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Protein

Spermidine synthase 1

Gene

SPDSYN1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

S-adenosyl 3-(methylthio)propylamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine.

Pathwayi: spermidine biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes spermidine from putrescine.
Proteins known to be involved in this subpathway in this organism are:
  1. Spermidine synthase 1 (SPDSYN1), Spermidine synthase 2 (SPDSYN2)
This subpathway is part of the pathway spermidine biosynthesis, which is itself part of Amine and polyamine biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes spermidine from putrescine, the pathway spermidine biosynthesis and in Amine and polyamine biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei76 – 761S-adenosylmethioninamineBy similarity
Binding sitei106 – 1061PutrescineBy similarity
Binding sitei107 – 1071S-adenosylmethioninamineBy similarity
Binding sitei131 – 1311S-adenosylmethioninamineBy similarity
Binding sitei151 – 1511S-adenosylmethioninamineBy similarity
Active sitei201 – 2011Proton acceptorBy similarity
Binding sitei201 – 2011S-adenosylmethioninamineBy similarity
Binding sitei270 – 2701PutrescineBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Polyamine biosynthesis, Spermidine biosynthesis

Enzyme and pathway databases

BioCyciARA:GQT-2854-MONOMER.
ReactomeiR-ATH-351202. Metabolism of polyamines.
UniPathwayiUPA00248; UER00314.

Names & Taxonomyi

Protein namesi
Recommended name:
Spermidine synthase 1 (EC:2.5.1.16)
Short name:
SPDSY 1
Alternative name(s):
Putrescine aminopropyltransferase 1
Gene namesi
Name:SPDSYN1
Ordered Locus Names:At1g23820
ORF Names:F5O8.38
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 1

Organism-specific databases

TAIRiAT1G23820.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 334334Spermidine synthase 1PRO_0000156448Add
BLAST

Proteomic databases

PaxDbiQ9ZUB3.
PRIDEiQ9ZUB3.

PTM databases

iPTMnetiQ9ZUB3.

Expressioni

Gene expression databases

ExpressionAtlasiQ9ZUB3. baseline and differential.
GenevisibleiQ9ZUB3. AT.

Interactioni

Subunit structurei

Homotetramer and heterodimer. Component of a multiprotein complex. Interacts with SPMS and SPDSYN2.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
SPDSYN2O486617EBI-1770123,EBI-1770100
SPMSQ94BN24EBI-1770123,EBI-1770109

Protein-protein interaction databases

BioGridi24231. 3 interactions.
IntActiQ9ZUB3. 2 interactions.
STRINGi3702.AT1G23820.1.

Structurei

Secondary structure

1
334
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi45 – 506Combined sources
Beta strandi58 – 7215Combined sources
Beta strandi77 – 8610Combined sources
Beta strandi88 – 925Combined sources
Beta strandi95 – 995Combined sources
Turni100 – 1023Combined sources
Helixi103 – 11513Combined sources
Beta strandi123 – 1275Combined sources
Beta strandi130 – 1323Combined sources
Helixi133 – 1386Combined sources
Beta strandi146 – 1527Combined sources
Helixi154 – 16310Combined sources
Helixi165 – 1684Combined sources
Helixi169 – 1724Combined sources
Beta strandi176 – 1816Combined sources
Helixi183 – 1886Combined sources
Beta strandi195 – 2006Combined sources
Beta strandi205 – 2073Combined sources
Helixi208 – 2136Combined sources
Helixi215 – 22410Combined sources
Beta strandi225 – 23410Combined sources
Turni238 – 2403Combined sources
Helixi242 – 25514Combined sources
Beta strandi260 – 2667Combined sources
Helixi271 – 2733Combined sources
Beta strandi274 – 2818Combined sources
Beta strandi283 – 2853Combined sources
Beta strandi289 – 2913Combined sources
Helixi299 – 3013Combined sources
Turni302 – 3043Combined sources
Helixi312 – 3176Combined sources
Helixi323 – 3297Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1XJ5X-ray2.70A/B/C/D2-334[»]
2Q41X-ray2.70A/B/C/D2-334[»]
ProteinModelPortaliQ9ZUB3.
SMRiQ9ZUB3. Positions 41-330.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9ZUB3.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini45 – 282238PABSAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni182 – 1832S-adenosylmethioninamine bindingBy similarity
Regioni201 – 2044Putrescine bindingBy similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG1562. Eukaryota.
COG0421. LUCA.
HOGENOMiHOG000256147.
InParanoidiQ9ZUB3.
KOiK00797.
PhylomeDBiQ9ZUB3.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
HAMAPiMF_00198. Spermidine_synth.
InterProiIPR030374. PABS.
IPR030373. PABS_CS.
IPR029063. SAM-dependent_MTases.
IPR001045. Spermi_synthase.
IPR030668. Spermi_synthase_euk.
[Graphical view]
PIRSFiPIRSF000502. Spermidine_synth. 1 hit.
SUPFAMiSSF53335. SSF53335. 1 hit.
TIGRFAMsiTIGR00417. speE. 1 hit.
PROSITEiPS01330. PABS_1. 1 hit.
PS51006. PABS_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

This entry describes 1 isoform i produced by alternative splicing. AlignAdd to basket

Note: A number of isoforms are produced. According to EST sequences.

Isoform 1 (identifier: Q9ZUB3-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MDAKETSATD LKRPREEDDN GGAATMETEN GDQKKEPACF STVIPGWFSE
60 70 80 90 100
MSPMWPGEAH SLKVEKVLFQ GKSDYQDVIV FQSATYGKVL VLDGVIQLTE
110 120 130 140 150
RDECAYQEMI THLPLCSIPN PKKVLVIGGG DGGVLREVAR HASIEQIDMC
160 170 180 190 200
EIDKMVVDVS KQFFPDVAIG YEDPRVNLVI GDGVAFLKNA AEGSYDAVIV
210 220 230 240 250
DSSDPIGPAK ELFEKPFFQS VARALRPGGV VCTQAESLWL HMDIIEDIVS
260 270 280 290 300
NCREIFKGSV NYAWTSVPTY PSGVIGFMLC STEGPDVDFK HPLNPIDESS
310 320 330
SKSNGPLKFY NAEIHSAAFC LPSFAKKVIE SKAN
Length:334
Mass (Da):36,553
Last modified:May 1, 1999 - v1
Checksum:iDE94F23DAE63FC2E
GO

Sequence cautioni

The sequence AEE30436.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ252215 Genomic DNA. Translation: CAB64644.1.
AJ251296 mRNA. Translation: CAB61614.1.
AC005990 Genomic DNA. Translation: AAC98040.1.
CP002684 Genomic DNA. Translation: AEE30436.1. Different initiation.
AY062593 mRNA. Translation: AAL32671.1.
AY093360 mRNA. Translation: AAM13359.1.
PIRiF86372.
RefSeqiNP_173794.2. NM_102230.4.
UniGeneiAt.10951.
At.22492.

Genome annotation databases

EnsemblPlantsiAT1G23820.1; AT1G23820.1; AT1G23820.
GeneIDi838993.
GrameneiAT1G23820.1; AT1G23820.1; AT1G23820.
KEGGiath:AT1G23820.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ252215 Genomic DNA. Translation: CAB64644.1.
AJ251296 mRNA. Translation: CAB61614.1.
AC005990 Genomic DNA. Translation: AAC98040.1.
CP002684 Genomic DNA. Translation: AEE30436.1. Different initiation.
AY062593 mRNA. Translation: AAL32671.1.
AY093360 mRNA. Translation: AAM13359.1.
PIRiF86372.
RefSeqiNP_173794.2. NM_102230.4.
UniGeneiAt.10951.
At.22492.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1XJ5X-ray2.70A/B/C/D2-334[»]
2Q41X-ray2.70A/B/C/D2-334[»]
ProteinModelPortaliQ9ZUB3.
SMRiQ9ZUB3. Positions 41-330.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi24231. 3 interactions.
IntActiQ9ZUB3. 2 interactions.
STRINGi3702.AT1G23820.1.

PTM databases

iPTMnetiQ9ZUB3.

Proteomic databases

PaxDbiQ9ZUB3.
PRIDEiQ9ZUB3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT1G23820.1; AT1G23820.1; AT1G23820.
GeneIDi838993.
GrameneiAT1G23820.1; AT1G23820.1; AT1G23820.
KEGGiath:AT1G23820.

Organism-specific databases

TAIRiAT1G23820.

Phylogenomic databases

eggNOGiKOG1562. Eukaryota.
COG0421. LUCA.
HOGENOMiHOG000256147.
InParanoidiQ9ZUB3.
KOiK00797.
PhylomeDBiQ9ZUB3.

Enzyme and pathway databases

UniPathwayiUPA00248; UER00314.
BioCyciARA:GQT-2854-MONOMER.
ReactomeiR-ATH-351202. Metabolism of polyamines.

Miscellaneous databases

EvolutionaryTraceiQ9ZUB3.
PROiQ9ZUB3.

Gene expression databases

ExpressionAtlasiQ9ZUB3. baseline and differential.
GenevisibleiQ9ZUB3. AT.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
HAMAPiMF_00198. Spermidine_synth.
InterProiIPR030374. PABS.
IPR030373. PABS_CS.
IPR029063. SAM-dependent_MTases.
IPR001045. Spermi_synthase.
IPR030668. Spermi_synthase_euk.
[Graphical view]
PIRSFiPIRSF000502. Spermidine_synth. 1 hit.
SUPFAMiSSF53335. SSF53335. 1 hit.
TIGRFAMsiTIGR00417. speE. 1 hit.
PROSITEiPS01330. PABS_1. 1 hit.
PS51006. PABS_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Plant aminopropyltransferase families."
    Franceschetti M., Michael A.J.
    Submitted (NOV-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA].
    Strain: cv. Columbia.
  2. "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana."
    Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K.
    , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.
    Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  5. "A polyamine metabolon involving aminopropyl transferase complexes in Arabidopsis."
    Panicot M., Minguet E.G., Ferrando A., Alcazar R., Blazquez M.A., Carbonell J., Altabella T., Koncz C., Tiburcio A.F.
    Plant Cell 14:2539-2551(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH SPMS AND SPDSYN2.
  6. "X-ray structure of spermidine synthase from Arabidopsis thaliana gene AT1G23820."
    Center for eukaryotic structural genomics (CESG)
    Submitted (FEB-2005) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) OF 2-334, SUBUNIT.

Entry informationi

Entry nameiSPD1_ARATH
AccessioniPrimary (citable) accession number: Q9ZUB3
Secondary accession number(s): F4I7M4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: May 1, 1999
Last modified: June 8, 2016
This is version 123 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.