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Protein

Gag-Pol polyprotein

Gene

gag-pol

Organism
Jembrana disease virus (JDV)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Protein inferred from homologyi

Functioni

Matrix protein p16 forms the outer shell of the core of the virus, lining the inner surface of the viral membrane.By similarity
Capsid protein p26 forms the conical core of the virus that encapsulates the genomic RNA-nucleocapsid complex.By similarity
The aspartyl protease 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.PROSITE-ProRule annotation
Reverse transcriptase/ribonuclease H (RT) is a multifunctional enzyme that converts the viral 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 primer. 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 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 (By similarity).By similarity

Catalytic activityi

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).PROSITE-ProRule annotation
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei457For protease activity; shared with dimeric partnerPROSITE-ProRule annotation1
Metal bindingi645Magnesium; catalyticBy similarity1
Metal bindingi720Magnesium; catalyticBy similarity1
Metal bindingi721Magnesium; catalyticBy similarity1
Metal bindingi968MagnesiumPROSITE-ProRule annotation1
Metal bindingi999MagnesiumPROSITE-ProRule annotation1
Metal bindingi1019MagnesiumPROSITE-ProRule annotation1
Metal bindingi1071MagnesiumPROSITE-ProRule annotation1
Metal bindingi1219Magnesium; catalyticBy similarity1
Metal bindingi1271Magnesium; catalyticBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri368 – 385CCHC-type 1PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri386 – 403CCHC-type 2PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri1157 – 1198Integrase-typePROSITE-ProRule annotationAdd BLAST42
DNA bindingi1376 – 1422Integrase-typePROSITE-ProRule annotationAdd BLAST47

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, Viral genome integration, Virion maturation, Virus entry into host cell, Virus exit from host cell

Keywords - Ligandi

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

Names & Taxonomyi

Protein namesi
Recommended name:
Gag-Pol polyprotein
Alternative name(s):
Pr170Gag-Pol
Cleaved into the following 6 chains:
Matrix protein p16
Short name:
MA
Capsid protein p26
Short name:
CA
Alternative name(s):
p11
Alternative name(s):
P119
Retropepsin
Alternative name(s):
Exoribonuclease H (EC:3.1.13.2)
P72
Integrase (EC:2.7.7.-By similarity, EC:3.1.-.-By similarity)
Short name:
IN
Gene namesi
Name:gag-pol
OrganismiJembrana disease virus (JDV)
Taxonomic identifieri36370 [NCBI]
Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeLentivirusBovine lentivirus group
Virus hostiBos javanicus (Wild banteng) [TaxID: 9906]

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Viral matrix protein, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002723531 – 1432Gag-Pol polyproteinAdd BLAST1432
ChainiPRO_00002723541 – 125Matrix protein p16Sequence analysisAdd BLAST125
ChainiPRO_0000272355126 – 351Capsid protein p26Sequence analysisAdd BLAST226
ChainiPRO_0000272356352 – 432Transframe peptideSequence analysisAdd BLAST81
ChainiPRO_0000272357433 – 522ProteaseSequence analysisAdd BLAST90
ChainiPRO_0000272358523 – 1151Reverse transcriptase/ribonuclease HSequence analysisAdd BLAST629
ChainiPRO_00002723591152 – 1432IntegraseSequence analysisAdd BLAST281

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
Sitei125 – 126Cleavage; by viral proteaseSequence analysis2
Sitei351 – 352Cleavage; by viral proteaseSequence analysis2
Sitei432 – 433Cleavage; by viral proteaseSequence analysis2
Sitei522 – 523Cleavage; by viral proteaseSequence analysis2
Sitei1151 – 1152Cleavage; by viral proteaseSequence analysis2

Proteomic databases

PRIDEiQ82851.

Structurei

3D structure databases

ProteinModelPortaliQ82851.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini452 – 525Peptidase A2PROSITE-ProRule annotationAdd BLAST74
Domaini579 – 766Reverse transcriptasePROSITE-ProRule annotationAdd BLAST188
Domaini959 – 1079RNase HPROSITE-ProRule annotationAdd BLAST121
Domaini1206 – 1358Integrase catalyticPROSITE-ProRule annotationAdd BLAST153

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili815 – 843Sequence analysisAdd BLAST29

Sequence similaritiesi

Contains 2 CCHC-type zinc fingers.PROSITE-ProRule annotation
Contains 1 integrase catalytic domain.PROSITE-ProRule annotation
Contains 1 integrase-type DNA-binding domain.PROSITE-ProRule annotation
Contains 1 integrase-type zinc finger.PROSITE-ProRule annotation
Contains 1 peptidase A2 domain.PROSITE-ProRule annotation
Contains 1 reverse transcriptase domain.PROSITE-ProRule annotation
Contains 1 RNase H domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri368 – 385CCHC-type 1PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri386 – 403CCHC-type 2PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri1157 – 1198Integrase-typePROSITE-ProRule annotationAdd BLAST42

Keywords - Domaini

Coiled coil, Repeat, Zinc-finger

Family and domain databases

Gene3Di1.10.10.200. 1 hit.
1.10.1200.30. 1 hit.
1.10.375.10. 1 hit.
2.30.30.10. 1 hit.
2.40.70.10. 1 hit.
3.30.420.10. 2 hits.
4.10.60.10. 1 hit.
InterProiIPR001969. Aspartic_peptidase_AS.
IPR000721. Gag_p24.
IPR001037. Integrase_C_retrovir.
IPR001584. Integrase_cat-core.
IPR017856. Integrase_Zn-bd_dom-like_N.
IPR003308. Integrase_Zn-bd_dom_N.
IPR001995. Peptidase_A2_cat.
IPR021109. Peptidase_aspartic_dom.
IPR018061. Retropepsins.
IPR008916. Retrov_capsid_C.
IPR008919. Retrov_capsid_N.
IPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR000477. RT_dom.
IPR010661. RVT_thumb.
IPR001878. Znf_CCHC.
[Graphical view]
PfamiPF00607. Gag_p24. 1 hit.
PF00552. IN_DBD_C. 1 hit.
PF02022. Integrase_Zn. 1 hit.
PF00075. RNase_H. 1 hit.
PF00665. rve. 1 hit.
PF00077. RVP. 1 hit.
PF00078. RVT_1. 1 hit.
PF06817. RVT_thumb. 1 hit.
PF00098. zf-CCHC. 2 hits.
[Graphical view]
SMARTiSM00343. ZnF_C2HC. 2 hits.
[Graphical view]
SUPFAMiSSF46919. SSF46919. 1 hit.
SSF47353. SSF47353. 1 hit.
SSF47943. SSF47943. 1 hit.
SSF50122. SSF50122. 1 hit.
SSF50630. SSF50630. 1 hit.
SSF53098. SSF53098. 2 hits.
SSF57756. SSF57756. 1 hit.
PROSITEiPS50175. ASP_PROT_RETROV. 1 hit.
PS00141. ASP_PROTEASE. 1 hit.
PS50994. INTEGRASE. 1 hit.
PS51027. INTEGRASE_DBD. 1 hit.
PS50879. RNASE_H. 1 hit.
PS50878. RT_POL. 1 hit.
PS50158. ZF_CCHC. 2 hits.
PS50876. ZF_INTEGRASE. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

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

This entry describes 2 isoformsi produced by ribosomal frameshifting. AlignAdd to basket

Note: This strategy of translation probably allows the virus to modulate the quantity of each viral protein.
Isoform Gag-Pol polyprotein (identifier: Q82851-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MKLSKLEKAL KKVRVTPQRD DTYTIGNVLW AIRMCRLMGL DCCIDEATAA
60 70 80 90 100
EVAILIGRFQ SLDLQDSPLK GKDEKAILTT LKVLWSLLAG HHPENSDMAE
110 120 130 140 150
KYWEAWTIRE RESQKEEEGE ITSIYPQLRK NFPAVSTSDG SPRYDPDLTK
160 170 180 190 200
QLKIWADATE KHGVDHHAVN ILGVITANLT QSEIRLLLQS TPQWRLDIQL
210 220 230 240 250
IESKLNAREH AHRVWKESHP EAPKTDEIIG KGLTAAEQAT LTTQECRDTY
260 270 280 290 300
RQWVLEAALE VAQGKHDRPG PINIHQGPKE PYPEFVNKLV TALEGMAAPE
310 320 330 340 350
TTKQYLLDHL SVDHANEDCR AVLLPLGPSA PMERKLEACR AVGSSKQKMQ
360 370 380 390 400
FLAEAFAAIN VKGDGEVQRC YGCGKPGHIR RDCKNQKCFK CGKPGHLQRN
410 420 430 440 450
CKSKNREALL CPFWAEERIP SGEDFCDPVC SPVGIRLNRQ PFIKIFLGGR
460 470 480 490 500
WVRALIDTGA DEVVLKDIHW DRIKGVPAAS VVQVGVTGRN IARRKSNVEW
510 520 530 540 550
RFKNRYGIVD VLFSNTPVNL LGRSVLQSIV TKFTLAAHTK QIQPLPVKLH
560 570 580 590 600
GPGPRVPQWP LTLEKYKALK EIVEELLKDG KISRTPWDNP FNTPVFVIKK
610 620 630 640 650
KGGSKWRMLM DFRALNKVTN KGQEFQIGLP YPPGIQQCEH ITAIDIKDAY
660 670 680 690 700
FTIPLDENFR QYTAFSVVPV NREGPLERYH WNVLPQGWVC SPAIYQTTTQ
710 720 730 740 750
EIIAEIKDRF PDIVLYQYMD DLLIGSDRPD HKRVVSEIRE ELGAYGFKTP
760 770 780 790 800
EEKIQEEQVQ WLGYELTPKR WRFQPRQIKI KKVVTVNELQ QMIGNCVWVQ
810 820 830 840 850
PEVKIPLSPL SDLLKGKTDL KDKIKLTEEA IQCLETVNKR LKDPEWKERI
860 870 880 890 900
KEGTELVVKI QLIPEGVVYD LLQDGNPIWG GVKGWDYNHA NKIKKMLSIM
910 920 930 940 950
KKLSRIVMIM TGREVSFLIP GDSEDWESAL QRINTLTEIP EVKFYKHACR
960 970 980 990 1000
WTSVCGPVIE RYPTYYTDGG KKGSKAAAAY WREGKIRREV FPGTNQQAEL
1010 1020 1030 1040 1050
KAVLMALQDG PAKMNIITDS RYAFEGMREE PETWGREGLW KEIGEELRRK
1060 1070 1080 1090 1100
EYVGVSWVPG HKGIGGNTEV DQEVQKALQG PITVSLPQEI LLEAGETKLV
1110 1120 1130 1140 1150
KTGIFWEGLR PCKLRPEEGL KLKGSLIDEE LQLEITNTQN SRVGIRQGQT
1160 1170 1180 1190 1200
IGTCFIEAIP QAIEEHEKWH TTAEILAREF QLPRRVAREI VHRCQACKRT
1210 1220 1230 1240 1250
VSCPRRGTNP RERFLWQMDN THLEGKIIWV AVETNSGLIE ARVIPEESAQ
1260 1270 1280 1290 1300
SIVFCILMLV YRYTVYHIHS DNGPCFIAQK VEALCKYLKI TKTTGIPYNP
1310 1320 1330 1340 1350
QAQAIVERTH RDIKDKIAAF REDCETVEAA LSLTLVALNK KRGGIGGHTP
1360 1370 1380 1390 1400
YEIYLESEYN KYQEQQNHYN NFKTEKWAYV RDKRKVWKGP YKVLWDGEGA
1410 1420 1430
AVVEENAMPT LYPHRHMRFI PPPNTDTQDG NL
Note: Produced by ribosomal frameshifting at the gag-pol genes boundary.
Length:1,432
Mass (Da):163,421
Last modified:November 1, 1996 - v1
Checksum:i06FF2F3E0E14EED4
GO
Isoform Gag polyprotein (identifier: Q82850-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry Q82850.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by conventional translation.
Length:436
Mass (Da):48,785
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U21603 Genomic RNA. Translation: AAA64389.1.
L32870 Genomic RNA. Translation: AAA64521.1.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U21603 Genomic RNA. Translation: AAA64389.1.
L32870 Genomic RNA. Translation: AAA64521.1.

3D structure databases

ProteinModelPortaliQ82851.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiQ82851.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Family and domain databases

Gene3Di1.10.10.200. 1 hit.
1.10.1200.30. 1 hit.
1.10.375.10. 1 hit.
2.30.30.10. 1 hit.
2.40.70.10. 1 hit.
3.30.420.10. 2 hits.
4.10.60.10. 1 hit.
InterProiIPR001969. Aspartic_peptidase_AS.
IPR000721. Gag_p24.
IPR001037. Integrase_C_retrovir.
IPR001584. Integrase_cat-core.
IPR017856. Integrase_Zn-bd_dom-like_N.
IPR003308. Integrase_Zn-bd_dom_N.
IPR001995. Peptidase_A2_cat.
IPR021109. Peptidase_aspartic_dom.
IPR018061. Retropepsins.
IPR008916. Retrov_capsid_C.
IPR008919. Retrov_capsid_N.
IPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR000477. RT_dom.
IPR010661. RVT_thumb.
IPR001878. Znf_CCHC.
[Graphical view]
PfamiPF00607. Gag_p24. 1 hit.
PF00552. IN_DBD_C. 1 hit.
PF02022. Integrase_Zn. 1 hit.
PF00075. RNase_H. 1 hit.
PF00665. rve. 1 hit.
PF00077. RVP. 1 hit.
PF00078. RVT_1. 1 hit.
PF06817. RVT_thumb. 1 hit.
PF00098. zf-CCHC. 2 hits.
[Graphical view]
SMARTiSM00343. ZnF_C2HC. 2 hits.
[Graphical view]
SUPFAMiSSF46919. SSF46919. 1 hit.
SSF47353. SSF47353. 1 hit.
SSF47943. SSF47943. 1 hit.
SSF50122. SSF50122. 1 hit.
SSF50630. SSF50630. 1 hit.
SSF53098. SSF53098. 2 hits.
SSF57756. SSF57756. 1 hit.
PROSITEiPS50175. ASP_PROT_RETROV. 1 hit.
PS00141. ASP_PROTEASE. 1 hit.
PS50994. INTEGRASE. 1 hit.
PS51027. INTEGRASE_DBD. 1 hit.
PS50879. RNASE_H. 1 hit.
PS50878. RT_POL. 1 hit.
PS50158. ZF_CCHC. 2 hits.
PS50876. ZF_INTEGRASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPOL_JEMBR
AccessioniPrimary (citable) accession number: Q82851
Secondary accession number(s): Q82859
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 23, 2007
Last sequence update: November 1, 1996
Last modified: September 7, 2016
This is version 92 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

Gag proteins are synthesized on both gag and gag-pol polyproteins. Gag polyprotein (AC Q82850) is produced from conventional translation of the gag ORF. Gag-Pol polyprotein is generated by a -1 ribosomal frameshift occurring at the gag-pol genes boundary. This strategy of translation probably allows the virus to modulate the quantity of each viral protein (By similarity).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 switching 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 (By similarity).By similarity

Keywords - Technical termi

Multifunctional enzyme

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.