Spermidine synthase - Escherichia coli (strain K12)

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P09158 (SPEE_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 123. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Spermidine synthase
EC=2.5.1.16

Alternative name(s):
Putrescine aminopropyltransferase
Short name=PAPT
SPDSY

Gene names

Name:	speE
Ordered Locus Names:	b0121, JW0117

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	288 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the production of spermidine from putrescine and decarboxylated S-adenosylmethionine (dcSAM), which serves as an aminopropyl donor. HAMAP-Rule MF_00198
Catalytic activity	S-adenosylmethioninamine + putrescine = S-methyl-5'-thioadenosine + spermidine. HAMAP-Rule MF_00198
Enzyme regulation	The activity is thought to be regulated mainly by the availability of decarboxylated S-adenosylmethionine. HAMAP-Rule MF_00198
Pathway	Amine and polyamine biosynthesis; spermidine biosynthesis; spermidine from putrescine: step 1/1. HAMAP-Rule MF_00198
Subunit structure	Homodimer. Ref.7 Ref.8
Sequence similarities	Belongs to the spermidine/spermine synthase family.
Biophysicochemical properties	pH dependence: Optimum pH is 10.4. HAMAP-Rule MF_00198

Ontologies

Keywords
Biological process	Polyamine biosynthesis Spermidine biosynthesis
Molecular function	Transferase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	spermidine biosynthetic process Inferred from mutant phenotype Ref.6. Source: EcoCyc
Cellular_component	cytosol Inferred from direct assay PubMed 16858726. Source: UniProtKB
Molecular_function	spermidine synthase activity Inferred from direct assay PubMed 23001854. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.6

Chain

2 – 288

287

Spermidine synthase HAMAP-Rule MF_00198

PRO_0000156479

Regions

Region

140 – 141

S-adenosylmethioninamine binding By similarity

Sites

Active site

158

Proton acceptor By similarity

Binding site

S-adenosylmethioninamine By similarity

Binding site

Putrescine By similarity

Binding site

S-adenosylmethioninamine By similarity

Binding site

108

S-adenosylmethioninamine By similarity

Binding site

161

Putrescine By similarity

Binding site

226

Putrescine By similarity

Secondary structure

288

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P09158 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: 31AE026FF6199E9F
Show »

FASTA

288

32,321

        10         20         30         40         50         60 
MAEKKQWHET LHDQFGQYFA VDNVLYHEKT DHQDLIIFEN AAFGRVMALD GVVQTTERDE 

        70         80         90        100        110        120 
FIYHEMMTHV PLLAHGHAKH VLIIGGGDGA MLREVTRHKN VESITMVEID AGVVSFCRQY 

       130        140        150        160        170        180 
LPNHNAGSYD DPRFKLVIDD GVNFVNQTSQ TFDVIISDCT DPIGPGESLF TSAFYEGCKR 

       190        200        210        220        230        240 
CLNPGGIFVA QNGVCFLQQE EAIDSHRKLS HYFSDVGFYQ AAIPTYYGGI MTFAWATDND 

       250        260        270        280 
ALRHLSTEII QARFLASGLK CRYYNPAIHT AAFALPQYLQ DALASQPS

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The speEspeD operon of Escherichia coli. Formation and processing of a proenzyme form of S-adenosylmethionine decarboxylase." Tabor C.W., Tabor H. J. Biol. Chem. 262:16037-16040(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Systematic sequencing of the Escherichia coli genome: analysis of the 2.4-4.1 min (110,917-193,643 bp) region." Fujita N., Mori H., Yura T., Ishihama A. Nucleic Acids Res. 22:1637-1639(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Spermidine biosynthesis in Escherichia coli: promoter and termination regions of the speED operon." Xie Q.W., Tabor C.W., Tabor H. J. Bacteriol. 171:4457-4465(1989) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-18.
[6]	"Spermidine synthase of Escherichia coli: localization of the speE gene." Tabor C.W., Tabor H., Xie Q.W. Proc. Natl. Acad. Sci. U.S.A. 83:6040-6044(1986) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-31.
[7]	"Spermidine biosynthesis. Purification and properties of propylamine transferase from Escherichia coli." Bowman W.H., Tabor C.W., Tabor H. J. Biol. Chem. 248:2480-2486(1973) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION, SUBUNIT.
[8]	"The crystal structure of Escherichia coli spermidine synthase SpeE reveals a unique substrate-binding pocket." Zhou X., Chua T.K., Tkaczuk K.L., Bujnicki J.M., Sivaraman J. J. Struct. Biol. 169:277-285(2010) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS), SUBUNIT.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J02804 Genomic DNA. Translation: AAA24643.1.
U00096 Genomic DNA. Translation: AAC73232.1.
AP009048 Genomic DNA. Translation: BAB96695.1.

PIR

SYECSD. A29778.

RefSeq

NP_414663.1. NC_000913.2.
YP_488424.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3O4F	X-ray	2.90	A/B/C/D/E/F/G/H	1-288	[»]

ProteinModelPortal

P09158.

SMR

P09158. Positions 4-287.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10908N.

IntAct

P09158. 10 interactions.

MINT

MINT-1231846.

STRING

511145.b0121.

2D gel databases

SWISS-2DPAGE

P09158.

Proteomic databases

PaxDb

P09158.

PRIDE

P09158.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC73232; AAC73232; b0121.
BAB96695; BAB96695; BAB96695.

GeneID

12933098.
947726.

KEGG

ecj:Y75_p0118.
eco:b0121.

PATRIC

32115343. VBIEscCol129921_0123.

Organism-specific databases

EchoBASE

EB0956.

EcoGene

EG10963. speE.

Phylogenomic databases

eggNOG

COG0421.

HOGENOM

HOG000256146.

K00797.

OMA

ELWYTEK.

ProtClustDB

PRK00811.

Enzyme and pathway databases

BioCyc

EcoCyc:SPERMIDINESYN-MONOMER.
ECOL316407:JW0117-MONOMER.
MetaCyc:SPERMIDINESYN-MONOMER.

UniPathway

UPA00248; UER00314.

Gene expression databases

Genevestigator

P09158.

Family and domain databases

HAMAP

MF_00198. Spermidine_synth.

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...

Entry information

Entry name

SPEE_ECOLI

Accession

Primary (citable) accession number: P09158

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 1989
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 123 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

2D gel databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents