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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)DescriptionActionsGraphical viewLength
Binding sitei76S-adenosylmethioninamineBy similarity1
Binding sitei106PutrescineBy similarity1
Binding sitei107S-adenosylmethioninamineBy similarity1
Binding sitei131S-adenosylmethioninamineBy similarity1
Binding sitei151S-adenosylmethioninamineBy similarity1
Active sitei201Proton acceptorBy similarity1
Binding sitei201S-adenosylmethioninamineBy similarity1
Binding sitei270PutrescineBy similarity1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Polyamine biosynthesis, Spermidine biosynthesis

Enzyme and pathway databases

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)DescriptionActionsGraphical viewLength
ChainiPRO_00001564481 – 334Spermidine synthase 1Add BLAST334

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 interactors.
IntActiQ9ZUB3. 2 interactors.
STRINGi3702.AT1G23820.1.

Structurei

Secondary structure

1334
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi45 – 50Combined sources6
Beta strandi58 – 72Combined sources15
Beta strandi77 – 86Combined sources10
Beta strandi88 – 92Combined sources5
Beta strandi95 – 99Combined sources5
Turni100 – 102Combined sources3
Helixi103 – 115Combined sources13
Beta strandi123 – 127Combined sources5
Beta strandi130 – 132Combined sources3
Helixi133 – 138Combined sources6
Beta strandi146 – 152Combined sources7
Helixi154 – 163Combined sources10
Helixi165 – 168Combined sources4
Helixi169 – 172Combined sources4
Beta strandi176 – 181Combined sources6
Helixi183 – 188Combined sources6
Beta strandi195 – 200Combined sources6
Beta strandi205 – 207Combined sources3
Helixi208 – 213Combined sources6
Helixi215 – 224Combined sources10
Beta strandi225 – 234Combined sources10
Turni238 – 240Combined sources3
Helixi242 – 255Combined sources14
Beta strandi260 – 266Combined sources7
Helixi271 – 273Combined sources3
Beta strandi274 – 281Combined sources8
Beta strandi283 – 285Combined sources3
Beta strandi289 – 291Combined sources3
Helixi299 – 301Combined sources3
Turni302 – 304Combined sources3
Helixi312 – 317Combined sources6
Helixi323 – 329Combined sources7

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiQ9ZUB3.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini45 – 282PABSAdd BLAST238

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni182 – 183S-adenosylmethioninamine bindingBy similarity2
Regioni201 – 204Putrescine bindingBy similarity4

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG1562. Eukaryota.
COG0421. LUCA.
HOGENOMiHOG000256147.
InParanoidiQ9ZUB3.
KOiK00797.
OrthoDBiEOG09360FON.
PhylomeDBiQ9ZUB3.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
HAMAPiMF_00198. Spermidine_synth. 1 hit.
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 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_173794.3. NM_102230.5.
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_173794.3. NM_102230.5.
UniGeneiAt.10951.
At.22492.

3D structure databases

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

Protein-protein interaction databases

BioGridi24231. 3 interactors.
IntActiQ9ZUB3. 2 interactors.
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.
OrthoDBiEOG09360FON.
PhylomeDBiQ9ZUB3.

Enzyme and pathway databases

UniPathwayiUPA00248; UER00314.
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. 1 hit.
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...

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: November 30, 2016
This is version 126 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.