skull.
	GO:0043085	positive regulation of catalytic activity	Any process that activates or increases the activity of an enzyme.
	GO:2001244	positive regulation of intrinsic apoptotic signaling pathway	Any process that activates or increases the frequency, rate or extent of intrinsic apoptotic signaling pathway.
	GO:0031054	pre-miRNA processing	Any process involved in the conversion of a pre-microRNA transcript into a mature microRNA molecule.
	GO:0035196	production of miRNAs involved in gene silencing by miRNA	Cleavage of stem-loop RNA precursors into microRNAs (miRNAs), a class of small RNAs that primarily silence genes by blocking the translation of mRNA transcripts into protein.
	GO:0030422	production of siRNA involved in RNA interference	Cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides, in the context of RNA interference.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0009615	response to virus	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a virus.
	GO:0048705	skeletal system morphogenesis	The process in which the anatomical structures of the skeleton are generated and organized.
cellular component
	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:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.

NMR Structure
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