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Protein

Genome polyprotein

Gene
N/A
Organism
Dengue virus type 2 (strain Puerto Rico/PR159-S1/1969) (DENV-2)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Protein C: Plays a role in virus budding by binding to membrane and gathering the viral RNA into a nucleocapsid that forms the core of a mature virus particle. During virus entry, may induce genome penetration in host cytoplasm after hemifusion induced by surface proteins. Can migrate tot cell nucleus where it modulates host functions.By similarity
Peptide pr: Prevents premature fusion activity of envelope proteins in trans Golgi by binding to envelope protein E at pH6.0. After virion release in extracellular space gets dissociated from E dimers.By similarity
Protein prM: Acts as a chaperone for envelope protein E during intracellular virion assembly by masking and inactivating envelope protein E fusion peptide. prM is the only viral peptide matured by host furin in the trans-Golgi network. Presumably to avoid catastrophic activation of the viral fusion activity in acidic GolGi compartment prior to virion release. prM-E cleavage is ineficient, and many virions are only partially matured. These uncleaved prM would play a role in immune evasion.By similarity
Small envelope protein M: May play a role in virus budding. Exerts cytotoxic effects by activating a mitochondrial apoptotic pathway through M extodomain. May display a viroporin activity.By similarity
Envelope protein E: Binds to host cell surface receptor and mediates fusion between viral and cellular membranes. Envelope protein is synthesized in the endoplasmic reticulum in the form of heterodimer with protein prM. They play a role in virion budding in the ER, and the newly formed immature particule is covered with 60 spikes composed of heterodimer between precursor prM and envelope protein E. The virion is transported to the Golgi apparatus where the low pH causes dissociation of PrM-E heterodimers and formation of E homodimers. prM-E cleavage is ineficient, and many virions are only partially matured. These uncleaved prM would play a role in immune evasion.By similarity
Non-structural protein 1: Involved in immune evasion, pathogenesis and viral replication. Once cleaved off the polyprotein, is targeted to three destinations: the viral replication cycle, the plasma membrane and the extracellular compartment. May plays a role in viral genome replication. Assist membrane bending and envelopment of genomic RNA at the endoplasmic reticulum. Excreted as a hexameric lipoparticle that plays a role against host immune responce.By similarity
Non-structural protein 2A: Component of the viral RNA replication complex that functions in virion assembly and antagonizes the host immune response.By similarity
Non-structural protein 2B: Required cofactor for the serine protease function of NS3 (By similarity). May have membrane-destabilizing activity and form viroporins (By similarity).PROSITE-ProRule annotationBy similarity
Serine protease NS3: Displays three enzymatic activities: serine protease, NTPase and RNA helicase. NS3 serine protease, in association with NS2B, performs its autocleavage and cleaves the polyprotein at dibasic sites in the cytoplasm: C-prM, NS2A-NS2B, NS2B-NS3, NS3-NS4A, NS4A-2K and NS4B-NS5. NS3 RNA helicase binds RNA and unwinds dsRNA in the 3' to 5' direction.PROSITE-ProRule annotation
Non-structural protein 4A: Induces host endoplasmic regulate the ATPase activity of the NS3 helicase.By similarity
Peptide 2k: Functions as a signal peptide for NS4B and is required for the interferon antagonism activity of the latter.By similarity
Non-structural protein 4B: Inhibits interferon (IFN)-induced host STAT1 phosphorylation and nuclear translocation, thereby preventing the establishment of cellular antiviral state by blocking the IFN-alpha/beta pathway.By similarity
RNA-directed RNA polymerase NS5: Replicates the viral (+) and (-) genome, and performs the capping of genomes in the cytoplasm. NS5 methylates viral RNA cap at guanine N-7 and ribose 2'-O positions. Besides its role in genome replication, also prevents the establishment of cellular antiviral state by blocking the interferon-alpha/beta (IFN-alpha/beta) signaling pathway. Inhibits host TYK2 and STAT2 phosphorylation, thereby preventing activation of JAK-STAT signaling pathway.By similarity

Catalytic activityi

Selective hydrolysis of -Xaa-Xaa-|-Yaa- bonds in which each of the Xaa can be either Arg or Lys and Yaa can be either Ser or Ala.
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).PROSITE-ProRule annotation
NTP + H2O = NDP + phosphate.
ATP + H2O = ADP + phosphate.
S-adenosyl-L-methionine + G(5')pppR-RNA = S-adenosyl-L-homocysteine + m7G(5')pppR-RNA.PROSITE-ProRule annotation
S-adenosyl-L-methionine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(purine-ribonucleotide)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-purine-ribonucleotide)-[mRNA].

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei1526Charge relay system; for serine protease NS3 activityPROSITE-ProRule annotation1
Active sitei1550Charge relay system; for serine protease NS3 activityPROSITE-ProRule annotation1
Active sitei1610Charge relay system; for serine protease NS3 activityPROSITE-ProRule annotation1
Binding sitei2502mRNA capPROSITE-ProRule annotation1
Binding sitei2505mRNA cap; via carbonyl oxygenPROSITE-ProRule annotation1
Binding sitei2506mRNA capPROSITE-ProRule annotation1
Binding sitei2508mRNA cap; via carbonyl oxygenPROSITE-ProRule annotation1
Sitei2513mRNA cap bindingPROSITE-ProRule annotation1
Binding sitei2517mRNA capPROSITE-ProRule annotation1
Binding sitei2544S-adenosyl-L-methionine1
Sitei2549Essential for 2'-O-methyltransferase activityPROSITE-ProRule annotation1
Binding sitei2574S-adenosyl-L-methionine; via carbonyl oxygen1
Binding sitei2575S-adenosyl-L-methionine; via carbonyl oxygen1
Binding sitei2592S-adenosyl-L-methionine1
Binding sitei2593S-adenosyl-L-methionine; via carbonyl oxygen1
Binding sitei2619S-adenosyl-L-methionine1
Binding sitei2620S-adenosyl-L-methionine; via carbonyl oxygen1
Sitei2634Essential for 2'-O-methyltransferase and N-7 methyltransferase activityPROSITE-ProRule annotation1
Sitei2635S-adenosyl-L-methionine binding1
Binding sitei2638mRNA capPROSITE-ProRule annotation1
Sitei2669Essential for 2'-O-methyltransferase activityPROSITE-ProRule annotation1
Binding sitei2700mRNA capPROSITE-ProRule annotation1
Binding sitei2702mRNA capPROSITE-ProRule annotation1
Sitei2705Essential for 2'-O-methyltransferase activityPROSITE-ProRule annotation1
Binding sitei2707S-adenosyl-L-methionine1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi1668 – 1675ATPPROSITE-ProRule annotation8

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase, Ion channel, Methyltransferase, Nucleotidyltransferase, Protease, RNA-directed RNA polymerase, Serine protease, Transferase, Viral ion channel

Keywords - Biological processi

Activation of host autophagy by virus, Clathrin-mediated endocytosis of virus by host, Fusion of virus membrane with host endosomal membrane, Fusion of virus membrane with host membrane, Host-virus interaction, Inhibition of host innate immune response by virus, Inhibition of host interferon signaling pathway by virus, Inhibition of host STAT2 by virus, Inhibition of host TYK2 by virus, Ion transport, mRNA capping, mRNA processing, Transcription, Transcription regulation, Transport, Viral attachment to host cell, Viral immunoevasion, Viral penetration into host cytoplasm, Viral RNA replication, Virus endocytosis by host, Virus entry into host cell

Keywords - Ligandi

ATP-binding, Metal-binding, Nucleotide-binding, RNA-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

BRENDAi2.1.1.57. 1867.

Names & Taxonomyi

Protein namesi
Recommended name:
Genome polyprotein
Cleaved into the following 14 chains:
Alternative name(s):
Core protein
Alternative name(s):
Matrix protein
Non-structural protein 2A-alpha
Short name:
NS2A-alpha
Alternative name(s):
Flavivirin protease NS2B regulatory subunit
Non-structural protein 2B
Alternative name(s):
Flavivirin protease NS3 catalytic subunit
Non-structural protein 3
Alternative name(s):
Non-structural protein 5
OrganismiDengue virus type 2 (strain Puerto Rico/PR159-S1/1969) (DENV-2)
Taxonomic identifieri11066 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stageFlaviviridaeFlavivirusDengue virus group
Virus hostiAedimorphus [TaxID: 53540]
Diceromyia [TaxID: 53539]
Erythrocebus patas (Red guenon) (Cercopithecus patas) [TaxID: 9538]
Homo sapiens (Human) [TaxID: 9606]
Stegomyia [TaxID: 53541]
Proteomesi
  • UP000007197 Componenti: Genome

Subcellular locationi

Protein C :
  • Virion By similarity
  • Host nucleus By similarity
Peptide pr :
  • Secreted By similarity
Small envelope protein M :
  • Virion membrane By similarity; Multi-pass membrane protein By similarity
  • Host endoplasmic reticulum membrane PROSITE-ProRule annotationBy similarity; Multi-pass membrane protein By similarity
Envelope protein E :
  • Virion membrane By similarity; Multi-pass membrane protein By similarity
  • Host endoplasmic reticulum membrane PROSITE-ProRule annotationBy similarity; Multi-pass membrane protein By similarity
Non-structural protein 1 :
  • Secreted By similarity
  • Host endoplasmic reticulum membrane PROSITE-ProRule annotation; Peripheral membrane protein PROSITE-ProRule annotation; Lumenal side By similarity
Non-structural protein 2A-alpha :
  • Host endoplasmic reticulum membrane PROSITE-ProRule annotation; Multi-pass membrane protein By similarity
Non-structural protein 2A :
  • Host endoplasmic reticulum membrane PROSITE-ProRule annotation; Multi-pass membrane protein By similarity
Serine protease subunit NS2B :
  • Host endoplasmic reticulum membrane PROSITE-ProRule annotation; Peripheral membrane protein PROSITE-ProRule annotation; Cytoplasmic side PROSITE-ProRule annotationBy similarity
Serine protease NS3 :
  • Host endoplasmic reticulum membrane PROSITE-ProRule annotation; Peripheral membrane protein PROSITE-ProRule annotation; Cytoplasmic side PROSITE-ProRule annotation

  • Note: Remains non-covalently associated to NS3 protease.PROSITE-ProRule annotation
Non-structural protein 4A :
  • Host endoplasmic reticulum membrane PROSITE-ProRule annotation; Multi-pass membrane protein By similarity

  • Note: Located in RE-associated vesicles hosting the replication complex.By similarity
Non-structural protein 4B :
  • Host endoplasmic reticulum membrane PROSITE-ProRule annotation; Multi-pass membrane protein By similarity
RNA-directed RNA polymerase NS5 :
  • Host endoplasmic reticulum membrane PROSITE-ProRule annotation; Peripheral membrane protein PROSITE-ProRule annotation; Cytoplasmic side PROSITE-ProRule annotation
  • Host nucleus By similarity

  • Note: Located in RE-associated vesicles hosting the replication complex.By similarity

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 101CytoplasmicSequence analysisAdd BLAST101
Transmembranei102 – 122HelicalSequence analysisAdd BLAST21
Topological domaini123 – 238ExtracellularSequence analysisAdd BLAST116
Transmembranei239 – 259HelicalSequence analysisAdd BLAST21
Topological domaini260 – 265CytoplasmicSequence analysis6
Transmembranei266 – 280HelicalSequence analysisAdd BLAST15
Topological domaini281 – 725ExtracellularSequence analysisAdd BLAST445
Intramembranei726 – 746HelicalSequence analysisAdd BLAST21
Topological domaini747 – 752ExtracellularSequence analysis6
Intramembranei753 – 773HelicalSequence analysisAdd BLAST21
Topological domaini774 – 1124ExtracellularSequence analysisAdd BLAST351
Transmembranei1125 – 1145HelicalSequence analysisAdd BLAST21
Topological domaini1146 – 1156CytoplasmicSequence analysisAdd BLAST11
Transmembranei1157 – 1177HelicalSequence analysisAdd BLAST21
Topological domaini1178 – 1184LumenalSequence analysis7
Transmembranei1185 – 1205HelicalSequence analysisAdd BLAST21
Topological domaini1206 – 1271CytoplasmicSequence analysisAdd BLAST66
Transmembranei1272 – 1292HelicalSequence analysisAdd BLAST21
Topological domaini1293 – 1317LumenalSequence analysisAdd BLAST25
Transmembranei1318 – 1338HelicalSequence analysisAdd BLAST21
Topological domaini1339 – 1346CytoplasmicSequence analysis8
Transmembranei1347 – 1367HelicalSequence analysisAdd BLAST21
Topological domaini1368 – 1370LumenalSequence analysis3
Transmembranei1371 – 1391HelicalSequence analysisAdd BLAST21
Topological domaini1392 – 1447CytoplasmicSequence analysisAdd BLAST56
Intramembranei1448 – 1468HelicalSequence analysisAdd BLAST21
Topological domaini1469 – 2144CytoplasmicSequence analysisAdd BLAST676
Transmembranei2145 – 2165HelicalSequence analysisAdd BLAST21
Topological domaini2166 – 2167LumenalSequence analysis2
Intramembranei2168 – 2188HelicalSequence analysisAdd BLAST21
Topological domaini2189LumenalSequence analysis1
Transmembranei2190 – 2210HelicalSequence analysisAdd BLAST21
Topological domaini2211 – 2225CytoplasmicSequence analysisAdd BLAST15
Transmembranei2226 – 2246Helical; Note=Signal for NS4BSequence analysisAdd BLAST21
Topological domaini2247 – 2274LumenalSequence analysisAdd BLAST28
Intramembranei2275 – 2292HelicalSequence analysisAdd BLAST18
Topological domaini2293 – 2313LumenalSequence analysisAdd BLAST21
Intramembranei2314 – 2334HelicalSequence analysisAdd BLAST21
Topological domaini2335 – 2344LumenalSequence analysis10
Transmembranei2345 – 2365HelicalSequence analysisAdd BLAST21
Topological domaini2366 – 2410CytoplasmicSequence analysisAdd BLAST45
Transmembranei2411 – 2431HelicalSequence analysisAdd BLAST21
Topological domaini2432 – 2456LumenalSequence analysisAdd BLAST25
Transmembranei2457 – 2477HelicalSequence analysisAdd BLAST21
Topological domaini2478 – 3388CytoplasmicSequence analysisAdd BLAST911

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Host endoplasmic reticulum, Host membrane, Host nucleus, Membrane, Secreted, Viral envelope protein, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004052171 – 3388Genome polyproteinAdd BLAST3388
ChainiPRO_00000379691 – 100Protein CBy similarityAdd BLAST100
PropeptideiPRO_0000037970101 – 114ER anchor for the protein C, removed in mature form by serine protease NS3By similarityAdd BLAST14
ChainiPRO_0000308286115 – 280prMBy similarityAdd BLAST166
ChainiPRO_0000308287115 – 205Peptide prBy similarityAdd BLAST91
ChainiPRO_0000037971206 – 280Small envelope protein MBy similarityAdd BLAST75
ChainiPRO_0000037972281 – 775Envelope protein EBy similarityAdd BLAST495
ChainiPRO_0000037973776 – 1127Non-structural protein 1By similarityAdd BLAST352
ChainiPRO_00000379741128 – 1345Non-structural protein 2ABy similarityAdd BLAST218
ChainiPRO_00003082881128 – 1315Non-structural protein 2A-alphaBy similarityAdd BLAST188
ChainiPRO_00000379751346 – 1475Serine protease subunit NS2BBy similarityAdd BLAST130
ChainiPRO_00000379761476 – 2090Serine protease NS3By similarityAdd BLAST615
ChainiPRO_00000379772091 – 2217Non-structural protein 4ABy similarityAdd BLAST127
PeptideiPRO_00003082892218 – 2240Peptide 2kBy similarityAdd BLAST23
ChainiPRO_00000379782241 – 2488Non-structural protein 4BBy similarityAdd BLAST248
ChainiPRO_00000379792489 – 3388RNA-directed RNA polymerase NS5By similarityAdd BLAST900

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi183N-linked (GlcNAc...); by hostSequence analysis1
Disulfide bondi283 ↔ 3101 Publication
Disulfide bondi340 ↔ 4011 Publication
Glycosylationi347N-linked (GlcNAc...); by hostSequence analysis1
Disulfide bondi354 ↔ 3851 Publication
Disulfide bondi372 ↔ 3961 Publication
Glycosylationi433N-linked (GlcNAc...); by hostSequence analysis1
Disulfide bondi465 ↔ 5651 Publication
Disulfide bondi582 ↔ 6131 Publication
Disulfide bondi779 ↔ 7901 Publication
Disulfide bondi830 ↔ 9181 Publication
Glycosylationi905N-linked (GlcNAc...); by hostSequence analysis1
Disulfide bondi954 ↔ 9981 Publication
Glycosylationi982N-linked (GlcNAc...); by hostSequence analysis1
Disulfide bondi1055 ↔ 11041 Publication
Disulfide bondi1066 ↔ 10881 Publication
Disulfide bondi1087 ↔ 10911 Publication
Glycosylationi2298N-linked (GlcNAc...); by hostSequence analysis1
Glycosylationi2302N-linked (GlcNAc...); by hostSequence analysis1

Post-translational modificationi

Genome polyprotein: Specific enzymatic cleavages in vivo yield mature proteins. Cleavages in the lumen of endoplasmic reticulum are performed by host signal peptidase, wereas cleavages in the cytoplasmic side are performed by the Serine protease NS3. Signal cleavage at the 2K-4B site requires a prior NS3 protease-mediated cleavage at the 4A-2K site.By similarity
Non-structural protein 2A-alpha: A C-terminally truncated form of non-structural protein 2A, results from partial cleavage by NS3.By similarity
Protein prM: Cleaved in post-Golgi vesicles by a host furin, releasing the mature small envelope protein M, and peptide pr. This cleavage is incomplete as up to 30% of viral particles still carry uncleaved prM.By similarity
Non-structural protein 1: The excreted form is glycosylated and this is required for efficient secretion of the protein from infected cells.By similarity
RNA-directed RNA polymerase NS5: Phosphorylated on serines residues. This phosphorylation may trigger NS5 nuclear localization.By similarity
Envelope protein E: N-glycosylated.By similarity
Non-structural protein 1: N-glycosylated.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei100 – 101Cleavage; by viral protease NS3Sequence analysis2
Sitei114 – 115Cleavage; by host signal peptidaseBy similarity2
Sitei205 – 206Cleavage; by host furinSequence analysis2
Sitei280 – 281Cleavage; by host signal peptidaseSequence analysis2
Sitei775 – 776Cleavage; by host signal peptidaseSequence analysis2
Sitei1127 – 1128Cleavage; by hostBy similarity2
Sitei1345 – 1346Cleavage; by viral protease NS3Sequence analysis2
Sitei1475 – 1476Cleavage; by autolysisSequence analysis2
Sitei2090 – 2091Cleavage; by autolysisSequence analysis2
Sitei2217 – 2218Cleavage; by viral protease NS3Sequence analysis2
Sitei2240 – 2241Cleavage; by host signal peptidaseSequence analysis2
Sitei2488 – 2489Cleavage; by viral protease NS3Sequence analysis2

Keywords - PTMi

Cleavage on pair of basic residues, Disulfide bond, Glycoprotein, Phosphoprotein

Interactioni

Subunit structurei

Protein C: Homodimerizes. Protein prM: Forms homodimers with envelope protein E in the endoplasmic reticulum and Golgi. Envelope protein E: Forms homodimers with envelope protein E in the endoplasmic reticulum and Golgi. Non-structural protein 1: Forms homodimers as well as homohexamers. NS1 may interact with NS4A. Non-structural protein 2B: Forms a heterodimer with Non-structural protein 3. May form homooligomers. Non-structural protein 3: Forms a heterodimer with Non-structural protein 2B. Interacts with Non-structural protein 4B. Interacts with unphosphorylated Non-structural protein 5; this interaction stimulates Non-structural protein 5 guanylyltransferase activity. Non-structural protein 4B: Interacts with non-structural protein 3. Non-structural protein 5: interacts with host STAT2; this interaction inhibits the phosphorylation of the latter, and, when all viral proteins are present (polyprotein), targets STAT2 for degradation.By similarity

Structurei

Secondary structure

13388
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi23 – 25Combined sources3
Helixi27 – 32Combined sources6
Beta strandi34 – 36Combined sources3
Helixi45 – 57Combined sources13
Helixi63 – 69Combined sources7
Helixi75 – 95Combined sources21
Turni282 – 285Combined sources4
Helixi288 – 290Combined sources3
Beta strandi291 – 293Combined sources3
Beta strandi295 – 306Combined sources12
Beta strandi311 – 315Combined sources5
Beta strandi320 – 332Combined sources13
Beta strandi334 – 352Combined sources19
Helixi363 – 366Combined sources4
Beta strandi370 – 379Combined sources10
Helixi381 – 383Combined sources3
Beta strandi389 – 409Combined sources21
Helixi412 – 414Combined sources3
Beta strandi415 – 424Combined sources10
Turni428 – 432Combined sources5
Beta strandi440 – 444Combined sources5
Beta strandi450 – 455Combined sources6
Turni456 – 458Combined sources3
Beta strandi459 – 467Combined sources9
Turni473 – 475Combined sources3
Beta strandi476 – 481Combined sources6
Beta strandi484 – 489Combined sources6
Helixi490 – 495Combined sources6
Beta strandi500 – 502Combined sources3
Helixi514 – 516Combined sources3
Beta strandi518 – 520Combined sources3
Beta strandi523 – 526Combined sources4
Beta strandi530 – 532Combined sources3
Helixi537 – 543Combined sources7
Turni544 – 546Combined sources3
Beta strandi547 – 550Combined sources4
Beta strandi552 – 559Combined sources8
Beta strandi562 – 571Combined sources10
Beta strandi586 – 594Combined sources9
Beta strandi600 – 606Combined sources7
Beta strandi608 – 610Combined sources3
Beta strandi612 – 614Combined sources3
Beta strandi617 – 624Combined sources8
Beta strandi631 – 633Combined sources3
Beta strandi645 – 649Combined sources5
Beta strandi653 – 661Combined sources9
Beta strandi667 – 673Combined sources7
Helixi2497 – 2507Combined sources11
Helixi2510 – 2517Combined sources8
Turni2518 – 2520Combined sources3
Beta strandi2522 – 2525Combined sources4
Helixi2527 – 2535Combined sources9
Beta strandi2543 – 2545Combined sources3
Helixi2546 – 2554Combined sources9
Turni2555 – 2557Combined sources3
Beta strandi2563 – 2568Combined sources6
Turni2571 – 2573Combined sources3
Helixi2574 – 2579Combined sources6
Beta strandi2585 – 2591Combined sources7
Helixi2609 – 2611Combined sources3
Beta strandi2612 – 2615Combined sources4
Helixi2620 – 2622Combined sources3
Beta strandi2629 – 2633Combined sources5
Helixi2642 – 2657Combined sources16
Beta strandi2665 – 2671Combined sources7
Helixi2676 – 2688Combined sources13
Beta strandi2692 – 2694Combined sources3
Beta strandi2706 – 2709Combined sources4
Helixi2716 – 2729Combined sources14
Beta strandi2739 – 2742Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1L9KX-ray2.40A2492-2784[»]
1OANX-ray2.75A/B281-674[»]
1OK8X-ray2.00A281-674[»]
1OKEX-ray2.40A/B281-674[»]
1P58electron microscopy9.50A/B/C281-775[»]
D/E/F206-280[»]
1R6AX-ray2.60A2492-2784[»]
1R6RNMR-A/B1-100[»]
1THDelectron microscopy9.50A/B/C281-675[»]
2P1DX-ray2.90A2492-2784[»]
2P3LX-ray2.20A2492-2784[»]
2P3OX-ray2.76A2492-2784[»]
2P3QX-ray2.75A2492-2784[»]
2P40X-ray2.70A2492-2784[»]
2P41X-ray1.80A2492-2784[»]
3J8Delectron microscopy26.00G/H/I281-674[»]
3ZKOelectron microscopy13.70A/B/C281-775[»]
5HHGX-ray2.20C3353-3388[»]
ProteinModelPortaliP12823.
SMRiP12823.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP12823.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1476 – 1653Peptidase S7PROSITE-ProRule annotationAdd BLAST178
Domaini1655 – 1811Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST157
Domaini1821 – 1988Helicase C-terminalPROSITE-ProRule annotationAdd BLAST168
Domaini2490 – 2752mRNA cap 0-1 NS5-type MTPROSITE-ProRule annotationAdd BLAST263
Domaini3017 – 3166RdRp catalyticPROSITE-ProRule annotationAdd BLAST150

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni33 – 74Hydrophobic; homodimerization of capsid protein CBy similarityAdd BLAST42
Regioni1398 – 1437Interacts with and activates NS3 proteasePROSITE-ProRule annotationAdd BLAST40

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi1759 – 1762DEAH box4

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi97 – 100Poly-Arg4
Compositional biasi1434 – 1437Poly-Glu4
Compositional biasi2145 – 2151Poly-Leu7
Compositional biasi2351 – 2354Poly-Leu4
Compositional biasi3380 – 3383Poly-Glu4

Domaini

Transmembrane domains of the small envelope protein M and envelope protein E contains an endoplasmic reticulum retention signals.By similarity

Sequence similaritiesi

In the N-terminal section; belongs to the class I-like SAM-binding methyltransferase superfamily. mRNA cap 0-1 NS5-type methyltransferase family.PROSITE-ProRule annotation
Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation
Contains 1 mRNA cap 0-1 NS5-type MT domain.PROSITE-ProRule annotation
Contains 1 peptidase S7 domain.PROSITE-ProRule annotation
Contains 1 RdRp catalytic domain.PROSITE-ProRule annotation

Keywords - Domaini

Transmembrane, Transmembrane helix

Family and domain databases

CDDicd12149. Flavi_E_C. 1 hit.
Gene3Di2.60.40.350. 1 hit.
2.60.98.10. 2 hits.
3.30.387.10. 1 hit.
3.40.50.150. 1 hit.
3.40.50.300. 2 hits.
InterProiIPR011492. DEAD_Flavivir.
IPR000069. Env_glycoprot_M_flavivir.
IPR013755. Flav_gly_cen_dom_subdom1.
IPR001122. Flavi_capsidC.
IPR027287. Flavi_E_Ig-like.
IPR026470. Flavi_E_Stem/Anchor_dom.
IPR001157. Flavi_NS1.
IPR000752. Flavi_NS2A.
IPR000487. Flavi_NS2B.
IPR000404. Flavi_NS4A.
IPR001528. Flavi_NS4B.
IPR002535. Flavi_propep.
IPR000336. Flavivir/Alphavir_Ig-like.
IPR001850. Flavivirus_NS3_S7.
IPR014412. Gen_Poly_FLV.
IPR011998. Glycoprot_cen/dimer.
IPR013754. GlyE_dim.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR014756. Ig_E-set.
IPR026490. mRNA_cap_0/1_MeTrfase.
IPR027417. P-loop_NTPase.
IPR009003. Peptidase_S1_PA.
IPR000208. RNA-dir_pol_flavivirus.
IPR007094. RNA-dir_pol_PSvirus.
IPR002877. rRNA_MeTrfase_FtsJ_dom.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF01003. Flavi_capsid. 1 hit.
PF07652. Flavi_DEAD. 1 hit.
PF02832. Flavi_glycop_C. 1 hit.
PF00869. Flavi_glycoprot. 1 hit.
PF01004. Flavi_M. 1 hit.
PF00948. Flavi_NS1. 1 hit.
PF01005. Flavi_NS2A. 1 hit.
PF01002. Flavi_NS2B. 1 hit.
PF01350. Flavi_NS4A. 1 hit.
PF01349. Flavi_NS4B. 1 hit.
PF00972. Flavi_NS5. 1 hit.
PF01570. Flavi_propep. 1 hit.
PF01728. FtsJ. 1 hit.
PF00949. Peptidase_S7. 1 hit.
[Graphical view]
PIRSFiPIRSF003817. Gen_Poly_FLV. 1 hit.
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 2 hits.
SSF53335. SSF53335. 1 hit.
SSF56983. SSF56983. 1 hit.
SSF81296. SSF81296. 1 hit.
TIGRFAMsiTIGR04240. flavi_E_stem. 1 hit.
PROSITEiPS51527. FLAVIVIRUS_NS2B. 1 hit.
PS51528. FLAVIVIRUS_NS3PRO. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS50507. RDRP_SSRNA_POS. 1 hit.
PS51591. RNA_CAP01_NS5_MT. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P12823-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNDQRKKARN TPFNMLKRER NRVSTVQQLT KRFSLGMLQG RGPLKLFMAL
60 70 80 90 100
VAFLRFLTIP PTAGILKRWG TIKKSKAINV LRGFRKEIGR MLNILNRRRR
110 120 130 140 150
TAGMIIMLIP TVMAFHLTTR NGEPHMIVSR QEKGKSLLFK TKDGTNMCTL
160 170 180 190 200
MAMDLGELCE DTITYKCPFL KQNEPEDIDC WCNSTSTWVT YGTCTTTGEH
210 220 230 240 250
RREKRSVALV PHVGMGLETR TETWMSSEGA WKHAQRIETW ILRHPGFTIM
260 270 280 290 300
AAILAYTIGT THFQRVLIFI LLTAIAPSMT MRCIGISNRD FVEGVSGGSW
310 320 330 340 350
VDIVLEHGSC VTTMAKNKPT LDFELIKTEA KQPATLRKYC IEAKLTNTTT
360 370 380 390 400
DSRCPTQGEP TLNEEQDKRF VCKHSMVDRG WGNGCGLFGK GGIVTCAMFT
410 420 430 440 450
CKKNMEGKIV QPENLEYTVV ITPHSGEEHA VGNDTGKHGK EVKITPQSSI
460 470 480 490 500
TEAELTGYGT VTMECSPRTG LDFNEMVLLQ MKDKAWLVHR QWFLDLPLPW
510 520 530 540 550
LPGADTQGSN WIQKETLVTF KNPHAKKQDV VVLGSQEGAM HTALTGATEI
560 570 580 590 600
QMSSGNLLFT GHLKCRLRMD KLQLKGMSYS MCTGKFKVVK EIAETQHGTI
610 620 630 640 650
VIRVQYEGDG SPCKTPFEIM DLEKRHVLGR LTTVNPIVTE KDSPVNIEAE
660 670 680 690 700
PPFGDSYIII GVEPGQLKLD WFKKGSSIGQ MFETTMRGAK RMAILGDTAW
710 720 730 740 750
DFGSLGGVFT SIGKALHQVF GAIYGAAFSG VSWTMKILIG VIITWIGMNS
760 770 780 790 800
RSTSLSVSLV LVGIVTLYLG VMVQADSGCV VSWKNKELKC GSGIFVTDNV
810 820 830 840 850
HTWTEQYKFQ PESPSKLASA IQKAHEEGIC GIRSVTRLEN LMWKQITSEL
860 870 880 890 900
NHILSENEVK LTIMTGDIKG IMQVGKRSLR PQPTELRYSW KTWGKAKMLS
910 920 930 940 950
TELHNQTFLI DGPETAECPN TNRAWNSLEV EDYGFGVFTT NIWLRLREKQ
960 970 980 990 1000
DAFCDSKLMS AAIKDNRAVH ADMGYWIESA LNDTWKIEKA SFIEVKSCHW
1010 1020 1030 1040 1050
PKSHTLWSNG VLESEMVIPK NFAGPVSQHN NRPGYHTQTA GPWHLGKLEM
1060 1070 1080 1090 1100
DFDFCEGTTV VVTEDCGNRG PSLRTTTASG KLITEWCCRS CTLPPLRYRG
1110 1120 1130 1140 1150
EDGCWYGMEI RPLKEKEENL VSSLVTAGHG QIDNFSLGIL GMALFLEEML
1160 1170 1180 1190 1200
RTRVGTKHAI LLVAVSFVTL ITGNMSFRDL GRVMVMVGAT MTDDIGMGVT
1210 1220 1230 1240 1250
YLALLAAFKV RPTFAAGLLL RKLTSKELMM TTIGIVLLSQ SSIPETILEL
1260 1270 1280 1290 1300
TDALALGMMV LKMVRNMEKY QLAVTIMAIL CVPNAVILQN AWKVSCTILA
1310 1320 1330 1340 1350
VVSVSPLFLT SSQQKADWIP LALTIKGLNP TAIFLTTLSR TSKKRSWPLN
1360 1370 1380 1390 1400
EAIMAVGMVS ILASSLLKND TPMTGPLVAG GLLTVCYVLT GRSADLELER
1410 1420 1430 1440 1450
ATDVKWDDQA EISGSSPILS ITISEDGSMS IKNEEEEQTL TILIRTGLLV
1460 1470 1480 1490 1500
ISGLFPVSIP ITAAAWYLWE VKKQRAGVLW DVPSPPPVGK AELEDGAYRI
1510 1520 1530 1540 1550
KQKGILGYSQ IGAGVYKEGT FHTMWHVTRG AVLMHKGKRI EPSWADVKKD
1560 1570 1580 1590 1600
LISYGGGWKL EGEWKEGEEV QVLALEPGKN PRAVQTKPGL FRTNTGTIGA
1610 1620 1630 1640 1650
VSLDFSPGTS GSPIVDKKGK VVGLYGNGVV TRSGAYVSAI AQTEKSIEDN
1660 1670 1680 1690 1700
PEIEDDIFRK RRLTIMDLHP GAGKTKRYLP AIVREAIKRG LRTLILAPTR
1710 1720 1730 1740 1750
VVAAEMEEAL RGLPIRYQTP AIRAEHTGRE IVDLMCHATF TMRLLSPIRV
1760 1770 1780 1790 1800
PNYNLIIMDE AHFTDPASIA ARGYISTRVE MGEAAGIFMT ATPPGSRDPF
1810 1820 1830 1840 1850
PQSNAPIMDE EREIPERSWN SGHEWVTDFK GKTVWFVPSI KTGNDIAACL
1860 1870 1880 1890 1900
RKNGKRVIQL SRKTFDSEYV KTRTNDWDFV VTTDISEMGA NFKAERVIDP
1910 1920 1930 1940 1950
RRCMKPVILT DGEERVILAG PMPVTHSSAA QRRGRIGRNP RNENDQYIYM
1960 1970 1980 1990 2000
GEPLENDEDC AHWKEAKMLL DNINTPEGII PSMFEPEREK VDAIDGEYRL
2010 2020 2030 2040 2050
RGEARKTFVD LMRRGDLPVW LAYKVAAEGI NYADRRWCFD GTRNNQILEE
2060 2070 2080 2090 2100
NVEVEIWTKE GERKKLKPRW LDARIYSDPL ALKEFAAGRK SLTLNLITEM
2110 2120 2130 2140 2150
GRLPTFMTQK ARDALDNLAV LHTAEAGGKA YNHALSELPE TLETLLLLTL
2160 2170 2180 2190 2200
LATVTGGIFL FLMSGRGIGK MTLGMCCIIT ASILLWYAQI QPHWIAASII
2210 2220 2230 2240 2250
LEFFLIVLLI PEPEKQRTPQ DNQLTYVIIA ILTVVAATMA NEMGFLEKTK
2260 2270 2280 2290 2300
KDLGLGNIAT QQPESNILDI DLRPASAWTL YAVATTFITP MLRHSIENSS
2310 2320 2330 2340 2350
VNVSLTAIAN QATVLMGLGK GWPLSKMDIG VPLLAIGCYS QVNPITLTAA
2360 2370 2380 2390 2400
LLLLVAHYAI IGPGLQAKAT REAQKRAAAG IMKNPTVDGI TVIDLDPIPY
2410 2420 2430 2440 2450
DPKFEKQLGQ VMLLVLCVTQ VLMMRTTWAL CEALTLATGP VSTLWEGNPG
2460 2470 2480 2490 2500
RFWNTTIAVS MANIFRGSYL AGAGLLFSIM KNTTSTRRGT GNIGETLGEK
2510 2520 2530 2540 2550
WKSRLNALGK SEFQIYKKSG IQEVDRTLAK EGIKRGETDH HAVSRGSAKL
2560 2570 2580 2590 2600
RWFVERNLVT PEGKVVDLGC GRGGWSYYCG GLKNVREVKG LTKGGPGHEE
2610 2620 2630 2640 2650
PIPMSTYGWN LVRLQSGVDV FFVPPEKCDT LLCDIGESSP NPTVEAGRTL
2660 2670 2680 2690 2700
RVLNLVENWL NNNTQFCVKV LNPYMPSVIE RMETLQRKYG GALVRNPLSR
2710 2720 2730 2740 2750
NSTHEMYWVS NASGNIVSSV NMISRMLINR FTMRHKKATY EPDVDLGSGT
2760 2770 2780 2790 2800
RNIGIESETP NLDIIGKRIE KIKQEHETSW HYDQDHPYKT WAYHGSYETK
2810 2820 2830 2840 2850
QTGSASSMVN GVVRLLTKPW DVVPMVTQMA MTDTTPFGQQ RVFKEKVDTR
2860 2870 2880 2890 2900
TQEPKEGTKK LMKITAEWLW KELGKKKTPR MCTREEFTKK VRSNAALGAI
2910 2920 2930 2940 2950
FTDENKWKSA REAVEDSRFW ELVDKERNLH LEGKCETCVY NMMGKREKKL
2960 2970 2980 2990 3000
GEFGKAKGSR AIWYMWLGAR FLEFEALGFL NEDHWFSREN SLSGVEGEGL
3010 3020 3030 3040 3050
HKLGYILREV SKKEGGAMYA DDTAGWDTRI TIEDLKNEEM ITNHMAGEHK
3060 3070 3080 3090 3100
KLAEAIFKLT YQNKVVRVQR PTPRGTVMDI ISRRDQRGSG QVGTYGLNTF
3110 3120 3130 3140 3150
TNMEAQLIRQ MEGEGIFKSI QHLTASEEIA VQDWLARVGR ERLSRMAISG
3160 3170 3180 3190 3200
DDCVVKPLDD RFARALTALN DMGKVRKDIQ QWEPSRGWND WTQVPFCSHH
3210 3220 3230 3240 3250
FHELIMKDGR TLVVPCRNQD ELIGRARISQ GAGWSLRETA CLGKSYAQMW
3260 3270 3280 3290 3300
SLMYFHRRDL RLAANAICSA VPSHWVPTSR TTWSIHASHE WMTTEDMLTV
3310 3320 3330 3340 3350
WNKVWILENP WMEDKTPVES WEEIPYLGKR EDQWCGSLIG LTSRATWAKN
3360 3370 3380
IQTAINQVRS LIGNEEYTDY MPSMKRFRRE EEEAGVLW
Length:3,388
Mass (Da):379,219
Last modified:October 1, 1989 - v1
Checksum:i79B7C87BE64D2D8F
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti351D → E (PubMed:12759475).Curated1
Sequence conflicti615T → I (PubMed:12759475).Curated1
Sequence conflicti632T → I (PubMed:12759475).Curated1
Sequence conflicti670D → N (PubMed:12759475).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M19197 Genomic RNA. Translation: AAA42962.1.
PIRiA29972. GNWVDP.

Cross-referencesi

Web resourcesi

Virus Particle ExploreR db

Icosahedral capsid structure

Virus Pathogen Resource

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M19197 Genomic RNA. Translation: AAA42962.1.
PIRiA29972. GNWVDP.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1L9KX-ray2.40A2492-2784[»]
1OANX-ray2.75A/B281-674[»]
1OK8X-ray2.00A281-674[»]
1OKEX-ray2.40A/B281-674[»]
1P58electron microscopy9.50A/B/C281-775[»]
D/E/F206-280[»]
1R6AX-ray2.60A2492-2784[»]
1R6RNMR-A/B1-100[»]
1THDelectron microscopy9.50A/B/C281-675[»]
2P1DX-ray2.90A2492-2784[»]
2P3LX-ray2.20A2492-2784[»]
2P3OX-ray2.76A2492-2784[»]
2P3QX-ray2.75A2492-2784[»]
2P40X-ray2.70A2492-2784[»]
2P41X-ray1.80A2492-2784[»]
3J8Delectron microscopy26.00G/H/I281-674[»]
3ZKOelectron microscopy13.70A/B/C281-775[»]
5HHGX-ray2.20C3353-3388[»]
ProteinModelPortaliP12823.
SMRiP12823.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

BRENDAi2.1.1.57. 1867.

Miscellaneous databases

EvolutionaryTraceiP12823.
PROiP12823.

Family and domain databases

CDDicd12149. Flavi_E_C. 1 hit.
Gene3Di2.60.40.350. 1 hit.
2.60.98.10. 2 hits.
3.30.387.10. 1 hit.
3.40.50.150. 1 hit.
3.40.50.300. 2 hits.
InterProiIPR011492. DEAD_Flavivir.
IPR000069. Env_glycoprot_M_flavivir.
IPR013755. Flav_gly_cen_dom_subdom1.
IPR001122. Flavi_capsidC.
IPR027287. Flavi_E_Ig-like.
IPR026470. Flavi_E_Stem/Anchor_dom.
IPR001157. Flavi_NS1.
IPR000752. Flavi_NS2A.
IPR000487. Flavi_NS2B.
IPR000404. Flavi_NS4A.
IPR001528. Flavi_NS4B.
IPR002535. Flavi_propep.
IPR000336. Flavivir/Alphavir_Ig-like.
IPR001850. Flavivirus_NS3_S7.
IPR014412. Gen_Poly_FLV.
IPR011998. Glycoprot_cen/dimer.
IPR013754. GlyE_dim.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR014756. Ig_E-set.
IPR026490. mRNA_cap_0/1_MeTrfase.
IPR027417. P-loop_NTPase.
IPR009003. Peptidase_S1_PA.
IPR000208. RNA-dir_pol_flavivirus.
IPR007094. RNA-dir_pol_PSvirus.
IPR002877. rRNA_MeTrfase_FtsJ_dom.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF01003. Flavi_capsid. 1 hit.
PF07652. Flavi_DEAD. 1 hit.
PF02832. Flavi_glycop_C. 1 hit.
PF00869. Flavi_glycoprot. 1 hit.
PF01004. Flavi_M. 1 hit.
PF00948. Flavi_NS1. 1 hit.
PF01005. Flavi_NS2A. 1 hit.
PF01002. Flavi_NS2B. 1 hit.
PF01350. Flavi_NS4A. 1 hit.
PF01349. Flavi_NS4B. 1 hit.
PF00972. Flavi_NS5. 1 hit.
PF01570. Flavi_propep. 1 hit.
PF01728. FtsJ. 1 hit.
PF00949. Peptidase_S7. 1 hit.
[Graphical view]
PIRSFiPIRSF003817. Gen_Poly_FLV. 1 hit.
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 2 hits.
SSF53335. SSF53335. 1 hit.
SSF56983. SSF56983. 1 hit.
SSF81296. SSF81296. 1 hit.
TIGRFAMsiTIGR04240. flavi_E_stem. 1 hit.
PROSITEiPS51527. FLAVIVIRUS_NS2B. 1 hit.
PS51528. FLAVIVIRUS_NS3PRO. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS50507. RDRP_SSRNA_POS. 1 hit.
PS51591. RNA_CAP01_NS5_MT. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPOLG_DEN2P
AccessioniPrimary (citable) accession number: P12823
Secondary accession number(s): Q88646
, Q88647, Q88648, Q88649, Q88650, Q88651, Q88652, Q88653, Q88654, Q88655
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1989
Last sequence update: October 1, 1989
Last modified: November 30, 2016
This is version 171 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Multifunctional enzyme

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Peptidase families
    Classification of peptidase families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.