PPR25_ARATH
ID PPR25_ARATH Reviewed; 705 AA.
AC Q56XI1; O80524;
DT 01-JUL-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-2008, sequence version 2.
DT 03-AUG-2022, entry version 101.
DE RecName: Full=Pentatricopeptide repeat-containing protein At1g09410, mitochondrial;
DE Flags: Precursor;
GN Name=PCMP-H18; OrderedLocusNames=At1g09410; ORFNames=F14J9.7;
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 [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 [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RX PubMed=17147637; DOI=10.1111/j.1467-7652.2006.00183.x;
RA Underwood B.A., Vanderhaeghen R., Whitford R., Town C.D., Hilson P.;
RT "Simultaneous high-throughput recombinational cloning of open reading
RT frames in closed and open configurations.";
RL Plant Biotechnol. J. 4:317-324(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
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 [5]
RP GENE FAMILY.
RX PubMed=10809006; DOI=10.1023/a:1006352315928;
RA Aubourg S., Boudet N., Kreis M., Lecharny A.;
RT "In Arabidopsis thaliana, 1% of the genome codes for a novel protein family
RT unique to plants.";
RL Plant Mol. Biol. 42:603-613(2000).
RN [6]
RP GENE FAMILY.
RX PubMed=15269332; DOI=10.1105/tpc.104.022236;
RA Lurin C., Andres C., Aubourg S., Bellaoui M., Bitton F., Bruyere C.,
RA Caboche M., Debast C., Gualberto J., Hoffmann B., Lecharny A., Le Ret M.,
RA Martin-Magniette M.-L., Mireau H., Peeters N., Renou J.-P., Szurek B.,
RA Taconnat L., Small I.;
RT "Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins
RT reveals their essential role in organelle biogenesis.";
RL Plant Cell 16:2089-2103(2004).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND CLEAVAGE OF TRANSIT PEPTIDE AFTER
RP TYR-11.
RX PubMed=25732537; DOI=10.1093/jxb/erv064;
RA Carrie C., Venne A.S., Zahedi R.P., Soll J.;
RT "Identification of cleavage sites and substrate proteins for two
RT mitochondrial intermediate peptidases in Arabidopsis thaliana.";
RL J. Exp. Bot. 66:2691-2708(2015).
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000305|PubMed:25732537}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q56XI1-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q56XI1-2; Sequence=VSP_034545, VSP_034546;
CC -!- SIMILARITY: Belongs to the PPR family. PCMP-H subfamily. {ECO:0000305}.
CC -!- WEB RESOURCE: Name=Pentatricopeptide repeat proteins;
CC URL="https://ppr.plantenergy.uwa.edu.au";
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DR EMBL; AC003970; AAC33201.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE28438.1; -; Genomic_DNA.
DR EMBL; DQ446238; ABE65608.1; -; mRNA.
DR EMBL; AK221693; BAD95400.1; -; mRNA.
DR PIR; D86227; D86227.
DR RefSeq; NP_172412.1; NM_100811.2. [Q56XI1-1]
DR AlphaFoldDB; Q56XI1; -.
DR SMR; Q56XI1; -.
DR iPTMnet; Q56XI1; -.
DR PaxDb; Q56XI1; -.
DR PRIDE; Q56XI1; -.
DR ProteomicsDB; 234697; -. [Q56XI1-1]
DR EnsemblPlants; AT1G09410.1; AT1G09410.1; AT1G09410. [Q56XI1-1]
DR GeneID; 837463; -.
DR Gramene; AT1G09410.1; AT1G09410.1; AT1G09410. [Q56XI1-1]
DR KEGG; ath:AT1G09410; -.
DR Araport; AT1G09410; -.
DR TAIR; locus:2012295; AT1G09410.
DR eggNOG; KOG4197; Eukaryota.
DR HOGENOM; CLU_002706_15_5_1; -.
DR InParanoid; Q56XI1; -.
DR OMA; ACRTHSQ; -.
DR PhylomeDB; Q56XI1; -.
DR PRO; PR:Q56XI1; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q56XI1; baseline and differential.
DR Genevisible; Q56XI1; AT.
DR GO; GO:0043231; C:intracellular membrane-bounded organelle; IBA:GO_Central.
DR GO; GO:0005739; C:mitochondrion; IEA:UniProtKB-SubCell.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0009451; P:RNA modification; IBA:GO_Central.
DR Gene3D; 1.25.40.10; -; 5.
DR InterPro; IPR032867; DYW_dom.
DR InterPro; IPR002885; Pentatricopeptide_repeat.
DR InterPro; IPR011990; TPR-like_helical_dom_sf.
DR Pfam; PF14432; DYW_deaminase; 1.
DR Pfam; PF01535; PPR; 8.
DR Pfam; PF12854; PPR_1; 2.
DR Pfam; PF13041; PPR_2; 1.
DR SUPFAM; SSF48452; SSF48452; 1.
DR TIGRFAMs; TIGR00756; PPR; 10.
DR PROSITE; PS51375; PPR; 15.
PE 1: Evidence at protein level;
KW Alternative splicing; Mitochondrion; Reference proteome; Repeat;
KW Transit peptide.
FT TRANSIT 1..11
FT /note="Mitochondrion"
FT /evidence="ECO:0000269|PubMed:25732537"
FT CHAIN 12..705
FT /note="Pentatricopeptide repeat-containing protein
FT At1g09410, mitochondrial"
FT /id="PRO_0000342766"
FT REPEAT 16..46
FT /note="PPR 1"
FT REPEAT 47..77
FT /note="PPR 2"
FT REPEAT 78..112
FT /note="PPR 3"
FT REPEAT 113..139
FT /note="PPR 4"
FT REPEAT 140..170
FT /note="PPR 5"
FT REPEAT 171..205
FT /note="PPR 6"
FT REPEAT 206..232
FT /note="PPR 7"
FT REPEAT 233..267
FT /note="PPR 8"
FT REPEAT 268..294
FT /note="PPR 9"
FT REPEAT 295..329
FT /note="PPR 10"
FT REPEAT 330..364
FT /note="PPR 11"
FT REPEAT 365..395
FT /note="PPR 12"
FT REPEAT 396..430
FT /note="PPR 13"
FT REPEAT 432..462
FT /note="PPR 14"
FT REPEAT 468..498
FT /note="PPR 15"
FT REGION 503..578
FT /note="Type E motif"
FT REGION 579..610
FT /note="Type E(+) motif"
FT REGION 611..705
FT /note="Type DYW motif"
FT VAR_SEQ 351..375
FT /note="KQVHAQLVRCQFDVDVYVASVLMTM -> FLQRTLSCGIQSYLVMPHTVLER
FT KH (in isoform 2)"
FT /evidence="ECO:0000303|Ref.4"
FT /id="VSP_034545"
FT VAR_SEQ 376..705
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|Ref.4"
FT /id="VSP_034546"
SQ SEQUENCE 705 AA; 79794 MW; 474D6665D6EFF80D CRC64;
MKSQILLRRT YSTTIPPPTA NVRITHLSRI GKIHEARKLF DSCDSKSISS WNSMVAGYFA
NLMPRDARKL FDEMPDRNII SWNGLVSGYM KNGEIDEARK VFDLMPERNV VSWTALVKGY
VHNGKVDVAE SLFWKMPEKN KVSWTVMLIG FLQDGRIDDA CKLYEMIPDK DNIARTSMIH
GLCKEGRVDE AREIFDEMSE RSVITWTTMV TGYGQNNRVD DARKIFDVMP EKTEVSWTSM
LMGYVQNGRI EDAEELFEVM PVKPVIACNA MISGLGQKGE IAKARRVFDS MKERNDASWQ
TVIKIHERNG FELEALDLFI LMQKQGVRPT FPTLISILSV CASLASLHHG KQVHAQLVRC
QFDVDVYVAS VLMTMYIKCG ELVKSKLIFD RFPSKDIIMW NSIISGYASH GLGEEALKVF
CEMPLSGSTK PNEVTFVATL SACSYAGMVE EGLKIYESME SVFGVKPITA HYACMVDMLG
RAGRFNEAME MIDSMTVEPD AAVWGSLLGA CRTHSQLDVA EFCAKKLIEI EPENSGTYIL
LSNMYASQGR WADVAELRKL MKTRLVRKSP GCSWTEVENK VHAFTRGGIN SHPEQESILK
ILDELDGLLR EAGYNPDCSY ALHDVDEEEK VNSLKYHSER LAVAYALLKL SEGIPIRVMK
NLRVCSDCHT AIKIISKVKE REIILRDANR FHHFRNGECS CKDYW
