POL_IPHA
ID POL_IPHA Reviewed; 863 AA.
AC P04026;
DT 23-OCT-1986, integrated into UniProtKB/Swiss-Prot.
DT 23-OCT-1986, sequence version 1.
DT 03-AUG-2022, entry version 114.
DE RecName: Full=Intracisternal A-particle Pol-related polyprotein;
DE Contains:
DE RecName: Full=Reverse transcriptase/ribonuclease H;
DE Short=RT;
DE EC=2.7.7.49 {ECO:0000255|PROSITE-ProRule:PRU00405};
DE EC=2.7.7.7 {ECO:0000255|PROSITE-ProRule:PRU00405};
DE EC=3.1.26.4 {ECO:0000255|PROSITE-ProRule:PRU00408};
DE Contains:
DE RecName: Full=Integrase;
DE Short=IN;
DE Flags: Fragment;
GN Name=pol;
OS Hamster intracisternal a-particle H18 (IAP-H18).
OC Viruses; Riboviria; Pararnavirae; Artverviricota; Revtraviricetes;
OC Ortervirales; Retroviridae; Intracisternal A-particles.
OX NCBI_TaxID=11752;
OH NCBI_TaxID=10026; Cricetinae (hamsters).
RN [1]
RP NUCLEOTIDE SEQUENCE.
RX PubMed=2991563; DOI=10.1128/jvi.55.2.387-394.1985;
RA Ono M., Toh H., Miyata T., Awaya T.;
RT "Nucleotide sequence of the Syrian hamster intracisternal A-particle gene:
RT close evolutionary relationship of type A particle gene to types B and D
RT oncovirus genes.";
RL J. Virol. 55:387-394(1985).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) =
CC diphosphate + DNA(n+1); Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339,
CC Rhea:RHEA-COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560,
CC ChEBI:CHEBI:173112; EC=2.7.7.49; Evidence={ECO:0000255|PROSITE-
CC ProRule:PRU00405};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) =
CC diphosphate + DNA(n+1); Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339,
CC Rhea:RHEA-COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560,
CC ChEBI:CHEBI:173112; EC=2.7.7.7; Evidence={ECO:0000255|PROSITE-
CC ProRule:PRU00405};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Endonucleolytic cleavage to 5'-phosphomonoester.; EC=3.1.26.4;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00408};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00405};
CC Note=The RT polymerase active site binds 2 magnesium ions.
CC {ECO:0000255|PROSITE-ProRule:PRU00405};
CC -!- MISCELLANEOUS: [Intracisternal A-particle Pol-related polyprotein]:
CC Intracisternal A particles (IAPs) are defective retroviral elements.
CC Due to extensive mutations in the envelope coding sequence, IAPs can
CC only form defective viral particles confined to the intracisternae of
CC the Golgi. IAPs are an important class of transposable elements that
CC induce genomic mutations and cell transformation by disrupting gene
CC expression. {ECO:0000305}.
CC -!- MISCELLANEOUS: Reverse transcriptase/ribonuclease HThe reverse
CC transcriptase is an error-prone enzyme that lacks a proof-reading
CC function. High mutations rate is a direct consequence of this
CC characteristic. RT also displays frequent template swiching leading to
CC high recombination rate. Recombination mostly occurs between homologous
CC regions of the two copackaged RNA genomes. If these two RNA molecules
CC derive from different viral strains, reverse transcription will give
CC rise to highly recombinated proviral DNAs. {ECO:0000255|PROSITE-
CC ProRule:PRU00405}.
CC -!- MISCELLANEOUS: Readthrough of three terminators may occur: TAA between
CC codons ATT for Ile-660 and AAA for Lys-661, TAG between codons TCC for
CC Ser-832 and TAT for Tyr-833, and TAG between codons CCC for Pro-859 and
CC ATT for Ile-860.
CC -!- SIMILARITY: Belongs to the retroviral Pol polyprotein family.
CC {ECO:0000305}.
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DR PIR; A03964; GNHYIH.
DR SMR; P04026; -.
DR PRIDE; P04026; -.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-EC.
DR GO; GO:0003964; F:RNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
DR GO; GO:0004523; F:RNA-DNA hybrid ribonuclease activity; IEA:UniProtKB-EC.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0015074; P:DNA integration; IEA:UniProtKB-KW.
DR GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
DR GO; GO:0075713; P:establishment of integrated proviral latency; IEA:UniProtKB-KW.
DR GO; GO:0046718; P:viral entry into host cell; IEA:UniProtKB-KW.
DR GO; GO:0044826; P:viral genome integration into host DNA; IEA:UniProtKB-KW.
DR Gene3D; 1.10.10.200; -; 1.
DR Gene3D; 2.30.30.10; -; 1.
DR Gene3D; 3.30.420.10; -; 2.
DR Gene3D; 3.30.70.270; -; 2.
DR InterPro; IPR043502; DNA/RNA_pol_sf.
DR InterPro; IPR017856; Integrase-like_N.
DR InterPro; IPR036862; Integrase_C_dom_sf_retrovir.
DR InterPro; IPR001037; Integrase_C_retrovir.
DR InterPro; IPR001584; Integrase_cat-core.
DR InterPro; IPR003308; Integrase_Zn-bd_dom_N.
DR InterPro; IPR043128; Rev_trsase/Diguanyl_cyclase.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR002156; RNaseH_domain.
DR InterPro; IPR036397; RNaseH_sf.
DR InterPro; IPR000477; RT_dom.
DR InterPro; IPR010661; RVT_thumb.
DR Pfam; PF00552; IN_DBD_C; 1.
DR Pfam; PF02022; Integrase_Zn; 1.
DR Pfam; PF00075; RNase_H; 1.
DR Pfam; PF00665; rve; 1.
DR Pfam; PF00078; RVT_1; 1.
DR Pfam; PF06817; RVT_thumb; 1.
DR SUPFAM; SSF46919; SSF46919; 1.
DR SUPFAM; SSF50122; SSF50122; 1.
DR SUPFAM; SSF53098; SSF53098; 1.
DR SUPFAM; SSF56672; SSF56672; 1.
DR PROSITE; PS50994; INTEGRASE; 1.
DR PROSITE; PS51027; INTEGRASE_DBD; 1.
DR PROSITE; PS50879; RNASE_H_1; 1.
DR PROSITE; PS50878; RT_POL; 1.
DR PROSITE; PS50876; ZF_INTEGRASE; 1.
PE 3: Inferred from homology;
KW DNA integration; DNA recombination; DNA-binding; Endonuclease; Hydrolase;
KW Magnesium; Metal-binding; Multifunctional enzyme; Nuclease;
KW Nucleotidyltransferase; RNA-directed DNA polymerase; Transferase;
KW Transposable element; Viral genome integration; Virus entry into host cell;
KW Zinc; Zinc-finger.
FT CHAIN <1..863
FT /note="Intracisternal A-particle Pol-related polyprotein"
FT /id="PRO_0000125486"
FT CHAIN <1..546
FT /note="Reverse transcriptase/ribonuclease H"
FT /id="PRO_0000443269"
FT CHAIN 547..863
FT /note="Integrase"
FT /id="PRO_0000443270"
FT DOMAIN 41..229
FT /note="Reverse transcriptase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00405"
FT DOMAIN 408..538
FT /note="RNase H type-1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT DOMAIN 596..766
FT /note="Integrase catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT ZN_FING 542..583
FT /note="Integrase-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00450"
FT DNA_BIND 760..809
FT /note="Integrase-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00506"
FT REGION 800..840
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 817..836
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 106
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic; for reverse transcriptase
FT activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00405"
FT BINDING 181
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic; for reverse transcriptase
FT activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00405"
FT BINDING 182
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic; for reverse transcriptase
FT activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00405"
FT BINDING 417
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT BINDING 446
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT BINDING 466
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT BINDING 530
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT BINDING 551
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00450"
FT BINDING 555
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00450"
FT BINDING 579
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00450"
FT BINDING 582
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00450"
FT BINDING 607
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT BINDING 663
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT SITE 546..547
FT /note="Cleavage; by viral protease"
FT /evidence="ECO:0000250|UniProtKB:P03365"
FT NON_TER 1
SQ SEQUENCE 863 AA; 97037 MW; 704AEF7FC6B1D886 CRC64;
LGAVEASRPI PWKTEEPLWV SQWPLSSEKL EAVTRLVQEQ ERLGHLEPST SPWNTPIFVI
KKKSGKWRLL HDLRAINNQM HLFGPVQRGL PLLSALPQDW KLIIIDIKDC FFSIPLYPRD
RPRFAFTIPS LNHMEPDKRF QWKVLPQGMA NSPTICQLYV QEALEPIRKQ FTSLIVIHYM
DDILICHKEL DVLQKAFPML VAELKQWGLE IASEKVQIAD TGLFLGSKIT PKNIVPQKIE
IRKDHLQTLN DFQKLLGDIN WLRPFLKIPS ADLKPLFDLL EGEPHISSPR KFTPAAHRAL
QMVEEALQEA QITTNSPAKI IDWYPDAVAQ PRSRIKAAVT HFGRDPDSLI VPYTAAQVQT
LAATSSDWAV LVTSFSGQID NHFPKHPILQ FALNQAIVFP QVTAKDPLPD GTVVYTDGSK
TGLGAYVVKD RVISKQYNET SPQVVECLIV LEVLEAFPGP LNIVSDSSYV VNAVNLLEIA
GIIRSSSRVA NIFQKIQAAL LNRRFPVFIT HVRAHSGLPG PMSLGNDLAD KATKLVATAL
STHAQAAKEF HKRFHVTAET LRRRFALSRK EAREIVTQCQ NCCEFLPTPH MGINPRGIRP
LQMWQMDVTH IPSFGRLQYV HVSVDTCSGV MFATPLTGEK ASYVIQHCLE AWSAWGKPRI
KTDNGPAYTS QKFRQFCRQM DVTHLTGLPY NPQGQGIVER AHRTLKSYLI KQKGSIEDVL
PSVPRVAVSM ALFTLNFLNC DAQGHTAADR HSLEPDRPKE MVKWKDVLTD LWKGPDPILI
RSRGAVCVFP QEEENPLWIP ERLTRRAPSQ LQNKKDGGQV GDEDSPTRDD GSYDGRVTVG
HHVYLPPTDA SDAECPGVPI FHK
