POTD_ECOLI
ID POTD_ECOLI Reviewed; 348 AA.
AC P0AFK9; P23861;
DT 20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 20-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 121.
DE RecName: Full=Spermidine/putrescine-binding periplasmic protein;
DE Short=SPBP;
DE Flags: Precursor;
GN Name=potD; OrderedLocusNames=b1123, JW1109;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 24-53, FUNCTION, AND
RP SUBCELLULAR LOCATION.
RC STRAIN=K12;
RX PubMed=1939142; DOI=10.1016/s0021-9258(18)54799-2;
RA Furuchi T., Kashiwagi K., Kobayashi H., Igarashi K.;
RT "Characteristics of the gene for a spermidine and putrescine transport
RT system that maps at 15 min on the Escherichia coli chromosome.";
RL J. Biol. Chem. 266:20928-20933(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP PROTEIN SEQUENCE OF 24-33.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RA Pasquali C., Sanchez J.-C., Ravier F., Golaz O., Hughes G.J., Frutiger S.,
RA Paquet N., Wilkins M., Appel R.D., Bairoch A., Hochstrasser D.F.;
RL Submitted (SEP-1994) to UniProtKB.
RN [6]
RP PROTEIN SEQUENCE OF 24-35.
RC STRAIN=K12 / EMG2;
RX PubMed=9298646; DOI=10.1002/elps.1150180807;
RA Link A.J., Robison K., Church G.M.;
RT "Comparing the predicted and observed properties of proteins encoded in the
RT genome of Escherichia coli K-12.";
RL Electrophoresis 18:1259-1313(1997).
RN [7]
RP 3D-STRUCTURE MODELING.
RX PubMed=8194593; DOI=10.1016/0014-5793(94)00435-8;
RA Matsuo Y., Nishikawa K.;
RT "Prediction of the structural similarity between spermidine/putrescine-
RT binding protein and maltose-binding protein.";
RL FEBS Lett. 345:23-26(1994).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
RX PubMed=8621624; DOI=10.1074/jbc.271.16.9519;
RA Sugiyama S., Vassylyev D.G., Matsushima M., Kashiwagi K., Igarashi K.,
RA Morikawa K.;
RT "Crystal structure of PotD, the primary receptor of the polyamine transport
RT system in Escherichia coli.";
RL J. Biol. Chem. 271:9519-9525(1996).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH SPERMIDINE.
RX PubMed=8897598; DOI=10.1002/pro.5560051004;
RA Sugiyama S., Matsuo Y., Maenaka K., Vassylyev D.G., Matsushima M.,
RA Kashiwagi K., Igarashi K., Morikawa K.;
RT "The 1.8-A X-ray structure of the Escherichia coli PotD protein complexed
RT with spermidine and the mechanism of polyamine binding.";
RL Protein Sci. 5:1984-1990(1996).
CC -!- FUNCTION: Required for the activity of the bacterial periplasmic
CC transport system of putrescine and spermidine. Polyamine binding
CC protein. {ECO:0000269|PubMed:1939142}.
CC -!- SUBCELLULAR LOCATION: Periplasm {ECO:0000269|PubMed:1939142}.
CC -!- SIMILARITY: Belongs to the bacterial solute-binding protein PotD/PotF
CC family. {ECO:0000305}.
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DR EMBL; M64519; AAC37041.1; -; Genomic_DNA.
DR EMBL; U00096; AAC74207.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35943.1; -; Genomic_DNA.
DR PIR; D40840; D40840.
DR RefSeq; NP_415641.1; NC_000913.3.
DR RefSeq; WP_000759317.1; NZ_STEB01000016.1.
DR PDB; 1POT; X-ray; 1.80 A; A=24-348.
DR PDB; 1POY; X-ray; 2.50 A; 1/2/3/4=26-348.
DR PDBsum; 1POT; -.
DR PDBsum; 1POY; -.
DR AlphaFoldDB; P0AFK9; -.
DR SMR; P0AFK9; -.
DR BioGRID; 4261797; 57.
DR ComplexPortal; CPX-4383; Spermidine ABC transporter complex.
DR IntAct; P0AFK9; 7.
DR STRING; 511145.b1123; -.
DR DrugBank; DB03566; Spermidine.
DR TCDB; 3.A.1.11.1; the atp-binding cassette (abc) superfamily.
DR SWISS-2DPAGE; P0AFK9; -.
DR jPOST; P0AFK9; -.
DR PaxDb; P0AFK9; -.
DR PRIDE; P0AFK9; -.
DR EnsemblBacteria; AAC74207; AAC74207; b1123.
DR EnsemblBacteria; BAA35943; BAA35943; BAA35943.
DR GeneID; 66670610; -.
DR GeneID; 945682; -.
DR KEGG; ecj:JW1109; -.
DR KEGG; eco:b1123; -.
DR PATRIC; fig|1411691.4.peg.1144; -.
DR EchoBASE; EB0745; -.
DR eggNOG; COG0687; Bacteria.
DR HOGENOM; CLU_026974_1_3_6; -.
DR InParanoid; P0AFK9; -.
DR OMA; FWMDNYA; -.
DR PhylomeDB; P0AFK9; -.
DR BioCyc; EcoCyc:POTD-MON; -.
DR BioCyc; MetaCyc:POTD-MON; -.
DR EvolutionaryTrace; P0AFK9; -.
DR PRO; PR:P0AFK9; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0016020; C:membrane; IC:ComplexPortal.
DR GO; GO:0030288; C:outer membrane-bounded periplasmic space; IDA:EcoCyc.
DR GO; GO:0019810; F:putrescine binding; IDA:EcoCyc.
DR GO; GO:0019809; F:spermidine binding; IDA:EcoCyc.
DR GO; GO:0015847; P:putrescine transport; IDA:EcoCyc.
DR GO; GO:1903711; P:spermidine transmembrane transport; IC:ComplexPortal.
DR GO; GO:0015848; P:spermidine transport; IDA:EcoCyc.
DR InterPro; IPR006059; SBP.
DR InterPro; IPR001188; Sperm_putr-bd.
DR Pfam; PF13416; SBP_bac_8; 1.
DR PIRSF; PIRSF019574; Periplasmic_polyamine_BP; 1.
DR PRINTS; PR00909; SPERMDNBNDNG.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Periplasm; Reference proteome;
KW Signal; Transport.
FT SIGNAL 1..23
FT /evidence="ECO:0000269|PubMed:1939142,
FT ECO:0000269|PubMed:9298646, ECO:0000269|Ref.5"
FT CHAIN 24..348
FT /note="Spermidine/putrescine-binding periplasmic protein"
FT /id="PRO_0000031837"
FT BINDING 36
FT /ligand="spermidine"
FT /ligand_id="ChEBI:CHEBI:57834"
FT /evidence="ECO:0000269|PubMed:8897598"
FT BINDING 85
FT /ligand="spermidine"
FT /ligand_id="ChEBI:CHEBI:57834"
FT /evidence="ECO:0000269|PubMed:8897598"
FT BINDING 168..171
FT /ligand="spermidine"
FT /ligand_id="ChEBI:CHEBI:57834"
FT /evidence="ECO:0000269|PubMed:8897598"
FT BINDING 327
FT /ligand="spermidine"
FT /ligand_id="ChEBI:CHEBI:57834"
FT /evidence="ECO:0000269|PubMed:8897598"
FT STRAND 27..38
FT /evidence="ECO:0007829|PDB:1POT"
FT HELIX 42..50
FT /evidence="ECO:0007829|PDB:1POT"
FT STRAND 52..60
FT /evidence="ECO:0007829|PDB:1POT"
FT HELIX 62..69
FT /evidence="ECO:0007829|PDB:1POT"
FT STRAND 73..75
FT /evidence="ECO:0007829|PDB:1POT"
FT STRAND 77..80
FT /evidence="ECO:0007829|PDB:1POT"
FT HELIX 84..86
FT /evidence="ECO:0007829|PDB:1POT"
FT HELIX 87..93
FT /evidence="ECO:0007829|PDB:1POT"
FT HELIX 101..103
FT /evidence="ECO:0007829|PDB:1POY"
FT HELIX 107..109
FT /evidence="ECO:0007829|PDB:1POT"
FT HELIX 112..114
FT /evidence="ECO:0007829|PDB:1POT"
FT STRAND 127..139
FT /evidence="ECO:0007829|PDB:1POT"
FT TURN 140..142
FT /evidence="ECO:0007829|PDB:1POT"
FT TURN 145..147
FT /evidence="ECO:0007829|PDB:1POT"
FT HELIX 152..155
FT /evidence="ECO:0007829|PDB:1POT"
FT HELIX 157..159
FT /evidence="ECO:0007829|PDB:1POT"
FT STRAND 163..165
FT /evidence="ECO:0007829|PDB:1POT"
FT HELIX 169..179
FT /evidence="ECO:0007829|PDB:1POT"
FT HELIX 189..201
FT /evidence="ECO:0007829|PDB:1POT"
FT HELIX 203..205
FT /evidence="ECO:0007829|PDB:1POT"
FT STRAND 206..209
FT /evidence="ECO:0007829|PDB:1POT"
FT HELIX 215..219
FT /evidence="ECO:0007829|PDB:1POT"
FT STRAND 224..229
FT /evidence="ECO:0007829|PDB:1POT"
FT HELIX 230..237
FT /evidence="ECO:0007829|PDB:1POT"
FT STRAND 243..246
FT /evidence="ECO:0007829|PDB:1POT"
FT STRAND 253..260
FT /evidence="ECO:0007829|PDB:1POT"
FT HELIX 268..279
FT /evidence="ECO:0007829|PDB:1POT"
FT HELIX 281..291
FT /evidence="ECO:0007829|PDB:1POT"
FT STRAND 296..298
FT /evidence="ECO:0007829|PDB:1POT"
FT TURN 299..303
FT /evidence="ECO:0007829|PDB:1POT"
FT HELIX 306..309
FT /evidence="ECO:0007829|PDB:1POT"
FT TURN 312..314
FT /evidence="ECO:0007829|PDB:1POT"
FT HELIX 318..323
FT /evidence="ECO:0007829|PDB:1POT"
FT STRAND 324..326
FT /evidence="ECO:0007829|PDB:1POT"
FT HELIX 331..333
FT /evidence="ECO:0007829|PDB:1POT"
FT HELIX 334..344
FT /evidence="ECO:0007829|PDB:1POT"
SQ SEQUENCE 348 AA; 38867 MW; 1E6EB7A6B4EC63AB CRC64;
MKKWSRHLLA AGALALGMSA AHADDNNTLY FYNWTEYVPP GLLEQFTKET GIKVIYSTYE
SNETMYAKLK TYKDGAYDLV VPSTYYVDKM RKEGMIQKID KSKLTNFSNL DPDMLNKPFD
PNNDYSIPYI WGATAIGVNG DAVDPKSVTS WADLWKPEYK GSLLLTDDAR EVFQMALRKL
GYSGNTTDPK EIEAAYNELK KLMPNVAAFN SDNPANPYME GEVNLGMIWN GSAFVARQAG
TPIDVVWPKE GGIFWMDSLA IPANAKNKEG ALKLINFLLR PDVAKQVAET IGYPTPNLAA
RKLLSPEVAN DKTLYPDAET IKNGEWQNDV GAASSIYEEY YQKLKAGR
