ID Q6F2Q6_ORYSJ Unreviewed; 1516 AA.
AC Q6F2Q6;
DT 16-AUG-2004, integrated into UniProtKB/TrEMBL.
DT 16-AUG-2004, sequence version 1.
DT 27-MAR-2024, entry version 111.
DE RecName: Full=RNA-directed DNA polymerase {ECO:0000256|ARBA:ARBA00012493};
DE EC=2.7.7.49 {ECO:0000256|ARBA:ARBA00012493};
GN ORFNames=OSJNBa0088M06.2 {ECO:0000313|EMBL:AAT73689.1};
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947 {ECO:0000313|EMBL:AAT73689.1, ECO:0000313|Proteomes:UP000000763};
RN [1] {ECO:0000313|Proteomes:UP000000763}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare {ECO:0000313|Proteomes:UP000000763};
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RA Matsumoto T., Wu J., Kanamori H., Katayose Y., Fujisawa M., Namiki N.,
RA Mizuno H., Yamamoto K., Antonio B.A., Baba T., Sakata K., Nagamura Y.,
RA Aoki H., Arikawa K., Arita K., Bito T., Chiden Y., Fujitsuka N.,
RA Fukunaka R., Hamada M., Harada C., Hayashi A., Hijishita S., Honda M.,
RA Hosokawa S., Ichikawa Y., Idonuma A., Iijima M., Ikeda M., Ikeno M.,
RA Ito K., Ito S., Ito T., Ito Y., Ito Y., Iwabuchi A., Kamiya K.,
RA Karasawa W., Kurita K., Katagiri S., Kikuta A., Kobayashi H., Kobayashi N.,
RA Machita K., Maehara T., Masukawa M., Mizubayashi T., Mukai Y., Nagasaki H.,
RA Nagata Y., Naito S., Nakashima M., Nakama Y., Nakamichi Y., Nakamura M.,
RA Meguro A., Negishi M., Ohta I., Ohta T., Okamoto M., Ono N., Saji S.,
RA Sakaguchi M., Sakai K., Shibata M., Shimokawa T., Song J., Takazaki Y.,
RA Terasawa K., Tsugane M., Tsuji K., Ueda S., Waki K., Yamagata H.,
RA Yamamoto M., Yamamoto S., Yamane H., Yoshiki S., Yoshihara R., Yukawa K.,
RA Zhong H., Yano M., Yuan Q., Ouyang S., Liu J., Jones K.M., Gansberger K.,
RA Moffat K., Hill J., Bera J., Fadrosh D., Jin S., Johri S., Kim M.,
RA Overton L., Reardon M., Tsitrin T., Vuong H., Weaver B., Ciecko A.,
RA Tallon L., Jackson J., Pai G., Aken S.V., Utterback T., Reidmuller S.,
RA Feldblyum T., Hsiao J., Zismann V., Iobst S., de Vazeille A.R., Buell C.R.,
RA Ying K., Li Y., Lu T., Huang Y., Zhao Q., Feng Q., Zhang L., Zhu J.,
RA Weng Q., Mu J., Lu Y., Fan D., Liu Y., Guan J., Zhang Y., Yu S., Liu X.,
RA Zhang Y., Hong G., Han B., Choisne N., Demange N., Orjeda G., Samain S.,
RA Cattolico L., Pelletier E., Couloux A., Segurens B., Wincker P., D'Hont A.,
RA Scarpelli C., Weissenbach J., Salanoubat M., Quetier F., Yu Y., Kim H.R.,
RA Rambo T., Currie J., Collura K., Luo M., Yang T., Ammiraju J.S.S.,
RA Engler F., Soderlund C., Wing R.A., Palmer L.E., de la Bastide M.,
RA Spiegel L., Nascimento L., Zutavern T., O'Shaughnessy A., Dike S.,
RA Dedhia N., Preston R., Balija V., McCombie W.R., Chow T., Chen H.,
RA Chung M., Chen C., Shaw J., Wu H., Hsiao K., Chao Y., Chu M., Cheng C.,
RA Hour A., Lee P., Lin S., Lin Y., Liou J., Liu S., Hsing Y., Raghuvanshi S.,
RA Mohanty A., Bharti A.K., Gaur A., Gupta V., Kumar D., Ravi V., Vij S.,
RA Kapur A., Khurana P., Khurana P., Khurana J.P., Tyagi A.K., Gaikwad K.,
RA Singh A., Dalal V., Srivastava S., Dixit A., Pal A.K., Ghazi I.A.,
RA Yadav M., Pandit A., Bhargava A., Sureshbabu K., Batra K., Sharma T.R.,
RA Mohapatra T., Singh N.K., Messing J., Nelson A.B., Fuks G., Kavchok S.,
RA Keizer G., Linton E., Llaca V., Song R., Tanyolac B., Young S., Ho-Il K.,
RA Hahn J.H., Sangsakoo G., Vanavichit A., de Mattos Luiz.A.T., Zimmer P.D.,
RA Malone G., Dellagostin O., de Oliveira A.C., Bevan M., Bancroft I.,
RA Minx P., Cordum H., Wilson R., Cheng Z., Jin W., Jiang J., Leong S.A.,
RA Iwama H., Gojobori T., Itoh T., Niimura Y., Fujii Y., Habara T., Sakai H.,
RA Sato Y., Wilson G., Kumar K., McCouch S., Juretic N., Hoen D., Wright S.,
RA Bruskiewich R., Bureau T., Miyao A., Hirochika H., Nishikawa T.,
RA Kadowaki K., Sugiura M., Burr B., Sasaki T.;
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [2] {ECO:0000313|Proteomes:UP000000763}
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare {ECO:0000313|Proteomes:UP000000763};
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
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DR EMBL; AC135916; AAT73689.1; -; Genomic_DNA.
DR Proteomes; UP000000763; Chromosome 5.
DR GO; GO:0004190; F:aspartic-type endopeptidase activity; IEA:InterPro.
DR GO; GO:0003676; F:nucleic acid binding; IEA:InterPro.
DR GO; GO:0003964; F:RNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0015074; P:DNA integration; IEA:InterPro.
DR GO; GO:0006508; P:proteolysis; IEA:InterPro.
DR CDD; cd00303; retropepsin_like; 1.
DR CDD; cd09274; RNase_HI_RT_Ty3; 1.
DR CDD; cd01647; RT_LTR; 1.
DR Gene3D; 1.10.340.70; -; 1.
DR Gene3D; 3.30.70.270; -; 2.
DR Gene3D; 2.40.70.10; Acid Proteases; 1.
DR Gene3D; 3.10.10.10; HIV Type 1 Reverse Transcriptase, subunit A, domain 1; 1.
DR Gene3D; 3.30.420.10; Ribonuclease H-like superfamily/Ribonuclease H; 1.
DR Gene3D; 4.10.60.10; Zinc finger, CCHC-type; 1.
DR InterPro; IPR001969; Aspartic_peptidase_AS.
DR InterPro; IPR016197; Chromo-like_dom_sf.
DR InterPro; IPR043502; DNA/RNA_pol_sf.
DR InterPro; IPR001584; Integrase_cat-core.
DR InterPro; IPR041588; Integrase_H2C2.
DR InterPro; IPR021109; Peptidase_aspartic_dom_sf.
DR InterPro; IPR005162; Retrotrans_gag_dom.
DR InterPro; IPR043128; Rev_trsase/Diguanyl_cyclase.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR InterPro; IPR000477; RT_dom.
DR InterPro; IPR041373; RT_RNaseH.
DR InterPro; IPR001878; Znf_CCHC.
DR InterPro; IPR036875; Znf_CCHC_sf.
DR PANTHER; PTHR45835:SF87; RNA-DIRECTED DNA POLYMERASE; 1.
DR PANTHER; PTHR45835; YALI0A06105P; 1.
DR Pfam; PF17921; Integrase_H2C2; 1.
DR Pfam; PF03732; Retrotrans_gag; 1.
DR Pfam; PF17917; RT_RNaseH; 1.
DR Pfam; PF00665; rve; 1.
DR Pfam; PF08284; RVP_2; 1.
DR Pfam; PF00078; RVT_1; 1.
DR SMART; SM00343; ZnF_C2HC; 1.
DR SUPFAM; SSF50630; Acid proteases; 1.
DR SUPFAM; SSF54160; Chromo domain-like; 1.
DR SUPFAM; SSF56672; DNA/RNA polymerases; 1.
DR SUPFAM; SSF57756; Retrovirus zinc finger-like domains; 1.
DR SUPFAM; SSF53098; Ribonuclease H-like; 1.
DR PROSITE; PS00141; ASP_PROTEASE; 1.
DR PROSITE; PS50994; INTEGRASE; 1.
DR PROSITE; PS50878; RT_POL; 1.
DR PROSITE; PS50158; ZF_CCHC; 1.
PE 4: Predicted;
KW Hydrolase {ECO:0000256|ARBA:ARBA00022801};
KW Metal-binding {ECO:0000256|PROSITE-ProRule:PRU00047};
KW Nucleotidyltransferase {ECO:0000256|ARBA:ARBA00022695};
KW RNA-directed DNA polymerase {ECO:0000256|ARBA:ARBA00022918};
KW Transferase {ECO:0000256|ARBA:ARBA00022679};
KW Zinc {ECO:0000256|PROSITE-ProRule:PRU00047};
KW Zinc-finger {ECO:0000256|PROSITE-ProRule:PRU00047}.
FT DOMAIN 350..365
FT /note="CCHC-type"
FT /evidence="ECO:0000259|PROSITE:PS50158"
FT DOMAIN 603..782
FT /note="Reverse transcriptase"
FT /evidence="ECO:0000259|PROSITE:PS50878"
FT DOMAIN 1147..1310
FT /note="Integrase catalytic"
FT /evidence="ECO:0000259|PROSITE:PS50994"
FT REGION 1..43
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 295..343
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..16
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 17..43
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 295..321
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 1516 AA; 173918 MW; 58FCAE65A0D2FA6F CRC64;
MMKTRNDPRD SNDASGSEEQ TDGAHVSGAS GSRSSPPPEN PTVTQMMTMM MQQMQQHYHQ
MLQQAQQNQQ FGPPPSHVSK LLDFLRIQPP TFSSTTNPME ANDWLRAIEK KLNLLQCNDR
EKVAFATHQL QGPASAWWDN YVATRLDATE VTWAEFCQSF RKAQIPEGIM AQQKREFRAL
QQGTRTVTEY LHEFNRLARY APEDVRTDAE KQEKFLFGLD DELTNQLISG VYEDFEKLVD
KAIRQEEQRN KMDRKRKAAQ ISFPQGNNQK PRFMTGQLGG PSTLIVCQHR PYHPSNFNND
YNGGSHNNSK QHNHNSTPPP LMAPAQSDPP AVSVQSEQPK KGAVGKPGPC FNCGKHGHFA
GKCPKLNRTR PRFIQARANH VSAEEAQAAP EVVLGTFPVN SYPATVLFDS GASHSFISKR
FAGMHGLSVV ELKIPMQVHT PGNDMRTAHY CPSVTIEIKR SPFLSNLILL ESKDLDVILG
MDWLTRNKGV IDCASRTITL TNDKGEKITF RSPVSQKSVA SLNQAAIEGQ TETVEKSPRK
LEDIPIVQEY PEVFPEDLTT MPPKREIEFR IDLAPGTAPI YKRPYRMAAN ELAEVKKQVD
EQLQKGYIRP STSPWGAPVI FVEKKDKTKR MCVDYRALNE VTIKNKYPLP RIDDLFDQLK
GAKVFSKIDL RSGYHQLRIR EEDIPKTAFT TRYGLFECTV MSFGLTNAPA FFMNLMNKVF
MEFLDKFVVV FIDDILIYSK SEKQHEQHLR LVLEKLKEHQ LYAKFSKCDF WLSEVKFLGH
VISAQGVAVD PSNVESVTKW TPPKTVSQIR SFLGLAGYYR RFIENFSKIA RPMTQLLKKD
EKFKWSAECN QSFEELKKKL VSAPVLILPD QTKDFQVYCD ASRQGLGCVL MQEGRVVAYA
SRQLRPHETN YPTHDLELAA VVHALKIWRH YLIGNRCEVY TDHKSLKYIF TQPDLNLRQR
RWLELIKDYD MGIHYHPGKA NVVADALSRK SYCNAVCTEG MCDKLQQDLE HLNLGIVEHG
FVAALEARPT LVDQVRAAQV NDPEIAELKK NMRVGKARDF HEDEHGTIWL GERLCVPDDK
ELKDLILTEA HQTQYSIHPG STKMYQDLKE KFWWVSMRRE IAEFVALCDV CQRVKAEHQR
PAGLLQPLQI PEWKWEEIGM DFITGLPRTS SGHDSIWVVV DRLTKVAHFI PVHTTYTGKR
LAELYLARIM CLHGVPKKIV SDRGSQFTSK FWQKLQEELG TRLNFSTAYH PQTDGQTERV
NQILEDMLRA CALDFGGAWD KSLPYAEFSY NNSYQASLQM APFEALYGRK CRTPLFWDQT
GERQLFGTEV LTEAEEKVRT IRERLRIAQS RQKSYADNRR RELTFEAGDY VYLRVTPLRG
VHRFQTKGKL APRFVGPYKI LERRGEVAYQ LELPSNMIGI HDVFHVSQLK KCLRVPEEQA
DSEHIDIQED LTYVEKPVRI LDTSERRTRN KVTRFCRVQW SHHSEEEATW EREDELKAAH
PHLFTSSSES RGRDSV
//
