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Protein

Gag-Pol polyprotein

Gene

gag-pol

Organism
Walleye dermal sarcoma virus (WDSV)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Matrix protein p10: targets Gag and gag-pol polyproteins to the plasma membrane via a multipartite membrane binding signal, that includes its myristoylated N-terminus. Also mediates nuclear localization of the preintegration complex (By similarity).By similarity
Capsid protein p25 forms the spherical core of the virion that encapsulates the genomic RNA-nucleocapsid complex.By similarity
Nucleocapsid protein p14: involved in the packaging and encapsidation of two copies of the genome. Binds with high affinity to conserved UCUG elements within the packaging signal, located near the 5'-end of the genome. This binding is dependent on genome dimerization (By similarity).By similarity
Protease p15: mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell (By similarity).By similarity
Reverse transcriptase/ribonuclease H p90: is a multifunctional enzyme that converts the viral dimeric RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell. This enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3' to 5' endonucleasic mode. Conversion of viral genomic RNA into dsDNA requires many steps. A tRNA binds to the primer-binding site (PBS) situated at the 5' end of the viral RNA. RT uses the 3' end of the tRNA primer to perform a short round of RNA-dependent minus-strand DNA synthesis. The reading proceeds through the U5 region and ends after the repeated (R) region which is present at both ends of viral RNA. The portion of the RNA-DNA heteroduplex is digested by the RNase H, resulting in a ssDNA product attached to the tRNA primer. This ssDNA/tRNA hybridizes with the identical R region situated at the 3' end of viral RNA. This template exchange, known as minus-strand DNA strong stop transfer, can be either intra- or intermolecular. RT uses the 3' end of this newly synthesized short ssDNA to perform the RNA-dependent minus-strand DNA synthesis of the whole template. RNase H digests the RNA template except for a polypurine tract (PPT) situated at the 5' end of the genome. It is not clear if both polymerase and RNase H activities are simultaneous. RNase H probably can proceed both in a polymerase-dependent (RNA cut into small fragments by the same RT performing DNA synthesis) and a polymerase-independent mode (cleavage of remaining RNA fragments by free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis using the PPT that has not been removed by RNase H as primers. PPT and tRNA primers are then removed by RNase H. The 3' and 5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate. Strand displacement synthesis by RT to the PBS and PPT ends produces a blunt ended, linear dsDNA copy of the viral genome that includes long terminal repeats (LTRs) at both ends (By similarity).By similarity
Integrase p46: catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising the viral genome, matrix protein and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from each 3' end of the viral DNA, leaving recessed CA OH's at the 3' ends. In the second step that requires cell division, the PIC enters cell nucleus. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. The last step is viral DNA integration into host chromosome.1 Publication
Gag-Pol polyprotein: plays a role in budding and is processed by the viral protease during virion maturation outside the cell.By similarity

Catalytic activityi

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).PROSITE-ProRule annotation
Endonucleolytic cleavage to 5'-phosphomonoester.PROSITE-ProRule annotation

Cofactori

Protein has several cofactor binding sites:
  • Mg2+By similarityNote: Binds 2 magnesium ions for reverse transcriptase polymerase activity.By similarity
  • Mg2+By similarityNote: Binds 2 magnesium ions for ribonuclease H (RNase H) activity.By similarity
  • Mg2+By similarityNote: Magnesium ions are required for integrase activity. Binds at least 1, maybe 2 magnesium ions.By similarity

pH dependencei

Optimum pH is 7.0 for protease p14.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei623Protease; shared with dimeric partnerBy similarity1
Metal bindingi861Magnesium; catalytic; for reverse transcriptase activityBy similarity1
Metal bindingi928Magnesium; catalytic; for reverse transcriptase activityBy similarity1
Metal bindingi929Magnesium; catalytic; for reverse transcriptase activityBy similarity1
Metal bindingi1231Magnesium; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1269Magnesium; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1290Magnesium; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1360Magnesium; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1493Magnesium; catalytic; for integrase activityBy similarity1
Metal bindingi1550Magnesium; catalytic; for integrase activityBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri501 – 518CCHC-typePROSITE-ProRule annotationAdd BLAST18

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Aspartyl protease, DNA-directed DNA polymerase, Endonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Protease, RNA-directed DNA polymerase, Transferase

Keywords - Biological processi

DNA integration, DNA recombination

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding, RNA-binding, Viral nucleoprotein, Zinc

Protein family/group databases

MEROPSiA02.063.

Names & Taxonomyi

Protein namesi
Recommended name:
Gag-Pol polyprotein
Cleaved into the following 7 chains:
Matrix protein p10
Short name:
MA
Capsid protein p25
Short name:
CA
Nucleocapsid protein p14
Short name:
NC-pol
Protease p15 (EC:3.4.23.-)
Short name:
PR
Integrase p46 (EC:2.7.7.-1 Publication, EC:3.1.-.-1 Publication)
Short name:
IN
Gene namesi
Name:gag-pol
OrganismiWalleye dermal sarcoma virus (WDSV)
Taxonomic identifieri39720 [NCBI]
Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeEpsilonretrovirus
Virus hostiSander vitreus (Walleye) (Perca vitrea) [TaxID: 283036]
Proteomesi
  • UP000008337 Componenti: Genome
  • UP000007081 Componenti: Genome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Host cell membrane, Host membrane, Membrane, Viral matrix protein, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedSequence analysis
ChainiPRO_00004105922 – 1752Gag-Pol polyproteinAdd BLAST1751
ChainiPRO_00004105932 – 95Matrix protein p10Add BLAST94
ChainiPRO_000041059496 – 251p20Add BLAST156
ChainiPRO_0000410595252 – 457Capsid protein p25Add BLAST206
ChainiPRO_0000410596458 – 584Nucleocapsid protein p14Add BLAST127
ChainiPRO_0000410597585 – 722Protease p15Add BLAST138
ChainiPRO_0000410598723 – 1372Reverse transcriptase/ribonuclease H p90By similarityAdd BLAST650
ChainiPRO_00004105991373 – 1752Integrase p46By similarityAdd BLAST380

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Lipidationi2N-myristoyl glycine; by hostBy similarity1

Post-translational modificationi

Specific enzymatic cleavages by the viral protease yield mature proteins. The protease is released by autocatalytic cleavage. The polyprotein is cleaved during and after budding, this process is termed maturation (By similarity).By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei95 – 96Cleavage; by viral proteaseBy similarity2
Sitei251 – 252Cleavage; by viral proteaseBy similarity2
Sitei457 – 458Cleavage; by viral proteaseBy similarity2
Sitei584 – 585Cleavage; by viral proteaseBy similarity2
Sitei722 – 723Cleavage; by viral proteaseBy similarity2
Sitei1372 – 1373Cleavage; by viral proteaseBy similarity2

Keywords - PTMi

Lipoprotein, Myristate, Phosphoprotein

Miscellaneous databases

PMAP-CutDBO92815.

Interactioni

Subunit structurei

Capsid protein p25 is a homohexamer, that further associates as homomultimer. The virus core is composed of a lattice formed from hexagonal rings, each containing six capsid monomers. The protease is a homodimer, whose active site consists of two apposed aspartic acid residues. The reverse transcriptase is a monomer (By similarity).By similarity

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini618 – 694Peptidase A2Add BLAST77
Domaini793 – 977Reverse transcriptasePROSITE-ProRule annotationAdd BLAST185
Domaini1222 – 1368RNase HPROSITE-ProRule annotationAdd BLAST147
Domaini1482 – 1638Integrase catalyticPROSITE-ProRule annotationAdd BLAST157

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili154 – 185Sequence analysisAdd BLAST32

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi147 – 170Gln-richAdd BLAST24
Compositional biasi181 – 184Poly-Lys4
Compositional biasi484 – 487Poly-Gln4

Sequence similaritiesi

Contains 1 CCHC-type zinc finger.PROSITE-ProRule annotation
Contains 1 integrase catalytic domain.PROSITE-ProRule annotation
Contains 1 peptidase A2 domain.Curated
Contains 1 reverse transcriptase domain.PROSITE-ProRule annotation
Contains 1 RNase H domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri501 – 518CCHC-typePROSITE-ProRule annotationAdd BLAST18

Keywords - Domaini

Coiled coil, Zinc-finger

Family and domain databases

Gene3Di3.30.420.10. 2 hits.
4.10.60.10. 1 hit.
InterProiIPR001584. Integrase_cat-core.
IPR021109. Peptidase_aspartic_dom.
IPR018061. Retropepsins.
IPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR000477. RT_dom.
IPR001878. Znf_CCHC.
[Graphical view]
PfamiPF00075. RNase_H. 1 hit.
PF00665. rve. 1 hit.
PF00077. RVP. 1 hit.
PF00078. RVT_1. 1 hit.
PF00098. zf-CCHC. 1 hit.
[Graphical view]
SMARTiSM00343. ZnF_C2HC. 1 hit.
[Graphical view]
SUPFAMiSSF50630. SSF50630. 1 hit.
SSF53098. SSF53098. 2 hits.
SSF57756. SSF57756. 1 hit.
PROSITEiPS50994. INTEGRASE. 1 hit.
PS50879. RNASE_H. 1 hit.
PS50878. RT_POL. 1 hit.
PS50158. ZF_CCHC. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

O92815-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGNSSSTPPP SALKNSDLFK TMLRTQYSGS VKTRRINQDI KKQYPLWPDQ
60 70 80 90 100
GTCATKHWEQ AVLIPLDSVS EETAKVLNFL RVKIQARKGE TARQMTAHTI
110 120 130 140 150
KKLIVGTIDK NKQQTEILQK TDESDEEMDT TNTMLFIARN KRERIAQQQQ
160 170 180 190 200
ADLAAQQQVL LLQREQQREQ REKDIKKRDE KKKKLLPDTT QKVEQTDIGE
210 220 230 240 250
ASSSDASAQK PISTDNNPDL KVDGVLTRSQ HTTVPSNITI KKDGTSVQYQ
260 270 280 290 300
HPIRNYPTGE GNLTAQVRNP FRPLELQQLR KDCPALPEGI PQLAEWLTQT
310 320 330 340 350
MAIYNCDEAD VEQLARVIFP TPVRQIAGVI NGHAAANTAA KIQNYVTACR
360 370 380 390 400
QHYPAVCDWG TIQAFTYKPP QTAHEYVKHA EIIFKNNSGL EWQHATVPFI
410 420 430 440 450
NMVVQGLPPK VTRSLMSGNP DWSTKTIPQI IPLMQHYLNL QSRQDAKIKQ
460 470 480 490 500
TPLVLQLAMP AQTMNGNKGY VGSYPTNEPY YSFQQQQRPA PRAPPGNVPS
510 520 530 540 550
NTCFFCKQPG HWKADCPNKT RNLRNMGNMG RGGRMGGPPY RSQPYPAFIQ
560 570 580 590 600
PPQNHQNQYN GRMDRSQLQA SAQEWLPGTY PAXDPIDCPY EKSGTKTTQD
610 620 630 640 650
VITTKNAEIM VTVNHTKIPM LVDTGACLTA IGGAATVVPD LKLTNTEIIA
660 670 680 690 700
VGISAEPVPH VLAKPTKIQI ENTNIDISPW YNPDQTFHIL GRDTLSKMRA
710 720 730 740 750
IVSFEKNGEM TVLLPPTYHK QLSCQTKNTL NIDEYLLQFP DQLWASLPTD
760 770 780 790 800
IGRMLVPPIT IKIKDNASLP SIRQYPLPKD KTEGLRPLIS SLENQGILIK
810 820 830 840 850
CHSPCNTPIF PIKKAGRDEY RMIHDLRAIN NIVAPLTAVV ASPTTVLSNL
860 870 880 890 900
APSLHWFTVI DLSNAFFSVP IHKDSQYLFA FTFEGHQYTW TVLPQGFIHS
910 920 930 940 950
PTLFSQALYQ SLHKIKFKIS SEICIYMDDV LIASKDRDTN LKDTAVMLQH
960 970 980 990 1000
LASEGHKVSK KKLQLCQQEV VYLGQLLTPE GRKILPDRKV TVSQFQQPTT
1010 1020 1030 1040 1050
IRQIRAFLGL VGYCRHWIPE FSIHSKFLEK QLKKDTAEPF QLDDQQVEAF
1060 1070 1080 1090 1100
NKLKHAITTA PVLVVPDPAK PFQLYTSHSE HASIAVLTQK HAGRTRPIAF
1110 1120 1130 1140 1150
LSSKFDAIES GLPPCLKACA SIHRSLTQAD SFILGAPLII YTTHAICTLL
1160 1170 1180 1190 1200
QRDRSQLVTA SRFSKWEADL LRPELTFVAC SAVSPAHLYM QSCENNIPPH
1210 1220 1230 1240 1250
DCVLLTHTIS RPRPDLSDLP IPDPDMTLFS DGSYTTGRGG AAVVMHRPVT
1260 1270 1280 1290 1300
DDFIIIHQQP GGASAQTAEL LALAAACHLA TDKTVNIYTD SRYAYGVVHD
1310 1320 1330 1340 1350
FGHLWMHRGF VTSAGTPIKN HKEIEYLLKQ IMKPKQVSVI KIEAHTKGVS
1360 1370 1380 1390 1400
MEVRGNAAAD EAAKNAVFLV QRVLKKGDAL ASTDLVMEYS ETDEKFTAGA
1410 1420 1430 1440 1450
ELHDGVFMRG DLIVPPLEML HAILLAIHGV SHTHKGGIMS YFSKFWTHPK
1460 1470 1480 1490 1500
ASQTIDLILG HCQICLKHNP KYKSRLQGHR PLPSRPFAHL QIDFVQMCVK
1510 1520 1530 1540 1550
KPMYALVIID VFSKWPEIIP CNKEDAKTVC DILMKDIIPR WGLPDQIDSD
1560 1570 1580 1590 1600
QGTHFTAKIS QELTHSIGVA WKLHCPGHPR SSGIVERTNR TLKSKIIKAQ
1610 1620 1630 1640 1650
EQLQLSKWTE VLPYVLLEMR ATPKKHGLSP HEIVMGRPMK TTYLSDMSPL
1660 1670 1680 1690 1700
WATDTLVTYM NKLTRQLSAY HQQVVDQWPS TSLPPGPEPG SWCMLRNPKK
1710 1720 1730 1740 1750
SSNWEGPFLI LLSTPTAVKV EGRPTWIHLD HCKLLRSSLS SSLGGPVNQL

LS
Length:1,752
Mass (Da):196,265
Last modified:June 28, 2011 - v2
Checksum:iA9DEF76316FBE4E0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L41838 Genomic RNA. No translation available.
AF033822 Genomic RNA. Translation: AAC82611.1.
PIRiT09394.
RefSeqiNP_045937.2. NC_001867.1.

Genome annotation databases

GeneIDi1403495.

Keywords - Coding sequence diversityi

RNA suppression of termination

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L41838 Genomic RNA. No translation available.
AF033822 Genomic RNA. Translation: AAC82611.1.
PIRiT09394.
RefSeqiNP_045937.2. NC_001867.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

MEROPSiA02.063.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1403495.

Miscellaneous databases

PMAP-CutDBO92815.

Family and domain databases

Gene3Di3.30.420.10. 2 hits.
4.10.60.10. 1 hit.
InterProiIPR001584. Integrase_cat-core.
IPR021109. Peptidase_aspartic_dom.
IPR018061. Retropepsins.
IPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR000477. RT_dom.
IPR001878. Znf_CCHC.
[Graphical view]
PfamiPF00075. RNase_H. 1 hit.
PF00665. rve. 1 hit.
PF00077. RVP. 1 hit.
PF00078. RVT_1. 1 hit.
PF00098. zf-CCHC. 1 hit.
[Graphical view]
SMARTiSM00343. ZnF_C2HC. 1 hit.
[Graphical view]
SUPFAMiSSF50630. SSF50630. 1 hit.
SSF53098. SSF53098. 2 hits.
SSF57756. SSF57756. 1 hit.
PROSITEiPS50994. INTEGRASE. 1 hit.
PS50879. RNASE_H. 1 hit.
PS50878. RT_POL. 1 hit.
PS50158. ZF_CCHC. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPOL_WDSV
AccessioniPrimary (citable) accession number: O92815
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 28, 2011
Last sequence update: June 28, 2011
Last modified: April 13, 2016
This is version 94 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

This protein is translated as a gag-pol fusion protein by episodic readthrough of the gag protein termination codon. Readthrough of the terminator codon TAG occurs between the codons for 582-Ala and 584-Asp (By similarity).By similarity
The nucleocapsid protein p14 released from Pol polyprotein (NC-pol) is a few amino acids longer than the nucleocapsid protein p14 released from Gag polyprotein (NC-gag).By similarity
The reverse transcriptase is an error-prone enzyme that lacks a proof-reading function. High mutations rate is a direct consequence of this characteristic. RT also displays frequent template swiching leading to high recombination rate. Recombination mostly occurs between homologous regions of the two copackaged RNA genomes. If these two RNA molecules derive from different viral strains, reverse transcription will give rise to highly recombinated proviral DNAs.PROSITE-ProRule annotation

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Multifunctional enzyme, Reference proteome

Documents

  1. Peptidase families
    Classification of peptidase families and list of entries
  2. 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.