PRAF1_ARATH
ID PRAF1_ARATH Reviewed; 1103 AA.
AC Q947D2; O49281; Q56WW7; Q8W111;
DT 30-AUG-2017, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 143.
DE RecName: Full=PH, RCC1 and FYVE domains-containing protein 1 {ECO:0000303|PubMed:11563980};
DE AltName: Full=Protein Praf4 {ECO:0000303|PubMed:15358268};
GN Name=PRAF1 {ECO:0000303|PubMed:11563980};
GN Synonyms=PRAF4 {ECO:0000303|PubMed:15358268};
GN OrderedLocusNames=At1g76950 {ECO:0000312|Araport:AT1G76950};
GN ORFNames=F22K20.5 {ECO:0000312|EMBL:AAC00618.1};
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 [MRNA], FUNCTION, MUTAGENESIS OF 653-ASN--LYS-655, AND
RP TISSUE SPECIFICITY.
RX PubMed=11563980; DOI=10.1042/0264-6021:3590165;
RA Jensen R.B., La Cour T., Albrethsen J., Nielsen M., Skriver K.;
RT "FYVE zinc-finger proteins in the plant model Arabidopsis thaliana:
RT identification of PtdIns3P-binding residues by comparison of classic and
RT variant FYVE domains.";
RL Biochem. J. 359:165-173(2001).
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 [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 909-1103.
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP GENE FAMILY.
RX PubMed=15358268; DOI=10.1016/j.tplants.2004.06.008;
RA van Leeuwen W., Oekresz L., Boegre L., Munnik T.;
RT "Learning the lipid language of plant signalling.";
RL Trends Plant Sci. 9:378-384(2004).
RN [7]
RP GENE FAMILY.
RX PubMed=20678208; DOI=10.1186/1471-2229-10-157;
RA Wywial E., Singh S.M.;
RT "Identification and structural characterization of FYVE domain-containing
RT proteins of Arabidopsis thaliana.";
RL BMC Plant Biol. 10:157-157(2010).
CC -!- FUNCTION: Binds to phosphatidic acid and to phosphoinositides such as
CC PtdIns3P, PtdIns(3,4)P(2), PtdIns(3,4,5)P(3) and PtdIns(4,5)P(2).
CC Catalyzes guanine nucleotide exchange on specific Rab proteins.
CC {ECO:0000269|PubMed:11563980}.
CC -!- TISSUE SPECIFICITY: Mostly expressed in flowers, and, to a lower
CC extent, in stems, leaves, siliques, seeds.
CC {ECO:0000269|PubMed:11563980}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC00618.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF323270; AAL08940.1; -; mRNA.
DR EMBL; AC002291; AAC00618.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE35908.1; -; Genomic_DNA.
DR EMBL; AF462811; AAL58903.1; -; mRNA.
DR EMBL; BT002726; AAO11642.1; -; mRNA.
DR EMBL; AK221913; BAD94309.1; -; mRNA.
DR PIR; D96798; D96798.
DR RefSeq; NP_565144.1; NM_106346.3.
DR AlphaFoldDB; Q947D2; -.
DR SMR; Q947D2; -.
DR STRING; 3702.AT1G76950.1; -.
DR iPTMnet; Q947D2; -.
DR PaxDb; Q947D2; -.
DR PRIDE; Q947D2; -.
DR ProteomicsDB; 226495; -.
DR EnsemblPlants; AT1G76950.1; AT1G76950.1; AT1G76950.
DR GeneID; 844030; -.
DR Gramene; AT1G76950.1; AT1G76950.1; AT1G76950.
DR KEGG; ath:AT1G76950; -.
DR Araport; AT1G76950; -.
DR TAIR; locus:2025277; AT1G76950.
DR eggNOG; ENOG502QT6C; Eukaryota.
DR HOGENOM; CLU_005343_0_0_1; -.
DR InParanoid; Q947D2; -.
DR OMA; ACNVDFV; -.
DR OrthoDB; 1062377at2759; -.
DR PhylomeDB; Q947D2; -.
DR PRO; PR:Q947D2; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q947D2; baseline and differential.
DR GO; GO:0005085; F:guanyl-nucleotide exchange factor activity; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0070300; F:phosphatidic acid binding; IDA:UniProtKB.
DR GO; GO:0035091; F:phosphatidylinositol binding; IDA:UniProtKB.
DR Gene3D; 2.130.10.30; -; 2.
DR Gene3D; 2.30.29.30; -; 1.
DR Gene3D; 3.30.40.10; -; 1.
DR InterPro; IPR013591; Brevis_radix_dom.
DR InterPro; IPR027988; BRX_N.
DR InterPro; IPR011993; PH-like_dom_sf.
DR InterPro; IPR001849; PH_domain.
DR InterPro; IPR009091; RCC1/BLIP-II.
DR InterPro; IPR000408; Reg_chr_condens.
DR InterPro; IPR000306; Znf_FYVE.
DR InterPro; IPR017455; Znf_FYVE-rel.
DR InterPro; IPR011011; Znf_FYVE_PHD.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR Pfam; PF08381; BRX; 1.
DR Pfam; PF13713; BRX_N; 1.
DR Pfam; PF01363; FYVE; 1.
DR Pfam; PF16457; PH_12; 1.
DR Pfam; PF00415; RCC1; 6.
DR PRINTS; PR00633; RCCNDNSATION.
DR SMART; SM00064; FYVE; 1.
DR SUPFAM; SSF50985; SSF50985; 1.
DR SUPFAM; SSF57903; SSF57903; 1.
DR PROSITE; PS51514; BRX; 1.
DR PROSITE; PS00626; RCC1_2; 3.
DR PROSITE; PS50012; RCC1_3; 7.
DR PROSITE; PS50178; ZF_FYVE; 1.
PE 1: Evidence at protein level;
KW Coiled coil; Guanine-nucleotide releasing factor; Lipid-binding;
KW Metal-binding; Reference proteome; Repeat; Zinc; Zinc-finger.
FT CHAIN 1..1103
FT /note="PH, RCC1 and FYVE domains-containing protein 1"
FT /id="PRO_0000441122"
FT DOMAIN 22..123
FT /note="PH"
FT /evidence="ECO:0000255"
FT REPEAT 237..298
FT /note="RCC1 1"
FT /evidence="ECO:0000255"
FT REPEAT 299..351
FT /note="RCC1 2"
FT /evidence="ECO:0000255"
FT REPEAT 353..406
FT /note="RCC1 3"
FT /evidence="ECO:0000255"
FT REPEAT 407..458
FT /note="RCC1 4"
FT /evidence="ECO:0000255"
FT REPEAT 471..522
FT /note="RCC1 5"
FT /evidence="ECO:0000255"
FT REPEAT 524..574
FT /note="RCC1 6"
FT /evidence="ECO:0000255"
FT REPEAT 575..626
FT /note="RCC1 7"
FT /evidence="ECO:0000255"
FT DOMAIN 1023..1078
FT /note="BRX"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00847"
FT ZN_FING 632..694
FT /note="FYVE-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00091"
FT REGION 144..233
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 783..818
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 962..988
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1079..1103
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 828..904
FT /evidence="ECO:0000255"
FT COMPBIAS 144..177
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 201..231
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 789..818
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1086..1103
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 638
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00091"
FT BINDING 641
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00091"
FT BINDING 654
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00091"
FT BINDING 657
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00091"
FT BINDING 662
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00091"
FT BINDING 665
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00091"
FT BINDING 686
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00091"
FT BINDING 689
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00091"
FT MUTAGEN 653..655
FT /note="NCY->HCR: Increased affinity for PtdIns3P."
FT /evidence="ECO:0000269|PubMed:11563980"
FT CONFLICT 134
FT /note="D -> N (in Ref. 4; AAL58903/AAO11642)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1103 AA; 120395 MW; DBACB727C761BB0B CRC64;
MADLVTYSNA DHNLEQALIT LKKGTQLLKY GRKGKPKFYP FRLSSDEKSL IWISSSGEKR
LKLASVSKIV PGQRTAVFQR YLRPEKDYLS FSLLYNGKKK SLDLICKDKV EAEIWIGGLK
TLISTGQGGR SKIDGWSGGG LSVDASRELT SSSPSSSSAS ASRGHSSPGT PFNIDPITSP
KSAEPEVPPT DSEKSHVALD NKNMQTKVSG SDGFRVSVSS AQSSSSHGSA ADDSDALGDV
YIWGEVICDN VVKVGIDKNA SYLTTRTDVL VPKPLESNIV LDVHQIACGV RHAAFVTRQG
EIFTWGEESG GRLGHGIGKD VFHPRLVESL TATSSVDFVA CGEFHTCAVT LAGELYTWGD
GTHNVGLLGH GSDISHWIPK RIAGSLEGLH VASVSCGPWH TALITSYGRL FTFGDGTFGV
LGHGDKETVQ YPREVESLSG LRTIAVSCGV WHTAAVVEII VTQSNSSSVS SGKLFTWGDG
DKNRLGHGDK DPRLKPTCVP ALIDYNFHKI ACGHSLTVGL TTSGQVFTMG STVYGQLGNL
QTDGKLPCLV EDKLASEFVE EISCGAYHVA ALTSRNEVYT WGKGANGRLG HGDLEDRKVP
TIVEALKDRH VKYIACGSNY TAAICLHKWV SGAEQSQCST CRLAFGFTRK RHNCYNCGLV
HCHSCSSKKA FRAALAPSAG RLYRVCDSCY VKLSKVSEIN DTNRRNSAVP RLSGENRDRL
DKSEIRLAKF GTSNMDLIKQ LDSKAAKQGK KTDTFSLGRN SQLPSLLQLK DAVQSNIGDM
RRATPKLAQA PSGISSRSVS PFSRRSSPPR SATPMPSTSG LYFPVGIADN MKKTNEILNQ
EIVKLRTQVD SLTQKCEFQE VELQNSVKKT QEALALAEEE SAKSRAAKEA IKSLIAQLKD
VAEKLPPGES VKLACLQNGL DQNGFHFPEE NGFHPSRSES MTSSISSVAP FDFAFANASW
SNLQSPKQTP RASERNSNAY PADPRLSSSG SVISERIEPF QFQNNSDNGS SQTGVNNTNQ
VEAEWIEQYE PGVYITLVAL HDGTRDLRRV RFSRRRFGEH QAETWWSENR EKVYEKYNVR
VSEKSTASQT HRDRDEEEED IPH
