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Protein

Spermidine/putrescine-binding periplasmic protein

Gene

potD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Required for the activity of the bacterial periplasmic transport system of putrescine and spermidine. Polyamine binding protein.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei36 – 361Spermidine1 Publication
Binding sitei85 – 851Spermidine1 Publication
Binding sitei327 – 3271Spermidine1 Publication

GO - Molecular functioni

  • polyamine binding Source: InterPro
  • polyamine-transporting ATPase activity Source: EcoCyc

GO - Biological processi

  • polyamine transmembrane transport Source: GOC
  • polyamine transport Source: EcoCyc
Complete GO annotation...

Keywords - Biological processi

Transport

Enzyme and pathway databases

BioCyciEcoCyc:POTD-MONOMER.
ECOL316407:JW1109-MONOMER.
MetaCyc:POTD-MONOMER.

Protein family/group databases

TCDBi3.A.1.11.1. the atp-binding cassette (abc) superfamily.

Names & Taxonomyi

Protein namesi
Recommended name:
Spermidine/putrescine-binding periplasmic protein
Short name:
SPBP
Gene namesi
Name:potD
Ordered Locus Names:b1123, JW1109
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10752. potD.

Subcellular locationi

  • Periplasm 1 Publication

GO - Cellular componenti

  • outer membrane-bounded periplasmic space Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 23233 PublicationsAdd
BLAST
Chaini24 – 348325Spermidine/putrescine-binding periplasmic proteinPRO_0000031837Add
BLAST

Proteomic databases

EPDiP0AFK9.
PaxDbiP0AFK9.
PRIDEiP0AFK9.

2D gel databases

SWISS-2DPAGEP0AFK9.

Interactioni

Protein-protein interaction databases

BioGridi4261797. 10 interactions.
IntActiP0AFK9. 7 interactions.
STRINGi511145.b1123.

Structurei

Secondary structure

1
348
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi27 – 3812Combined sources
Helixi42 – 509Combined sources
Beta strandi52 – 609Combined sources
Helixi62 – 698Combined sources
Beta strandi73 – 753Combined sources
Beta strandi77 – 804Combined sources
Helixi84 – 863Combined sources
Helixi87 – 937Combined sources
Helixi101 – 1033Combined sources
Helixi107 – 1093Combined sources
Helixi112 – 1143Combined sources
Beta strandi127 – 13913Combined sources
Turni140 – 1423Combined sources
Turni145 – 1473Combined sources
Helixi152 – 1554Combined sources
Helixi157 – 1593Combined sources
Beta strandi163 – 1653Combined sources
Helixi169 – 17911Combined sources
Helixi189 – 20113Combined sources
Helixi203 – 2053Combined sources
Beta strandi206 – 2094Combined sources
Helixi215 – 2195Combined sources
Beta strandi224 – 2296Combined sources
Helixi230 – 2378Combined sources
Beta strandi243 – 2464Combined sources
Beta strandi253 – 2608Combined sources
Helixi268 – 27912Combined sources
Helixi281 – 29111Combined sources
Beta strandi296 – 2983Combined sources
Turni299 – 3035Combined sources
Helixi306 – 3094Combined sources
Turni312 – 3143Combined sources
Helixi318 – 3236Combined sources
Beta strandi324 – 3263Combined sources
Helixi331 – 3333Combined sources
Helixi334 – 34411Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1POTX-ray1.80A24-348[»]
1POYX-ray2.501/2/3/426-348[»]
ProteinModelPortaliP0AFK9.
SMRiP0AFK9. Positions 26-348.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AFK9.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni168 – 1714Spermidine-binding1 Publication

Sequence similaritiesi

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4107RUE. Bacteria.
COG0687. LUCA.
HOGENOMiHOG000263814.
InParanoidiP0AFK9.
KOiK11069.
OMAiMDDSREV.
OrthoDBiEOG66XBH9.
PhylomeDBiP0AFK9.

Family and domain databases

InterProiIPR001188. Sperm_putr-bd.
[Graphical view]
PIRSFiPIRSF019574. Periplasmic_polyamine_BP. 1 hit.
PRINTSiPR00909. SPERMDNBNDNG.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0AFK9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKWSRHLLA AGALALGMSA AHADDNNTLY FYNWTEYVPP GLLEQFTKET
60 70 80 90 100
GIKVIYSTYE SNETMYAKLK TYKDGAYDLV VPSTYYVDKM RKEGMIQKID
110 120 130 140 150
KSKLTNFSNL DPDMLNKPFD PNNDYSIPYI WGATAIGVNG DAVDPKSVTS
160 170 180 190 200
WADLWKPEYK GSLLLTDDAR EVFQMALRKL GYSGNTTDPK EIEAAYNELK
210 220 230 240 250
KLMPNVAAFN SDNPANPYME GEVNLGMIWN GSAFVARQAG TPIDVVWPKE
260 270 280 290 300
GGIFWMDSLA IPANAKNKEG ALKLINFLLR PDVAKQVAET IGYPTPNLAA
310 320 330 340
RKLLSPEVAN DKTLYPDAET IKNGEWQNDV GAASSIYEEY YQKLKAGR
Length:348
Mass (Da):38,867
Last modified:December 20, 2005 - v1
Checksum:i1E6EB7A6B4EC63AB
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M64519 Genomic DNA. Translation: AAC37041.1.
U00096 Genomic DNA. Translation: AAC74207.1.
AP009048 Genomic DNA. Translation: BAA35943.1.
PIRiD40840.
RefSeqiNP_415641.1. NC_000913.3.
WP_000759317.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74207; AAC74207; b1123.
BAA35943; BAA35943; BAA35943.
GeneIDi945682.
KEGGiecj:JW1109.
eco:b1123.
PATRICi32117493. VBIEscCol129921_1169.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M64519 Genomic DNA. Translation: AAC37041.1.
U00096 Genomic DNA. Translation: AAC74207.1.
AP009048 Genomic DNA. Translation: BAA35943.1.
PIRiD40840.
RefSeqiNP_415641.1. NC_000913.3.
WP_000759317.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1POTX-ray1.80A24-348[»]
1POYX-ray2.501/2/3/426-348[»]
ProteinModelPortaliP0AFK9.
SMRiP0AFK9. Positions 26-348.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261797. 10 interactions.
IntActiP0AFK9. 7 interactions.
STRINGi511145.b1123.

Protein family/group databases

TCDBi3.A.1.11.1. the atp-binding cassette (abc) superfamily.

2D gel databases

SWISS-2DPAGEP0AFK9.

Proteomic databases

EPDiP0AFK9.
PaxDbiP0AFK9.
PRIDEiP0AFK9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74207; AAC74207; b1123.
BAA35943; BAA35943; BAA35943.
GeneIDi945682.
KEGGiecj:JW1109.
eco:b1123.
PATRICi32117493. VBIEscCol129921_1169.

Organism-specific databases

EchoBASEiEB0745.
EcoGeneiEG10752. potD.

Phylogenomic databases

eggNOGiENOG4107RUE. Bacteria.
COG0687. LUCA.
HOGENOMiHOG000263814.
InParanoidiP0AFK9.
KOiK11069.
OMAiMDDSREV.
OrthoDBiEOG66XBH9.
PhylomeDBiP0AFK9.

Enzyme and pathway databases

BioCyciEcoCyc:POTD-MONOMER.
ECOL316407:JW1109-MONOMER.
MetaCyc:POTD-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0AFK9.
PROiP0AFK9.

Family and domain databases

InterProiIPR001188. Sperm_putr-bd.
[Graphical view]
PIRSFiPIRSF019574. Periplasmic_polyamine_BP. 1 hit.
PRINTSiPR00909. SPERMDNBNDNG.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Characteristics of the gene for a spermidine and putrescine transport system that maps at 15 min on the Escherichia coli chromosome."
    Furuchi T., Kashiwagi K., Kobayashi H., Igarashi K.
    J. Biol. Chem. 266:20928-20933(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 24-53, FUNCTION, SUBCELLULAR LOCATION.
    Strain: K12.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. 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. Cited for: PROTEIN SEQUENCE OF 24-33.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  6. "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12."
    Link A.J., Robison K., Church G.M.
    Electrophoresis 18:1259-1313(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 24-35.
    Strain: K12 / EMG2.
  7. "Prediction of the structural similarity between spermidine/putrescine-binding protein and maltose-binding protein."
    Matsuo Y., Nishikawa K.
    FEBS Lett. 345:23-26(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: 3D-STRUCTURE MODELING.
  8. "Crystal structure of PotD, the primary receptor of the polyamine transport system in Escherichia coli."
    Sugiyama S., Vassylyev D.G., Matsushima M., Kashiwagi K., Igarashi K., Morikawa K.
    J. Biol. Chem. 271:9519-9525(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
  9. "The 1.8-A X-ray structure of the Escherichia coli PotD protein complexed with spermidine and the mechanism of polyamine binding."
    Sugiyama S., Matsuo Y., Maenaka K., Vassylyev D.G., Matsushima M., Kashiwagi K., Igarashi K., Morikawa K.
    Protein Sci. 5:1984-1990(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH SPERMIDINE.

Entry informationi

Entry nameiPOTD_ECOLI
AccessioniPrimary (citable) accession number: P0AFK9
Secondary accession number(s): P23861
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: December 20, 2005
Last modified: March 16, 2016
This is version 90 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.