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Q9TTC1

- POL_KORV

UniProt

Q9TTC1 - POL_KORV

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Protein

Pro-Pol polyprotein

Gene
pro-pol
Organism
Koala retrovirus (KoRV)
Status
Reviewed - Annotation score: 5 out of 5 - Protein inferred from homologyi

Functioni

The aspartyl protease activity mediates proteolytic cleavages of Gag and Pol polyproteins. The reverse transcriptase (RT) activity converts the viral RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell (early reverse transcription) or after proviral DNA transcription (late reverse transcription). RT consists of 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 and near the center 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.
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. 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. In the second step, the PIC access cell chromosomes during cell division. 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 5'-ends are produced by integrase-catalyzed staggered cuts, 5 bp apart. A Y-shaped, gapped, recombination intermediate results, with the 5'-ends of the viral DNA strands and the 3' ends of target DNA strands remaining unjoined, flanking a gap of 5 bp. The last step is viral DNA integration into host chromosome. This involves host DNA repair synthesis in which the 5 bp gaps between the unjoined strands (see above) are filled in and then ligated By similarity.

Catalytic activityi

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

Cofactori

Binds 2 magnesium ions for reverse transcriptase polymerase activity By similarity.
Binds 2 magnesium ions for ribonuclease H (RNase H) activity. Substrate-binding is a precondition for magnesium binding By similarity.
Magnesium ions for integrase activity. Binds at least 1, maybe 2 magnesium ions By similarity.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi229 – 2291Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal bindingi303 – 3031Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal bindingi304 – 3041Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal bindingi661 – 6611Magnesium; catalytic; for RNase H activity By similarity
Metal bindingi731 – 7311Magnesium; catalytic; for RNase H activity By similarity
Sitei?742 – ?7432Cleavage; by viral protease By similarity
Metal bindingi904 – 9041Magnesium; catalytic; for integrase activity By similarity

GO - Molecular functioni

  1. aspartic-type endopeptidase activity Source: UniProtKB-KW
  2. DNA-directed DNA polymerase activity Source: UniProtKB-KW
  3. metal ion binding Source: UniProtKB-KW
  4. RNA binding Source: UniProtKB-KW
  5. RNA-directed DNA polymerase activity Source: UniProtKB-KW
  6. RNA-DNA hybrid ribonuclease activity Source: UniProtKB-EC

GO - Biological processi

  1. DNA integration Source: UniProtKB-KW
  2. DNA recombination Source: UniProtKB-KW
  3. establishment of integrated proviral latency Source: UniProtKB-KW
  4. viral entry into host cell Source: UniProtKB-KW
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, Virus entry into host cell

Keywords - Ligandi

Magnesium, Metal-binding, RNA-binding

Protein family/group databases

MEROPSiA02.020.

Names & Taxonomyi

Protein namesi
Recommended name:
Pro-Pol polyprotein
Alternative name(s):
Pr125Pol
Cleaved into the following 2 chains:
Alternative name(s):
p87Pro-RT-RNaseH
Integrase
Short name:
IN
Alternative name(s):
p42In
Gene namesi
Name:pro-pol
OrganismiKoala retrovirus (KoRV)
Taxonomic identifieri394239 [NCBI]
Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeGammaretrovirusunclassified Gammaretrovirus
Virus hostiPhascolarctos cinereus (Koala) [TaxID: 38626]
ProteomesiUP000007765: Genome

Subcellular locationi

Chain Integrase : Virion Reviewed prediction. Host nucleus By similarity. Host cytoplasm Reviewed prediction
Note: Nuclear at initial phase, cytoplasmic at assembly Reviewed prediction.
Chain Protease/Reverse transcriptase/ribonuclease H : Host nucleus By similarity. Host cytoplasm Reviewed prediction
Note: Nuclear at initial phase, cytoplasmic at assembly Reviewed prediction.

GO - Cellular componenti

  1. host cell cytoplasm Source: UniProtKB-SubCell
  2. host cell nucleus Source: UniProtKB-SubCell
  3. virion Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Host cytoplasm, Host nucleus, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 11271127Pro-Pol polyproteinPRO_0000249431Add
BLAST
Chaini1 – ?742742Protease/Reverse transcriptase/ribonuclease H By similarityPRO_0000249432Add
BLAST
Chaini?743 – 1127385Integrase By similarityPRO_0000249433Add
BLAST

Post-translational modificationi

Specific enzymatic cleavages in vivo by viral protease yield mature proteins. The protease is not cleaved off from Pol. Since cleavage efficiency is not optimal for all sites, long and active p65Pro-RT, p87Pro-RT-RNaseH and even some Pr125Pol are detected in infected cells By similarity.

Structurei

3D structure databases

ProteinModelPortaliQ9TTC1.
SMRiQ9TTC1. Positions 103-552, 583-738.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini22 – 9271Peptidase A2Add
BLAST
Domaini202 – 393192Reverse transcriptaseAdd
BLAST
Domaini635 – 781147RNase HAdd
BLAST
Domaini905 – 1063159Integrase catalyticAdd
BLAST

Domaini

The reverse transcriptase/ribonuclease H (RT) is structured in five subdomains: finger, palm, thumb, connection and RNase H. Within the palm subdomain, the "primer grip" region is thought to be involved in the positioning of the primer terminus for accommodating the incoming nucleotide. The RNase H domain stabilizes the association of RT with primer-template By similarity.
Integrase core domain contains the D-x(n)-D-x(35)-E motif, named for the phylogenetically conserved glutamic acid and aspartic acid residues and the invariant 35 amino acid spacing between the second and third acidic residues. Each acidic residue of the D,D(35)E motif is independently essential for the 3'-processing and strand transfer activities of purified integrase protein By similarity.

Sequence similaritiesi

Contains 1 RNase H domain.

Family and domain databases

Gene3Di3.30.420.10. 2 hits.
InterProiIPR001584. Integrase_cat-core.
IPR018061. Pept_A2A_retrovirus_sg.
IPR001995. Peptidase_A2_cat.
IPR021109. Peptidase_aspartic_dom.
IPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR000477. RT_dom.
[Graphical view]
PfamiPF00075. RNase_H. 1 hit.
PF00665. rve. 1 hit.
PF00077. RVP. 1 hit.
PF00078. RVT_1. 1 hit.
[Graphical view]
SUPFAMiSSF50630. SSF50630. 1 hit.
SSF53098. SSF53098. 2 hits.
PROSITEiPS50175. ASP_PROT_RETROV. 1 hit.
PS50994. INTEGRASE. 1 hit.
PS50879. RNASE_H. 1 hit.
PS50878. RT_POL. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q9TTC1-1 [UniParc]FASTAAdd to Basket

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MGKMGSKRTV VAGATGSKVY PWTTKRLLKI GQKQVTHSFL VIPECPAPLL     50
GRDLLTKLKA QIQFSTEGPQ VTWEDRPAMC LVLNLEEEYR LHEKPVPPSI 100
DPSWLQLFPM VWAEKAGMGL ANQVPPVVVE LKSDASPVAV RQYPMSKEAR 150
EGIRPHIQRF LDLGILVPCQ SPWNTPLLPV KKPGTNDYRP VQDLREVNKR 200
VQDIHPTVPN PYNLLSSLPP SHTWYSVLDL KDAFFCLKLH PNSQPLFAFE 250
WRDPEKGNTG QLTWTRLPQG FKNSPTLFDE ALHRDLASFR ALNPQVVMLQ 300
YVDDLLVAAP TYRDCKEGTR RLLQELSKLG YRVSAKKAQL CREEVTYLGY 350
LLKGGKRWLT PARKATVMKI PTPTTPRQVR EFLGTAGFCR LWIPGFASLA 400
APLYPLTREK VPFTWTEAHQ EAFGRIKEAL LSAPALALPD LTKPFALYVD 450
EKEGVARGVL TQTLGPWRRP VAYLSKKLDP VASGWPTCLK AIAAVALLLK 500
DADKLTLGQN VLVIAPHNLE SIVRQPPDRW MTNARMTHYQ SLLLNERVSF 550
APPAILNPAT LLPVESDDTP IHICSEILAE ETGTRPDLRD QPLPGVPAWY 600
TDGSSFIMDG RRQAGAAIVD NKRTVWASNL PEGTSAQKAE LIALTQALRL 650
AEGKSINIYT DSRYAFATAH VHGAIYKQRG LLTSAGKDIK NKEEILALLE 700
AIHLPKRVAI IHCPGHQRGT DPVATGNRKA DEAAKQAAQS TRILTETTKN 750
QEHFEPTRGK IKPRELTPDQ GREFIQRLHQ LTHLGPDKLL QLVGRTSFHI 800
PNLQSVVREI TSKCQVCAVT NAVTTYREPG RRQRGDRPGV YWEVDFTEVK 850
PGRYGNRYLL VFIDTFSGWV EAFPTKTETA LTVCKKILEE ILPRFGIPKV 900
LGSDNGPAFV AQVSQGLATQ LGIDWKLHCA YRPQSSGQVE RMNRTIKETL 950
TKLALETGGK DWVTLLPLAL LRARNTPGQF GLTPYEILHG GPPPVLASGE 1000
VVGSNGDFFP VLFTHLKALE VVRTQIWDQI KEAYRPGTVA IPHPFQVGDR 1050
VLVRRHRSGS LEPRWKGPYL VLLTTPTAVK VDGIAAWVHA SHLKPAPPGA 1100
PDESWELEKT DHPLKLRVRR RRNESTA 1127
Length:1,127
Mass (Da):125,817
Last modified:May 1, 2000 - v1
Checksum:i010ADD971CA957BF
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF151794 Genomic DNA. Translation: AAF15098.1.

Keywords - Coding sequence diversityi

RNA suppression of termination

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF151794 Genomic DNA. Translation: AAF15098.1 .

3D structure databases

ProteinModelPortali Q9TTC1.
SMRi Q9TTC1. Positions 103-552, 583-738.
ModBasei Search...
MobiDBi Search...

Protein family/group databases

MEROPSi A02.020.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Family and domain databases

Gene3Di 3.30.420.10. 2 hits.
InterProi IPR001584. Integrase_cat-core.
IPR018061. Pept_A2A_retrovirus_sg.
IPR001995. Peptidase_A2_cat.
IPR021109. Peptidase_aspartic_dom.
IPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR000477. RT_dom.
[Graphical view ]
Pfami PF00075. RNase_H. 1 hit.
PF00665. rve. 1 hit.
PF00077. RVP. 1 hit.
PF00078. RVT_1. 1 hit.
[Graphical view ]
SUPFAMi SSF50630. SSF50630. 1 hit.
SSF53098. SSF53098. 2 hits.
PROSITEi PS50175. ASP_PROT_RETROV. 1 hit.
PS50994. INTEGRASE. 1 hit.
PS50879. RNASE_H. 1 hit.
PS50878. RT_POL. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "The nucleotide sequence of koala (Phascolarctos cinereus) retrovirus: a novel type C endogenous virus related to Gibbon ape leukemia virus."
    Hanger J.J., Bromham L.D., McKee J.J., O'Brien T.M., Robinson W.F.
    J. Virol. 74:4264-4272(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].

Entry informationi

Entry nameiPOL_KORV
AccessioniPrimary (citable) accession number: Q9TTC1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 5, 2006
Last sequence update: May 1, 2000
Last modified: May 14, 2014
This is version 77 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

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.
Koala retrovirus is both a circulating virus and an endogenous retrovirus of koala, except in some isolated populations in south Australia.

Keywords - Technical termi

Complete proteome, Multifunctional enzyme

Documents

  1. Peptidase families
    Classification of peptidase families and list of entries
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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