Escherichia coli K-12 substr. MG1655 Polypeptide: putrescine ABC transporter - periplasmic binding protein

Gene: potF Accession Numbers: EG11629 (EcoCyc), b0854, ECK0845

Regulation Summary Diagram

Regulation summary diagram for potF

Component of: putrescine ABC transporter (extended summary available)

Gene Citations: [Pistocchi93]

Locations: periplasmic space, inner membrane

Map Position: [893,007 -> 894,119] (19.25 centisomes, 69°)
Length: 1113 bp / 370 aa

Molecular Weight of Polypeptide: 40.84 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0002913, CGSC:31694, DIP:DIP-10531N, EchoBASE:EB1586, EcoGene:EG11629, EcoliWiki:b0854, ModBase:P31133, OU-Microarray:b0854, PortEco:potF, PR:PRO_000023572, Pride:P31133, Protein Model Portal:P31133, RefSeq:NP_415375, RegulonDB:EG11629, SMR:P31133, String:511145.b0854, UniProt:P31133

Relationship Links: InterPro:IN-FAMILY:IPR001188, Panther:IN-FAMILY:PTHR30222:SF5, PDB:Structure:1A99, PDB:Structure:4JDF, Pfam:IN-FAMILY:PF13416, Prints:IN-FAMILY:PR00909

In Paralogous Gene Group: 216 (4 members)

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for potF

GO Terms:
Biological Process:
Inferred from experimentGO:0015847 - putrescine transport [Pistocchi93]
Inferred by computational analysisGO:0006810 - transport [UniProtGOA11a]
Inferred by computational analysisGO:0015846 - polyamine transport [GOA01a]
Molecular Function:
Inferred by computational analysisInferred from experimentGO:0015594 - putrescine-importing ATPase activity [Pistocchi93]
Inferred by computational analysisGO:0019808 - polyamine binding [GOA01a]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0030288 - outer membrane-bounded periplasmic space [DiazMejia09, LopezCampistrou05]
Inferred by computational analysisGO:0042597 - periplasmic space [UniProtGOA11, UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0043190 - ATP-binding cassette (ABC) transporter complex [Pistocchi93]

MultiFun Terms: metabolismcarbon utilizationamines
transportChannel-type TransportersPyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active TransportersThe ATP-binding Cassette (ABC) Superfamily + ABC-type Uptake PermeasesABC superfamily, periplasmic binding component

Essentiality data for potF knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enrichedYes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Subunit of: putrescine ABC transporter

Subunit composition of putrescine ABC transporter = [PotG]2[PotH][PotI][PotF]
         putrescine ABC transporter - ATP binding subunit = PotG
         putrescine ABC transporter - membrane subunit = PotH
         putrescine ABC transporter - membrane subunit = PotI
         putrescine ABC transporter - periplasmic binding protein = PotF

The PotFGHI ATP-dependent putrescine transporter is a member of the ATP Binding Cassette (ABC) Superfamily of transporters [Wu95]. PotFGHI is similar in sequence and subunit composition to the PotABCD putrescine/spermidine uptake system. Based on sequence similarity, PotG is the ATP-binding component, PotH and PotI are the membrane components, and PotF is the periplasmic binding component of the ABC transporter. Knockout and complementation studies showed that the expression of all four proteins was necessary for maximal putrescine transport activity [Pistocchi93]. The PotFGHI transporter is primarily responsible for importing putrescine necessary for cell growth in the presence of glucose whereas the putrescine symporter, PuuP, is required when putrescine is utilised as an energy source in the absence of glucose [Terui13].

Gradual inhibition of PotFGHI mediated putrescine transport occurs as the intracellular level of putrescine increases. PotFGHI enhances cell growth more effectively than PuuP in media containing 0.4% glucose and 10mM putrescine [Terui13].

The PotF protein possesses a high binding affinity to putrescine (Kd=2.0 μM) [Vassylyev98]. Site-directed mutagenesis have shown that PotF is the putrescine-binding protein [Vassylyev98], and gel filtration studies have show that in the presence of 1mM magnesium ion and 100mM potassium ion, PotF bound putrescine, but not spermidine, in a 1:1 ratio [Pistocchi93]. A high resolution structure of PotF has been determined by x-ray crystallography [Vassylyev98].

In addition to PotFGHI, PuuP and the spermidine preferential ABC transporter (PotABCD), E. coli K-12 may contain a fourth putrescine uptake system [Terui13].

Locations: inner membrane

GO Terms:
Biological Process:
Inferred from experimentGO:0015847 - putrescine transport [Pistocchi93]
Molecular Function:
Inferred by computational analysisInferred from experimentGO:0015594 - putrescine-importing ATPase activity [Pistocchi93]
Cellular Component:
Inferred by computational analysisGO:0043190 - ATP-binding cassette (ABC) transporter complex [Pistocchi93]

Enzymatic reaction of: transport of putresince (putrescine ABC transporter)

Inferred from experimentInferred by computational analysis

Synonyms: Transport of putrescine

EC Number:

Transport reaction diagram for transport of putresince

Kinetic Parameters:
Substrate Km (μM) Vmax (µmol mg-1 min-1) Citations
putrescine 0.57 0.023 [Terui13]

Sequence Features

Protein sequence of putrescine ABC transporter - periplasmic binding protein with features indicated

Feature Class Location Citations Comment
Signal-Sequence 1 -> 26
Inferred from experiment[Link97, Pistocchi93]
Chain 27 -> 370
Author statement[UniProt15]
UniProt: Putrescine-binding periplasmic protein.
Sequence-Conflict 29
Inferred by curator[Link97, UniProt15]
UniProt: (in Ref. 5; AA sequence).
Amino-Acid-Sites-That-Bind 38
Inferred from experiment[Vassylyev98]
UniProt: Putrescine.
Pfam PF13416 45 -> 335
Inferred by computational analysis[Finn14]
SBP_bac_8 : Bacterial extracellular solute-binding protein
Disulfide-Bond-Site 175, 239
Inferred from experiment[Vassylyev98]
Sequence-Conflict 216 -> 217
Inferred by curator[Pistocchi93, UniProt15]
UniProt: (in Ref. 1; AAA24409).
Amino-Acid-Sites-That-Bind 247
Inferred from experiment[Vassylyev98]
UniProt: Putrescine.
Amino-Acid-Sites-That-Bind 278
Inferred from experiment[Vassylyev98]
UniProt: Putrescine.

Gene Local Context (not to scale -- see Genome Browser for correct scale)

Gene local context diagram

Transcription Units

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b0854 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11629; confirmed by SwissProt match.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Link97: Link AJ, Robison K, Church GM (1997). "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Electrophoresis 18(8);1259-313. PMID: 9298646

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Pistocchi93: Pistocchi R, Kashiwagi K, Miyamoto S, Nukui E, Sadakata Y, Kobayashi H, Igarashi K (1993). "Characteristics of the operon for a putrescine transport system that maps at 19 minutes on the Escherichia coli chromosome." J Biol Chem 1993;268(1);146-52. PMID: 8416922

Terui13: Terui Y, Saroj SD, Sakamoto A, Yoshida T, Higashi K, Kurihara S, Suzuki H, Toida T, Kashiwagi K, Igarashi K (2013). "Properties of putrescine uptake by PotFGHI and PuuP and their physiological significance in Escherichia coli." Amino Acids. PMID: 23719730

UniProt15: UniProt Consortium (2015). "UniProt version 2015-08 released on 2015-07-22." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Vassylyev98: Vassylyev DG, Tomitori H, Kashiwagi K, Morikawa K, Igarashi K (1998). "Crystal structure and mutational analysis of the Escherichia coli putrescine receptor. Structural basis for substrate specificity." J Biol Chem 1998;273(28);17604-9. PMID: 9651355

Wu95: Wu LF, Mandrand-Berthelot MA (1995). "A family of homologous substrate-binding proteins with a broad range of substrate specificity and dissimilar biological functions." Biochimie 1995;77(9);744-50. PMID: 8789466

Other References Related to Gene Regulation

Barrios99: Barrios H, Valderrama B, Morett E (1999). "Compilation and analysis of sigma(54)-dependent promoter sequences." Nucleic Acids Res 27(22);4305-13. PMID: 10536136

Reitzer01: Reitzer L, Schneider BL (2001). "Metabolic context and possible physiological themes of sigma(54)-dependent genes in Escherichia coli." Microbiol Mol Biol Rev 65(3);422-44, table of contents. PMID: 11528004

Zimmer00: Zimmer DP, Soupene E, Lee HL, Wendisch VF, Khodursky AB, Peter BJ, Bender RA, Kustu S (2000). "Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation." Proc Natl Acad Sci U S A 97(26);14674-9. PMID: 11121068

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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