SPD1_ARATH
ID SPD1_ARATH Reviewed; 684 AA.
AC F4J3R7; Q0WWY6; Q940C8; Q9CAE6;
DT 26-FEB-2020, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 78.
DE RecName: Full=Protein SEEDLING PLASTID DEVELOPMENT 1 {ECO:0000303|PubMed:21045120};
DE Flags: Precursor;
GN Name=SPD1 {ECO:0000303|PubMed:21045120};
GN OrderedLocusNames=At3g10420 {ECO:0000312|Araport:AT3G10420};
GN ORFNames=F13M14.30 {ECO:0000312|EMBL:AAG51387.1};
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(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;
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 (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 9-684 (ISOFORM 1).
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 FUNCTION, DISRUPTION PHENOTYPE, AND SUBCELLULAR LOCATION.
RC STRAIN=cv. Columbia;
RX PubMed=21045120; DOI=10.1104/pp.110.161414;
RA Ruppel N.J., Logsdon C.A., Whippo C.W., Inoue K., Hangarter R.P.;
RT "A mutation in Arabidopsis seedling plastid development1 affects plastid
RT differentiation in embryo-derived tissues during seedling growth.";
RL Plant Physiol. 155:342-353(2011).
CC -!- FUNCTION: Required during eoplast (a highly reduced plastid type
CC present during the degreening and dehydration stages of seed
CC maturation) development in embryos and early stages of eoplast
CC redifferentiation during seedling growth.
CC {ECO:0000269|PubMed:21045120}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast membrane
CC {ECO:0000269|PubMed:21045120}; Peripheral membrane protein
CC {ECO:0000269|PubMed:21045120}; Intermembrane side
CC {ECO:0000269|PubMed:21045120}. Plastid, chloroplast envelope
CC {ECO:0000269|PubMed:21045120}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=F4J3R7-1; Sequence=Displayed;
CC Name=2 {ECO:0000312|EMBL:AEE74904.1};
CC IsoId=F4J3R7-2; Sequence=VSP_060460, VSP_060461;
CC -!- DISRUPTION PHENOTYPE: Albino seedlings with defects in etioplast and
CC amyloplast development leading to degenerate organelle-like structures,
CC but normal green vegetative tissues (PubMed:21045120). Reduced
CC hypocotyl gravitropism probably due to the lack of amyloplasts
CC (PubMed:21045120). {ECO:0000269|PubMed:21045120}.
CC -!- SIMILARITY: Belongs to the ycf45 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAL06991.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=BAE98362.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=BAE98362.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; AC011560; AAG51387.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE74903.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE74904.1; -; Genomic_DNA.
DR EMBL; AK226197; BAE98362.1; ALT_FRAME; mRNA.
DR EMBL; AY056103; AAL06991.1; ALT_INIT; mRNA.
DR EMBL; BT004529; AAO42775.1; -; mRNA.
DR RefSeq; NP_566373.2; NM_111877.3. [F4J3R7-1]
DR RefSeq; NP_850553.1; NM_180222.1. [F4J3R7-2]
DR AlphaFoldDB; F4J3R7; -.
DR STRING; 3702.AT3G10420.2; -.
DR PaxDb; F4J3R7; -.
DR PRIDE; F4J3R7; -.
DR ProteomicsDB; 197235; -. [F4J3R7-1]
DR EnsemblPlants; AT3G10420.1; AT3G10420.1; AT3G10420. [F4J3R7-2]
DR EnsemblPlants; AT3G10420.2; AT3G10420.2; AT3G10420. [F4J3R7-1]
DR GeneID; 820206; -.
DR Gramene; AT3G10420.1; AT3G10420.1; AT3G10420. [F4J3R7-2]
DR Gramene; AT3G10420.2; AT3G10420.2; AT3G10420. [F4J3R7-1]
DR KEGG; ath:AT3G10420; -.
DR Araport; AT3G10420; -.
DR TAIR; locus:2075825; AT3G10420.
DR eggNOG; ENOG502QQ4X; Eukaryota.
DR HOGENOM; CLU_022515_2_0_1; -.
DR InParanoid; F4J3R7; -.
DR OMA; NHWIRNV; -.
DR OrthoDB; 1035234at2759; -.
DR PRO; PR:F4J3R7; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; F4J3R7; baseline and differential.
DR GO; GO:0009507; C:chloroplast; IDA:UniProtKB.
DR GO; GO:0009941; C:chloroplast envelope; IDA:UniProtKB.
DR GO; GO:0031972; C:chloroplast intermembrane space; IDA:UniProtKB.
DR GO; GO:0031969; C:chloroplast membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0009657; P:plastid organization; IMP:UniProtKB.
DR GO; GO:0090677; P:reversible differentiation; IMP:UniProtKB.
DR GO; GO:0010431; P:seed maturation; IMP:UniProtKB.
DR CDD; cd02645; R3H_AAA; 1.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR003593; AAA+_ATPase.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR034081; R3H_AAA.
DR InterPro; IPR045735; Spore_III_AA_AAA+_ATPase.
DR Pfam; PF19568; Spore_III_AA; 1.
DR SMART; SM00382; AAA; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; ATP-binding; Chloroplast; Developmental protein;
KW Membrane; Nucleotide-binding; Plastid; Reference proteome; Transit peptide.
FT TRANSIT 1..78
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 79..684
FT /note="Protein SEEDLING PLASTID DEVELOPMENT 1"
FT /evidence="ECO:0000255"
FT /id="PRO_0000448862"
FT REGION 33..91
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 651..684
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 33..64
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 71..91
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 651..674
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 220..227
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255"
FT VAR_SEQ 541..547
FT /note="STTMAQM -> VSFFLHG (in isoform 2)"
FT /id="VSP_060460"
FT VAR_SEQ 548..684
FT /note="Missing (in isoform 2)"
FT /id="VSP_060461"
SQ SEQUENCE 684 AA; 75061 MW; 49CF7AB0889AF2BE CRC64;
MRALNSRLVL IDINSSWQAS RRLISATATA FSSDSSSSFR RTRGARQRIA SSKSPASSPS
PVRRPSDGFS FDVRSPSSDS SISSRKSPTT APPTVELDAF LEILPPATRK ELVKHEAIEE
LIEVVMDLGR KPLARFPSGD WVISEQPVTH QDLELAVSKV GDFSDDNRSG IDRSLHRISA
IRNRKLQVIG LTCRVGRVVS GSAEIIRDLI EGGGSILVIG SPGVGKTTLI REIARMLADE
HRKRVVIVDT SNEIGGDGDV PHSGIGRARR MQVPNVNLQH DVMIEAVENH MPETIIIDEI
GTELEALAAS TIAQRGVQLV ATAHGMTIDN IIKNPSLQIL IGGIESVTLG DEEARKRKVQ
KTILERKGPP TFTCAVEMIS RTECRVHQRL DVTVDAILAG KSAPFEIRQI RGEDDVPHKL
VTPIPLENLE EEPAPLLNRD FVSELLSDDE DEDFLLIRSN KARSNTYTSP RSSPVHVYTY
NVLEADLLQV AEVMGLDDEI EVTDDVGEAD VILASSSELK QNSSIRRVAK LHKLPIFVIK
STTMAQMVKA VRMILGRESF GSAPKAIEKS SVDDIEIKDD APESKPSLEE LDALEEVRLA
IEYIVIPGGE PVELLPRRSD IIVRQLELVE SYQLAVENLG THLNPRLQIL PRRSTKKTLT
SSSPQKSADG SMGTTGTRLP FLKD
