1PX5 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE 2'-SPECIFIC AND DOUBLE-STRANDED RNA-ACTIVATED INTERFERON-INDUCED ANTIVIRAL PROTEIN 2'-5'-OLIGOADENYLATE SYNTHETASE

Authors :   R. Hartmann, J. Justesen, S. N. Sarkar, G. C. Sen, V. C. Yee

Date :   02 Jul 03 (Deposition) - 25 Nov 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.74

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   5-Stranded Antiparalel Beta Sheet, Four Helix Bundle, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Hartmann, J. Justesen, S. N. Sarkar, G. C. Sen, V. C. Yee
Crystal Structure Of The 2'-Specific And Double-Stranded Rna-Activated Interferon-Induced Antiviral Protein 2'-5'-Oligoadenylate Synthetase
Mol. Cell V. 12 1173 2003
PubMed-ID: 14636576 | Reference-DOI: 10.1016/S1097-2765(03)00433-7
(for further references see the PDB file header)

Molecule 1 - 2'-5'-OLIGOADENYLATE SYNTHETASE 1
	Chains	:	A, B
	EC Number	:	2.7.7.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	OAS1
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823
	Synonym	:	(2-5')OLIGO(A)SYNTHETASE 1, 2-5A SYNTHETASE 1, P42 OAS

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION
2	YCM	4	Mod. Amino Acid	S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION
2	YCM	2	Mod. Amino Acid	S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION
2	YCM	2	Mod. Amino Acid	S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:103 , ALA A:107 , ARG A:110 , LYS A:246 , HOH A:833 , HOH A:835 , HOH A:890 , HOH A:928 , HOH A:937 , HOH A:986	BINDING SITE FOR RESIDUE SO4 A 801
2	AC2	SOFTWARE	GLN B:46 , ARG B:53 , LYS B:246 , HOH B:894 , HOH B:1035	BINDING SITE FOR RESIDUE SO4 B 802
3	AC3	SOFTWARE	ARG A:295 , HOH A:1155	BINDING SITE FOR RESIDUE SO4 A 803
4	AC4	SOFTWARE	ARG B:38 , HOH B:849	BINDING SITE FOR RESIDUE SO4 B 804

(no "SS Bond" information available for 1PX5)

Asymmetric Unit

No.	Residues
1	Arg A:295	-	Pro A:296
2	Arg B:295	-	Pro B:296

(no "SAP(SNP)/Variant" information available for 1PX5)

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	25A_SYNTH_3	PS50152	2'-5'-oligoadenylate synthase N-terminal region profile.	OAS1_PIG	16-104	2	A:16-104 B:16-104
2	25A_SYNTH_1	PS00832	2'-5'-oligoadenylate synthases signature 1.	OAS1_PIG	61-80	2	A:61-80 B:61-80
3	25A_SYNTH_2	PS00833	2'-5'-oligoadenylate synthases signature 2.	OAS1_PIG	295-305	2	A:295-305 B:295-305

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	25A_SYNTH_3	PS50152	2'-5'-oligoadenylate synthase N-terminal region profile.	OAS1_PIG	16-104	1	A:16-104 -
2	25A_SYNTH_1	PS00832	2'-5'-oligoadenylate synthases signature 1.	OAS1_PIG	61-80	1	A:61-80 -
3	25A_SYNTH_2	PS00833	2'-5'-oligoadenylate synthases signature 2.	OAS1_PIG	295-305	1	A:295-305 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	25A_SYNTH_3	PS50152	2'-5'-oligoadenylate synthase N-terminal region profile.	OAS1_PIG	16-104	1	- B:16-104
2	25A_SYNTH_1	PS00832	2'-5'-oligoadenylate synthases signature 1.	OAS1_PIG	61-80	1	- B:61-80
3	25A_SYNTH_2	PS00833	2'-5'-oligoadenylate synthases signature 2.	OAS1_PIG	295-305	1	- B:295-305

(no "Exon" information available for 1PX5)

Asymmetric Unit

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	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:329
 aligned with OAS1_PIG | Q29599 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:346
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340      
             OAS1_PIG     1 MELRHTPARDLDKFIEDHLLPNTCFRTQVKEAIDIVCRFLKERCFQGTADPVRVSKVVKGGSSGKGTTLRGRSDADLVVFLTKLTSFEDQLRRRGEFIQEIRRQLEACQREQKFKVTFEVQSPRRENPRALSFVLSSPQLQQEVEFDVLPAFDALGQWTPGYKPNPEIYVQLIKECKSRGKEGEFSTCFTELQRDFLRNRPTKLKSLIRLVKHWYQTCKKTHGNKLPPQYALELLTVYAWEQGSRKTDFSTAQGFQTVLELVLKHQKLCIFWEAYYDFTNPVVGRCMLQQLKKPRPVILDPADPTGNVGGGDTHSWQRLAQEARVWLGYPCCKNLDGSLVGAWTML 346
               SCOP domains d1px5a2 A:1-200 2'-5'-oligoadenylate synthetase    1, OAS1, N-t        erminal domain                                                                                                                   d1px5a1 A:201-346 2'-5'-oligoadenylate synthetase 1, OAS1, second domain                                                                           SCOP domains
               CATH domains 1px5A01 A:1-160 Beta Polymerase, domain 2                                                                                                                       1px5A02 A:161-346 2'-5'-oligoadenylate synthetase 1, domain 2                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...---..eeeeeeeeee.--------.eeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh....eeee...------..eeeee......eeeeeeeeee............hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.ee.........hhhhhhhhhhhhh....ee.............hhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------25A_SYNTH_3  PDB: A:16-104 UniProt: 16-104                                               ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------25A_SYNTH_2----------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------25A_SYNTH_1         -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1px5 A   1 MELRHTPARDLDKFIEDHLLPNTcFRTQVKEAIDIVcRFLKERCFQG---PVRVSKVVKGGSS--------RSDADLVVFLTKLTSFEDQLRRRGEFIQEIRRQLEACQREQKFKVTFEVQSP------ALSFVLSSPQLQQEVEFDVLPAFDALGQWTPGYKPNPEIYVQLIKECKSRGKEGEFSTCFTELQRDFLRNRPTKLKSLIRLVKHWYQTCKKTHGNKLPPQYALELLTVYAWEQGSRKTDFSTAQGFQTVLELVLKHQKLCIFWEAYYDFTNPVVGRCMLQQLKKPRPVILDPADPTGNVGGGDTHSWQRLAQEARVWLGYPCCKNLDGSLVGAWTML 346
                                    10        20   |    30      | 40      |  -|       60  |      - |      80        90       100       110       120  |    130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340      
                                                  24-YCM       37-YCM    47  51          63       72                                                123    130

Chain B from PDB  Type:PROTEIN  Length:341
 aligned with OAS1_PIG | Q29599 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:349
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340         
             OAS1_PIG     1 MELRHTPARDLDKFIEDHLLPNTCFRTQVKEAIDIVCRFLKERCFQGTADPVRVSKVVKGGSSGKGTTLRGRSDADLVVFLTKLTSFEDQLRRRGEFIQEIRRQLEACQREQKFKVTFEVQSPRRENPRALSFVLSSPQLQQEVEFDVLPAFDALGQWTPGYKPNPEIYVQLIKECKSRGKEGEFSTCFTELQRDFLRNRPTKLKSLIRLVKHWYQTCKKTHGNKLPPQYALELLTVYAWEQGSRKTDFSTAQGFQTVLELVLKHQKLCIFWEAYYDFTNPVVGRCMLQQLKKPRPVILDPADPTGNVGGGDTHSWQRLAQEARVWLGYPCCKNLDGSLVGAWTMLQKI 349
               SCOP domains d1px5b2 B:1-200 2'-5'-oligoadenylate synthetase 1, OAS1, N-termina   l domain                                                                                                                           d1px5b1 B:201-349 2'-5'-oligoadenylate synthetase 1, OAS1, second domain                                                                              SCOP domains
               CATH domains 1px5B01 B:1-160 Beta Polymerase, domain 2                                                                                                                       1px5B02 B:161-349 2'-5'-oligoadenylate synthetase 1, domain 2                                                                                                                                 CATH domains
           Pfam domains (1) -----------------------------------NTP_transf_2-1px5B01 B:36-131                                                                   -----------------------------OAS1_C-1px5B03 B:161-349                                                                                                                                                                      Pfam domains (1)
           Pfam domains (2) -----------------------------------NTP_transf_2-1px5B02 B:36-131                                                                   -----------------------------OAS1_C-1px5B04 B:161-349                                                                                                                                                                      Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.........eeeeeeeee....---..eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh....eeee...-----...eeeeee....eeeeeeeeeee............hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.ee.........hhhhhhhhhhhhh....ee.............hhhhhhhhhhhhhhhhhhhhhh.........hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------25A_SYNTH_3  PDB: B:16-104 UniProt: 16-104                                               ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------25A_SYNTH_2-------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------25A_SYNTH_1         ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1px5 B   1 MELRHTPARDLDKFIEDHLLPNTcFRTQVKEAIDIVcRFLKERCFQGTADPVRVSKVVKGGSSGKG---RGRSDADLVVFLTKLTSFEDQLRRRGEFIQEIRRQLEACQREQKFKVTFEVQSP-----RALSFVLSSPQLQQEVEFDVLPAFDALGQWTPGYKPNPEIYVQLIKECKSRGKEGEFSTCFTELQRDFLRNRPTKLKSLIRLVKHWYQTCKKTHGNKLPPQYALELLTVYAWEQGSRKTDFSTAQGFQTVLELVLKHQKLCIFWEAYYDFTNPVVGRCMLQQLKKPRPVILDPADPTGNVGGGDTHSWQRLAQEARVWLGYPCCKNLDGSLVGAWTMLQKI 349
                                    10        20   |    30      | 40        50        60     |  70        80        90       100       110       120  |    130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340         
                                                  24-YCM       37-YCM                       66  70                                                  123   129

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 Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Beta Polymerase; domain 2 (187)

Homologous Superfamily: Beta Polymerase, domain 2 (183)

Pig (Sus scrofa) (1)

1a	1px5A01	A:1-160
1b	1px5B01	B:1-160

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Poly(a)-polymerase, middle domain (9)

Homologous Superfamily: 2'-5'-oligoadenylate synthetase 1, domain 2 (1)

Pig (Sus scrofa) (1)

2a	1px5A02	A:161-346
2b	1px5B02	B:161-349

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NTP_transf (45)

Family: NTP_transf_2 (35)

Sus scrofa (Pig) (1)

1a	NTP_transf_2-1px5B01	B:36-131
1b	NTP_transf_2-1px5B02	B:36-131

Clan: no clan defined [family: OAS1_C] (1)

Family: OAS1_C (1)

Sus scrofa (Pig) (1)

2a	OAS1_C-1px5B03	B:161-349
2b	OAS1_C-1px5B04	B:161-349

Asymmetric Unit(hide GO term definitions)

Chain A,B (OAS1_PIG | Q29599)

molecular function
	GO:0001730	2'-5'-oligoadenylate synthetase activity	Catalysis of the reaction: ATP = pppA(2'p5'A)n oligomers. This reaction requires the binding of double-stranded RNA.
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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: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:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0051607	defense response to virus	Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
	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:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0045071	negative regulation of viral genome replication	Any process that stops, prevents, or reduces the frequency, rate or extent of viral genome replication.
	GO:0006164	purine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	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:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	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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(no "Related Entries Specified in the PDB File" available for 1PX5)

Description

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