P19623 (SPEE_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Spermidine synthase
Short name=SPDSY
EC=2.5.1.16

Alternative name(s):
Putrescine aminopropyltransferase

Gene names

Name:	SRM
Synonyms:	SPS1, SRML1

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	302 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the production of spermidine from putrescine and decarboxylated S-adenosylmethionine (dcSAM). Has a strong preference for putrescine as substrate, and has very low activity towards 1,3-diaminopropane. Has extremely low activity towards spermidine. Ref.7
Catalytic activity	S-adenosylmethioninamine + putrescine = S-methyl-5'-thioadenosine + spermidine. Ref.7
Enzyme regulation	The activity is thought to be regulated mainly by the availability of decarboxylated S-adenosylmethionine.
Pathway	Amine and polyamine biosynthesis; spermidine biosynthesis; spermidine from putrescine: step 1/1.
Subunit structure	Homodimer or homotetramer. Ref.7
Sequence similarities	Belongs to the spermidine/spermine synthase family.
Biophysicochemical properties	Kinetic parameters: KM=20 µM for putrescine Ref.7 KM=0.9 µM for S-adenosylmethioninamine

Ontologies

Keywords
Biological process	Spermidine biosynthesis
Coding sequence diversity	Polymorphism
Molecular function	Transferase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	small molecule metabolic process Traceable author statement. Source: Reactome spermidine biosynthetic process Inferred from direct assay Ref.7. Source: UniProtKB
Cellular_component	cytosol Traceable author statement. Source: Reactome
Molecular_function	protein homodimerization activity Inferred from direct assay Ref.7. Source: UniProtKB spermidine synthase activity Inferred from direct assay Ref.7. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 302

302

Spermidine synthase

PRO_0000156445

Regions

Region

155 – 156

2

S-adenosylmethioninamine binding

Region

173 – 176

4

Putrescine binding

Sites

Active site

173

1

Proton acceptor Probable

Binding site

49

1

S-adenosylmethioninamine

Binding site

79

1

Putrescine

Binding site

80

1

S-adenosylmethioninamine

Binding site

104

1

S-adenosylmethioninamine

Binding site

124

1

S-adenosylmethioninamine

Binding site

173

1

S-adenosylmethioninamine

Binding site

241

1

Putrescine

Natural variations

Natural variant

149

1

L → V.
Corresponds to variant rs1049932 [ dbSNP | Ensembl ].

VAR_011807

Experimental info

Sequence conflict

210

1

Q → E in AAA36633. Ref.1

Secondary structure

1

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302

Helix Strand Turn

Details...

Beta strand

20 – 23

4

Beta strand

31 – 45

15

Beta strand

47 – 59

13

Beta strand

61 – 65

5

Beta strand

68 – 72

5

Turn

73 – 76

4

Helix

77 – 88

12

Beta strand

91 – 93

3

Beta strand

96 – 101

6

Helix

106 – 111

6

Beta strand

119 – 125

7

Helix

127 – 136

10

Helix

138 – 141

4

Helix

142 – 145

4

Beta strand

149 – 154

6

Helix

156 – 161

6

Beta strand

167 – 173

7

Turn

177 – 179

3

Helix

180 – 185

6

Helix

188 – 196

9

Beta strand

197 – 208

12

Turn

210 – 212

3

Helix

214 – 227

14

Beta strand

229 – 237

9

Helix

242 – 244

3

Beta strand

245 – 254

10

Beta strand

259 – 261

3

Helix

268 – 273

6

Helix

281 – 286

6

Helix

292 – 299

8

Sequences

	Sequence		Length	Mass (Da)
	P19623 [UniParc]. Last modified February 1, 1991. Version 1. Checksum: 3EF454D886F6425D	FASTA	302	33,825
	10 20 30 40 50 60 MEPGPDGPAA SGPAAIREGW FRETCSLWPG QALSLQVEQL LHHRRSRYQD ILVFRSKTYG 70 80 90 100 110 120 NVLVLDGVIQ CTERDEFSYQ EMIANLPLCS HPNPRKVLII GGGDGGVLRE VVKHPSVESV 130 140 150 160 170 180 VQCEIDEDVI QVSKKFLPGM AIGYSSSKLT LHVGDGFEFM KQNQDAFDVI ITDSSDPMGP 190 200 210 220 230 240 AESLFKESYY QLMKTALKED GVLCCQGECQ WLHLDLIKEM RQFCQSLFPV VAYAYCTIPT 250 260 270 280 290 300 YPSGQIGFML CSKNPSTNFQ EPVQPLTQQQ VAQMQLKYYN SDVHRAAFVL PEFARKALND VS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Human spermidine synthase: cloning and primary structure." Wahlfors J., Alhonen L., Kauppinen L., Hyvoenen T., Jaenne J., Eloranta T. DNA Cell Biol. 9:103-110(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]	"Human spermidine synthase gene: structure and chromosomal localization." Myoehaenen S., Kauppinen L., Wahlfors J., Alhonen L., Jaenne J. DNA Cell Biol. 10:467-474(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"The DNA sequence and biological annotation of human chromosome 1." Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K. , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R. Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Lung and Skin.
[6]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[7]	"Structure and mechanism of spermidine synthases." Wu H., Min J., Ikeguchi Y., Zeng H., Dong A., Loppnau P., Pegg A.E., Plotnikov A.N. Biochemistry 46:8331-8339(2007) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.89 ANGSTROMS) IN COMPLEXES WITH SPERMIDINE; PUTRESCINE; MTA AND S-ADENOSYLMETHIONINAMINE, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M34338 mRNA. Translation: AAA36633.1.
M64231 Genomic DNA. Translation: AAA60574.1.
AL109811 Genomic DNA. Translation: CAI22104.1.
CH471130 Genomic DNA. Translation: EAW71675.1.
BC000309 mRNA. Translation: AAH00309.1.
BC033106 mRNA. Translation: AAH33106.1.

IPI

IPI00292020.

PIR

A32610.

RefSeq

NP_003123.2. NM_003132.2.

UniGene

Hs.76244.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2O05	X-ray	2.00	A/B	1-302	[»]
2O06	X-ray	2.00	A/B	1-302	[»]
2O07	X-ray	1.89	A/B	1-302	[»]
2O0L	X-ray	1.99	A/B	1-302	[»]
3RW9	X-ray	2.00	A/B	1-302	[»]

ProteinModelPortal

P19623.

ModBase

Search...

Protein-protein interaction databases

IntAct

P19623. 4 interactions.

STRING

9606.ENSP00000366156.

PTM databases

PhosphoSite

P19623.

Polymorphism databases

DMDM

134811.

Proteomic databases

PaxDb

P19623.

PeptideAtlas

P19623.

PRIDE

P19623.

Protocols and materials databases

DNASU

6723.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000376957; ENSP00000366156; ENSG00000116649.

GeneID

6723.

KEGG

hsa:6723.

UCSC

uc001arz.1. human.

Organism-specific databases

CTD

6723.

GeneCards

GC01M011114.

HGNC

HGNC:11296. SRM.

HPA

HPA015746.
HPA029528.

MIM

182891. gene.

neXtProt

NX_P19623.

PharmGKB

PA36120.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG0421.

HOGENOM

HOG000256147.

HOVERGEN

HBG000834.

InParanoid

P19623.

KO

K00797.

OMA

ELWYTEK.

OrthoDB

EOG4H9XM0.

PhylomeDB

P19623.

Enzyme and pathway databases

BioCyc

MetaCyc:HS04027-MONOMER.

Reactome

REACT_111217. Metabolism.

SABIO-RK

P19623.

UniPathway

UPA00248; UER00314.

Gene expression databases

Bgee

P19623.

CleanEx

HS_SRM.

Genevestigator

P19623.

GermOnline

ENSG00000116649. Homo sapiens.

Family and domain databases

InterPro

IPR001045. Spermidine/spermine_synthase.
[Graphical view]

PANTHER

PTHR11558. PTHR11558. 1 hit.

Pfam

PF01564. Spermine_synth. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00417. speE. 1 hit.

PROSITE

PS01330. SPERMIDINE_SYNTHASE_1. 1 hit.
PS51006. SPERMIDINE_SYNTHASE_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

BindingDB

P19623.

ChEMBL

CHEMBL4232.

ChiTaRS

SRM. human.

DrugBank

DB00118. S-Adenosylmethionine.
DB00127. Spermine.

EvolutionaryTrace

P19623.

GenomeRNAi

6723.

NextBio

26226.

SOURCE

Search...

Entry information

Entry name

SPEE_HUMAN

Accession

Primary (citable) accession number: P19623
Secondary accession number(s): B1AKP9, Q15511

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1991
Last sequence update:	February 1, 1991
Last modified:	May 1, 2013
This is version 140 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.