SPDS1_ARATH
ID SPDS1_ARATH Reviewed; 334 AA.
AC Q9ZUB3; F4I7M4;
DT 01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1999, sequence version 1.
DT 03-AUG-2022, entry version 155.
DE RecName: Full=Spermidine synthase 1;
DE Short=SPDSY 1;
DE EC=2.5.1.16;
DE AltName: Full=Putrescine aminopropyltransferase 1;
GN Name=SPDSYN1; OrderedLocusNames=At1g23820; ORFNames=F5O8.38;
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 / MRNA].
RC STRAIN=cv. Columbia;
RA Franceschetti M., Michael A.J.;
RT "Plant aminopropyltransferase families.";
RL Submitted (NOV-1999) to the EMBL/GenBank/DDBJ databases.
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 INTERACTION WITH SPMS AND SPDSYN2.
RX PubMed=12368503; DOI=10.1105/tpc.004077;
RA Panicot M., Minguet E.G., Ferrando A., Alcazar R., Blazquez M.A.,
RA Carbonell J., Altabella T., Koncz C., Tiburcio A.F.;
RT "A polyamine metabolon involving aminopropyl transferase complexes in
RT Arabidopsis.";
RL Plant Cell 14:2539-2551(2002).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) OF 2-334, AND SUBUNIT.
RG Center for eukaryotic structural genomics (CESG);
RT "X-ray structure of spermidine synthase from Arabidopsis thaliana gene
RT AT1G23820.";
RL Submitted (FEB-2005) to the PDB data bank.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=putrescine + S-adenosyl 3-(methylsulfanyl)propylamine = H(+) +
CC S-methyl-5'-thioadenosine + spermidine; Xref=Rhea:RHEA:12721,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:17509, ChEBI:CHEBI:57443,
CC ChEBI:CHEBI:57834, ChEBI:CHEBI:326268; EC=2.5.1.16;
CC -!- PATHWAY: Amine and polyamine biosynthesis; spermidine biosynthesis;
CC spermidine from putrescine: step 1/1.
CC -!- SUBUNIT: Homotetramer and heterodimer. Component of a multiprotein
CC complex. Interacts with SPMS and SPDSYN2. {ECO:0000269|PubMed:12368503,
CC ECO:0000269|Ref.6}.
CC -!- INTERACTION:
CC Q9ZUB3; O48661: SPDSYN2; NbExp=7; IntAct=EBI-1770123, EBI-1770100;
CC Q9ZUB3; Q94BN2: SPMS; NbExp=4; IntAct=EBI-1770123, EBI-1770109;
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=Q9ZUB3-1; Sequence=Displayed;
CC -!- SIMILARITY: Belongs to the spermidine/spermine synthase family.
CC {ECO:0000305}.
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DR EMBL; AJ252215; CAB64644.1; -; Genomic_DNA.
DR EMBL; AJ251296; CAB61614.1; -; mRNA.
DR EMBL; AC005990; AAC98040.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE30436.2; -; Genomic_DNA.
DR EMBL; AY062593; AAL32671.1; -; mRNA.
DR EMBL; AY093360; AAM13359.1; -; mRNA.
DR PIR; F86372; F86372.
DR RefSeq; NP_173794.3; NM_102230.5. [Q9ZUB3-1]
DR PDB; 1XJ5; X-ray; 2.70 A; A/B/C/D=2-334.
DR PDB; 2Q41; X-ray; 2.70 A; A/B/C/D=2-334.
DR PDB; 6O63; X-ray; 1.80 A; A/B/C/D=1-334.
DR PDB; 6O65; X-ray; 1.80 A; A/B/C/D/E/F/G/H=34-334.
DR PDBsum; 1XJ5; -.
DR PDBsum; 2Q41; -.
DR PDBsum; 6O63; -.
DR PDBsum; 6O65; -.
DR AlphaFoldDB; Q9ZUB3; -.
DR SMR; Q9ZUB3; -.
DR BioGRID; 24231; 10.
DR IntAct; Q9ZUB3; 2.
DR STRING; 3702.AT1G23820.1; -.
DR iPTMnet; Q9ZUB3; -.
DR PaxDb; Q9ZUB3; -.
DR PRIDE; Q9ZUB3; -.
DR ProteomicsDB; 232482; -. [Q9ZUB3-1]
DR EnsemblPlants; AT1G23820.1; AT1G23820.1; AT1G23820. [Q9ZUB3-1]
DR GeneID; 838993; -.
DR Gramene; AT1G23820.1; AT1G23820.1; AT1G23820. [Q9ZUB3-1]
DR KEGG; ath:AT1G23820; -.
DR Araport; AT1G23820; -.
DR eggNOG; KOG1562; Eukaryota.
DR HOGENOM; CLU_048199_3_2_1; -.
DR InParanoid; Q9ZUB3; -.
DR OMA; LWPGQSF; -.
DR PhylomeDB; Q9ZUB3; -.
DR BRENDA; 2.5.1.16; 399.
DR UniPathway; UPA00248; UER00314.
DR EvolutionaryTrace; Q9ZUB3; -.
DR PRO; PR:Q9ZUB3; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9ZUB3; baseline and differential.
DR Genevisible; Q9ZUB3; AT.
DR GO; GO:0004766; F:spermidine synthase activity; IBA:GO_Central.
DR GO; GO:0006596; P:polyamine biosynthetic process; IBA:GO_Central.
DR GO; GO:0008295; P:spermidine biosynthetic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 2.30.140.10; -; 1.
DR Gene3D; 3.40.50.150; -; 1.
DR HAMAP; MF_00198; Spermidine_synth; 1.
DR InterPro; IPR030374; PABS.
DR InterPro; IPR030373; PABS_CS.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR InterPro; IPR001045; Spermi_synthase.
DR InterPro; IPR030668; Spermi_synthase_euk.
DR InterPro; IPR035246; Spermidine_synt_N.
DR InterPro; IPR037163; Spermidine_synt_N_sf.
DR PANTHER; PTHR11558; PTHR11558; 1.
DR Pfam; PF17284; Spermine_synt_N; 1.
DR PIRSF; PIRSF000502; Spermidine_synth; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR TIGRFAMs; TIGR00417; speE; 1.
DR PROSITE; PS01330; PABS_1; 1.
DR PROSITE; PS51006; PABS_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Polyamine biosynthesis;
KW Reference proteome; Spermidine biosynthesis; Transferase.
FT CHAIN 1..334
FT /note="Spermidine synthase 1"
FT /id="PRO_0000156448"
FT DOMAIN 45..282
FT /note="PABS"
FT REGION 1..35
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..22
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 201
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 76
FT /ligand="S-adenosyl 3-(methylsulfanyl)propylamine"
FT /ligand_id="ChEBI:CHEBI:57443"
FT /evidence="ECO:0000250"
FT BINDING 106
FT /ligand="putrescine"
FT /ligand_id="ChEBI:CHEBI:326268"
FT /evidence="ECO:0000250"
FT BINDING 107
FT /ligand="S-adenosyl 3-(methylsulfanyl)propylamine"
FT /ligand_id="ChEBI:CHEBI:57443"
FT /evidence="ECO:0000250"
FT BINDING 131
FT /ligand="S-adenosyl 3-(methylsulfanyl)propylamine"
FT /ligand_id="ChEBI:CHEBI:57443"
FT /evidence="ECO:0000250"
FT BINDING 151
FT /ligand="S-adenosyl 3-(methylsulfanyl)propylamine"
FT /ligand_id="ChEBI:CHEBI:57443"
FT /evidence="ECO:0000250"
FT BINDING 182..183
FT /ligand="S-adenosyl 3-(methylsulfanyl)propylamine"
FT /ligand_id="ChEBI:CHEBI:57443"
FT /evidence="ECO:0000250"
FT BINDING 201..204
FT /ligand="putrescine"
FT /ligand_id="ChEBI:CHEBI:326268"
FT /evidence="ECO:0000250"
FT BINDING 201
FT /ligand="S-adenosyl 3-(methylsulfanyl)propylamine"
FT /ligand_id="ChEBI:CHEBI:57443"
FT /evidence="ECO:0000250"
FT BINDING 270
FT /ligand="putrescine"
FT /ligand_id="ChEBI:CHEBI:326268"
FT /evidence="ECO:0000250"
FT STRAND 42..44
FT /evidence="ECO:0007829|PDB:6O65"
FT STRAND 45..50
FT /evidence="ECO:0007829|PDB:6O63"
FT STRAND 58..72
FT /evidence="ECO:0007829|PDB:6O63"
FT STRAND 77..86
FT /evidence="ECO:0007829|PDB:6O63"
FT STRAND 88..92
FT /evidence="ECO:0007829|PDB:6O63"
FT STRAND 95..99
FT /evidence="ECO:0007829|PDB:6O63"
FT TURN 100..102
FT /evidence="ECO:0007829|PDB:6O63"
FT HELIX 103..115
FT /evidence="ECO:0007829|PDB:6O63"
FT STRAND 118..120
FT /evidence="ECO:0007829|PDB:6O63"
FT STRAND 123..128
FT /evidence="ECO:0007829|PDB:6O63"
FT STRAND 130..132
FT /evidence="ECO:0007829|PDB:6O63"
FT HELIX 133..139
FT /evidence="ECO:0007829|PDB:6O63"
FT STRAND 146..152
FT /evidence="ECO:0007829|PDB:6O63"
FT HELIX 154..163
FT /evidence="ECO:0007829|PDB:6O63"
FT HELIX 165..168
FT /evidence="ECO:0007829|PDB:6O63"
FT HELIX 169..172
FT /evidence="ECO:0007829|PDB:6O63"
FT STRAND 176..181
FT /evidence="ECO:0007829|PDB:6O63"
FT HELIX 183..188
FT /evidence="ECO:0007829|PDB:6O63"
FT STRAND 195..200
FT /evidence="ECO:0007829|PDB:6O63"
FT STRAND 205..207
FT /evidence="ECO:0007829|PDB:6O63"
FT HELIX 210..213
FT /evidence="ECO:0007829|PDB:6O63"
FT HELIX 215..224
FT /evidence="ECO:0007829|PDB:6O63"
FT STRAND 225..234
FT /evidence="ECO:0007829|PDB:6O63"
FT TURN 238..240
FT /evidence="ECO:0007829|PDB:6O63"
FT HELIX 242..255
FT /evidence="ECO:0007829|PDB:6O63"
FT STRAND 260..266
FT /evidence="ECO:0007829|PDB:6O63"
FT HELIX 271..273
FT /evidence="ECO:0007829|PDB:6O63"
FT STRAND 274..281
FT /evidence="ECO:0007829|PDB:6O63"
FT STRAND 283..285
FT /evidence="ECO:0007829|PDB:6O63"
FT STRAND 289..291
FT /evidence="ECO:0007829|PDB:1XJ5"
FT HELIX 296..298
FT /evidence="ECO:0007829|PDB:6O63"
FT HELIX 299..301
FT /evidence="ECO:0007829|PDB:1XJ5"
FT TURN 302..304
FT /evidence="ECO:0007829|PDB:1XJ5"
FT HELIX 312..317
FT /evidence="ECO:0007829|PDB:6O63"
FT HELIX 323..329
FT /evidence="ECO:0007829|PDB:6O63"
SQ SEQUENCE 334 AA; 36553 MW; DE94F23DAE63FC2E CRC64;
MDAKETSATD LKRPREEDDN GGAATMETEN GDQKKEPACF STVIPGWFSE MSPMWPGEAH
SLKVEKVLFQ GKSDYQDVIV FQSATYGKVL VLDGVIQLTE RDECAYQEMI THLPLCSIPN
PKKVLVIGGG DGGVLREVAR HASIEQIDMC EIDKMVVDVS KQFFPDVAIG YEDPRVNLVI
GDGVAFLKNA AEGSYDAVIV DSSDPIGPAK ELFEKPFFQS VARALRPGGV VCTQAESLWL
HMDIIEDIVS NCREIFKGSV NYAWTSVPTY PSGVIGFMLC STEGPDVDFK HPLNPIDESS
SKSNGPLKFY NAEIHSAAFC LPSFAKKVIE SKAN
