POLR1_ARATH
ID POLR1_ARATH Reviewed; 1466 AA.
AC Q94HW2; F7J134; Q9SLU4;
DT 25-OCT-2017, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 113.
DE RecName: Full=Retrovirus-related Pol polyprotein from transposon RE1;
DE AltName: Full=Retro element 1 {ECO:0000303|PubMed:10689195};
DE Short=AtRE1 {ECO:0000303|PubMed:10689195};
DE Includes:
DE RecName: Full=Protease RE1;
DE EC=3.4.23.-;
DE Includes:
DE RecName: Full=Reverse transcriptase RE1;
DE EC=2.7.7.49;
DE Includes:
DE RecName: Full=Endonuclease RE1;
GN Name=RE1; Synonyms=RF12, RF28 {ECO:0000303|PubMed:10689195};
GN OrderedLocusNames=At1g58889 {ECO:0000305};
GN ORFNames=R18I {ECO:0000312|EMBL:BAB84015.1};
GN and
GN Name=RE1; OrderedLocusNames=At1g59265 {ECO:0000305};
GN ORFNames=T4M14.18 {ECO:0000312|EMBL:AAK62788.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=cv. C24;
RX PubMed=24770782; DOI=10.1007/s00438-014-0855-z;
RA Yamada M., Yamagishi Y., Akaoka M., Ito H., Kato A.;
RT "Genomic localization of AtRE1 and AtRE2, copia-type retrotransposons, in
RT natural variants of Arabidopsis thaliana.";
RL Mol. Genet. Genomics 289:821-835(2014).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=10548732; DOI=10.1016/s0378-1119(99)00403-5;
RA Kato A., Suzuki M., Kuwahara A., Ooe H., Higano-Inaba K., Komeda Y.;
RT "Isolation and analysis of cDNA within a 300 kb Arabidopsis thaliana
RT genomic region located around the 100 map unit of chromosome 1.";
RL Gene 239:309-316(1999).
RN [5]
RP GENE FAMILY, AND NOMENCLATURE.
RC STRAIN=cv. Columbia;
RX PubMed=10689195; DOI=10.1016/s0378-1119(99)00565-x;
RA Kuwahara A., Kato A., Komeda Y.;
RT "Isolation and characterization of copia-type retrotransposons in
RT Arabidopsis thaliana.";
RL Gene 244:127-136(2000).
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;
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA87949.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; AB605839; BAK41511.1; -; Genomic_DNA.
DR EMBL; AC027036; AAK62788.1; -; Genomic_DNA.
DR EMBL; AB078516; BAB84015.1; -; Genomic_DNA.
DR EMBL; CP002684; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AB028223; BAA87949.1; ALT_FRAME; mRNA.
DR PIR; T52436; T52436.
DR AlphaFoldDB; Q94HW2; -.
DR SMR; Q94HW2; -.
DR MEROPS; A11.004; -.
DR PeptideAtlas; Q94HW2; -.
DR PRIDE; Q94HW2; -.
DR Araport; AT1G58889; -.
DR Araport; AT1G59265; -.
DR PRO; PR:Q94HW2; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q94HW2; baseline and differential.
DR GO; GO:0004190; F:aspartic-type endopeptidase activity; IEA:UniProtKB-KW.
DR GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003676; F:nucleic acid binding; IEA:InterPro.
DR GO; GO:0003964; F:RNA-directed DNA polymerase activity; IEA:UniProtKB-EC.
DR GO; GO:0015074; P:DNA integration; IEA:UniProtKB-KW.
DR GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR Gene3D; 3.30.420.10; -; 1.
DR InterPro; IPR043502; DNA/RNA_pol_sf.
DR InterPro; IPR025724; GAG-pre-integrase_dom.
DR InterPro; IPR001584; Integrase_cat-core.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR InterPro; IPR013103; RVT_2.
DR Pfam; PF13976; gag_pre-integrs; 1.
DR Pfam; PF00665; rve; 1.
DR Pfam; PF07727; RVT_2; 1.
DR SUPFAM; SSF53098; SSF53098; 1.
DR SUPFAM; SSF56672; SSF56672; 1.
DR PROSITE; PS50994; INTEGRASE; 1.
PE 2: Evidence at transcript level;
KW Aspartyl protease; DNA integration; DNA recombination; Endonuclease;
KW Hydrolase; Magnesium; Metal-binding; Nuclease; Protease;
KW Reference proteome; Transferase; Zinc; Zinc-finger.
FT CHAIN 1..1466
FT /note="Retrovirus-related Pol polyprotein from transposon
FT RE1"
FT /id="PRO_0000441908"
FT DOMAIN 519..682
FT /note="Integrase catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT DOMAIN 982..1225
FT /note="Reverse transcriptase Ty1/copia-type"
FT /evidence="ECO:0000255"
FT ZN_FING 278..294
FT /note="CCHC-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00047"
FT REGION 227..270
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 772..927
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 795..831
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 839..901
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 913..927
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 334
FT /note="For protease activity"
FT /evidence="ECO:0000250"
FT BINDING 530
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT BINDING 592
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00457"
FT CONFLICT 149
FT /note="L -> F (in Ref. 1; BAK41511)"
FT /evidence="ECO:0000305"
FT CONFLICT 235
FT /note="N -> T (in Ref. 4; BAA87949)"
FT /evidence="ECO:0000305"
FT CONFLICT 1019
FT /note="A -> V (in Ref. 1; BAK41511)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1466 AA; 163905 MW; FF1A4143B1161D43 CRC64;
MAAHAEELVL NNTSILNVNM SNVTKLTSTN YLMWSRQVHA LFDGYELAGF LDGSTTMPPA
TIGTDAAPRV NPDYTRWKRQ DKLIYSAVLG AISMSVQPAV SRATTAAQIW ETLRKIYANP
SYGHVTQLRT QLKQWTKGTK TIDDYMQGLV TRFDQLALLG KPMDHDEQVE RVLENLPEEY
KPVIDQIAAK DTPPTLTEIH ERLLNHESKI LAVSSATVIP ITANAVSHRN TTTTNNNNNG
NRNNRYDNRN NNNNSKPWQQ SSTNFHPNNN QSKPYLGKCQ ICGVQGHSAK RCSQLQHFLS
SVNSQQPPSP FTPWQPRANL ALGSPYSSNN WLLDSGATHH ITSDFNNLSL HQPYTGGDDV
MVADGSTIPI SHTGSTSLST KSRPLNLHNI LYVPNIHKNL ISVYRLCNAN GVSVEFFPAS
FQVKDLNTGV PLLQGKTKDE LYEWPIASSQ PVSLFASPSS KATHSSWHAR LGHPAPSILN
SVISNYSLSV LNPSHKFLSC SDCLINKSNK VPFSQSTINS TRPLEYIYSD VWSSPILSHD
NYRYYVIFVD HFTRYTWLYP LKQKSQVKET FITFKNLLEN RFQTRIGTFY SDNGGEFVAL
WEYFSQHGIS HLTSPPHTPE HNGLSERKHR HIVETGLTLL SHASIPKTYW PYAFAVAVYL
INRLPTPLLQ LESPFQKLFG TSPNYDKLRV FGCACYPWLR PYNQHKLDDK SRQCVFLGYS
LTQSAYLCLH LQTSRLYISR HVRFDENCFP FSNYLATLSP VQEQRRESSC VWSPHTTLPT
RTPVLPAPSC SDPHHAATPP SSPSAPFRNS QVSSSNLDSS FSSSFPSSPE PTAPRQNGPQ
PTTQPTQTQT QTHSSQNTSQ NNPTNESPSQ LAQSLSTPAQ SSSSSPSPTT SASSSSTSPT
PPSILIHPPP PLAQIVNNNN QAPLNTHSMG TRAKAGIIKP NPKYSLAVSL AAESEPRTAI
QALKDERWRN AMGSEINAQI GNHTWDLVPP PPSHVTIVGC RWIFTKKYNS DGSLNRYKAR
LVAKGYNQRP GLDYAETFSP VIKSTSIRIV LGVAVDRSWP IRQLDVNNAF LQGTLTDDVY
MSQPPGFIDK DRPNYVCKLR KALYGLKQAP RAWYVELRNY LLTIGFVNSV SDTSLFVLQR
GKSIVYMLVY VDDILITGND PTLLHNTLDN LSQRFSVKDH EELHYFLGIE AKRVPTGLHL
SQRRYILDLL ARTNMITAKP VTTPMAPSPK LSLYSGTKLT DPTEYRGIVG SLQYLAFTRP
DISYAVNRLS QFMHMPTEEH LQALKRILRY LAGTPNHGIF LKKGNTLSLH AYSDADWAGD
KDDYVSTNGY IVYLGHHPIS WSSKKQKGVV RSSTEAEYRS VANTSSEMQW ICSLLTELGI
RLTRPPVIYC DNVGATYLCA NPVFHSRMKH IAIDYHFIRN QVQSGALRVV HVSTHDQLAD
TLTKPLSRTA FQNFASKIGV TRVPPS
