Escherichia coli K-12 substr. MG1655 Polypeptide: glycerol-3-phosphate ABC transporter - periplasmic binding protein

Gene: ugpB Accession Numbers: EG11047 (EcoCyc), b3453, ECK3437

Synonyms: psiB, psiC

Regulation Summary Diagram: ?

Regulation summary diagram for ugpB

Component of: glycerol-3-phosphate / glycerophosphodiester ABC transporter (extended summary available)

UgpB is the periplasmic binding component of the sn-glycerol-3-phosphate (G3P) ABC transporter in E. coli K-12. Purified UgpB binds G3P and glycerophosphocholine with dissociation constants of 0.68 µM and 5.1 µM respectively [Wuttge12]. UgpB binds glycerophosphoethanolamine [Brzoska88].

Gene Citations: [Overduin88]

Locations: inner membrane, periplasmic space

Map Position: [3,589,032 <- 3,590,348] (77.36 centisomes, 278°)
Length: 1317 bp / 438 aa

Molecular Weight of Polypeptide: 48.449 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0011274 , CGSC:39 , DIP:DIP-35942N , EchoBASE:EB1040 , EcoGene:EG11047 , EcoliWiki:b3453 , Mint:MINT-1291422 , ModBase:P0AG80 , OU-Microarray:b3453 , PortEco:ugpB , PR:PRO_000024165 , Pride:P0AG80 , Protein Model Portal:P0AG80 , RefSeq:NP_417910 , RegulonDB:EG11047 , SMR:P0AG80 , String:511145.b3453 , UniProt:P0AG80

Relationship Links: InterPro:IN-FAMILY:IPR006059 , InterPro:IN-FAMILY:IPR006061 , InterPro:IN-FAMILY:IPR030166 , Panther:IN-FAMILY:PTHR30061:SF7 , PDB:Structure:4AQ4 , Pfam:IN-FAMILY:PF01547 , Prosite:IN-FAMILY:PS01037

In Paralogous Gene Group: 274 (2 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for ugpB

GO Terms:

Biological Process: GO:0001407 - glycerophosphodiester transport Inferred from experiment Inferred by computational analysis [GOA01, Brzoska88]
GO:0015794 - glycerol-3-phosphate transport Inferred from experiment Inferred by computational analysis [GOA01, Wuttge12, Schweizer82]
GO:0006810 - transport Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0005215 - transporter activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0030288 - outer membrane-bounded periplasmic space Inferred from experiment Inferred by computational analysis [GOA01, DiazMejia09, LopezCampistrou05, Schweizer82a]
GO:0042597 - periplasmic space Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing Inferred by computational analysis [GOA01]

MultiFun Terms: metabolism biosynthesis of building blocks fatty acids and phosphatidic acid
metabolism biosynthesis of macromolecules (cellular constituents) phospholipid
metabolism central intermediary metabolism misc. glycerol metabolism
metabolism energy metabolism, carbon aerobic respiration
metabolism energy metabolism, carbon anaerobic respiration
transport Channel-type Transporters Pyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active Transporters The ATP-binding Cassette (ABC) Superfamily + ABC-type Uptake Permeases ABC superfamily, periplasmic binding component

Essentiality data for ugpB knockouts: ?

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

Revised 25-May-2011 by Brito D
Last-Curated ? 17-Oct-2013 by Mackie A , Macquarie University

Subunit of: glycerol-3-phosphate / glycerophosphodiester ABC transporter

Subunit composition of glycerol-3-phosphate / glycerophosphodiester ABC transporter = [UgpC]2[UgpA][UgpE][UgpB]
         glycerol-3-phosphate ABC transporter - ATP binding subunit = UgpC
         glycerol-3-phosphate ABC transporter - membrane subunit = UgpA
         glycerol-3-phosphate ABC transporter - membrane subunit = UgpE
         glycerol-3-phosphate ABC transporter - periplasmic binding protein = UgpB (summary available)

UgpBAEC is an ATP-dependent glycerol-3-phosphate (G3P) and glycerophosphodiester uptake system that is a member of the ATP-Binding Cassette (ABC) Superfamily of transporters [Schweizer82, Brzoska88, Saurin99]. Based on sequence similarity, UgpC is the ATP-binding protein, UgpA and UgpE are the membrane components, and UgpB is the periplasmic binding protein [Overduin88]. Glycerol-3-phosphate can be used as a carbon source and a phosphate source and is also an essential intermediate in phospholipid biosynthesis [Schweizer82, Boos98a].

The Ugp system can supply G3P as a sole phosphate source but is unable to supply enough carbon for bacterial growth [Schweizer82]. Ugp-mediated uptake of G3P is inhibited by increased internal phosphate concentration which may explain why G3P transported by the Ugp system can only serve as the sole phosphate source but not the sole carbon source [Schweizer82, Brzoska94, Xavier95]. The ATPase activity of the Ugp system reconstituted in vitro is insensitive to phosphate, PhoU or UgpQ [Wuttge12].

Glycerophosphodiesters, such as glycerophosphoethanolamaine (GPE), glycerophosphocholine (GPC) and glycerophosphoglycerol (GPG) are high affinity substrates of the Ugp transport system. Glycerophosphodiesters transported by the Ugp system are hydrolysed very quickly at the inner face of the cytoplasmic membrane, the G3P moiety can be detected in the cytoplasm whereas the corresponding alcohol is usually found in the culture medium [Brzoska88].

G3P uptake via the Ugp system does not operate in membrane vesicles but can be observed in whole cell experiments [Schweizer82, Brzoska94]. Purified UgpAEC2 displays UgpB/G3P stimulated ATPase activity in proteoliposomes [Wuttge12].

Transcription of the ugp system is under the control of the pho regulon [Brzoska94].

E. coli ΔphoA strains containing deletions of ugpB, ugpA, ugpE, ugpC or ugpBAEC are unable to utilise glycerol-2-phosphate as a phosphate source. This suggests that the Ugp system is also capable of transporting glycerol-2-phosphate [Yang09a]. Purified UgpB does not bind glycerol-2-phosphate [Wuttge12].

Review: [Brzoska89]

Citations: [Schweizer82a, Hekstra93, Kasahara91, Ames90]

Locations: inner membrane

GO Terms:

Biological Process: GO:0001407 - glycerophosphodiester transport Inferred from experiment [Brzoska88]
GO:0015794 - glycerol-3-phosphate transport Inferred from experiment [Wuttge12, Schweizer82a]
Molecular Function: GO:0001406 - glycerophosphodiester transmembrane transporter activity Inferred from experiment [Brzoska88]
GO:0015430 - glycerol-3-phosphate-transporting ATPase activity Inferred by computational analysis Inferred from experiment [Wuttge12, Overduin88]
Cellular Component: GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing Inferred from experiment Inferred by computational analysis [Wuttge12]
GO:0005887 - integral component of plasma membrane Inferred by computational analysis [Overduin88]

Last-Curated ? 26-Nov-2013 by Mackie A , Macquarie University

Enzymatic reaction of: transport of a glycerophosphodiester (glycerol-3-phosphate / glycerophosphodiester ABC transporter)

Transport reaction diagram for transport of a glycerophosphodiester

Enzymatic reaction of: transport of glycerol-3-phosphate (glycerol-3-phosphate / glycerophosphodiester ABC transporter)

EC Number:

Transport reaction diagram for transport of glycerol-3-phosphate

Sequence Features

Protein sequence of glycerol-3-phosphate ABC transporter - periplasmic binding protein with features indicated

Feature Class Location Citations Comment
Signal-Sequence 1 -> 23
Chain 24 -> 438
UniProt: sn-glycerol-3-phosphate-binding periplasmic protein ugpB;
Amino-Acid-Sites-That-Bind 169
Sequence-Conflict 334
[Overduin88, UniProt10a]
UniProt: (in Ref. 1; CAA31531);

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b3453 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11047; confirmed by SwissProt match.


Ames90: Ames GF, Mimura CS, Shyamala V (1990). "Bacterial periplasmic permeases belong to a family of transport proteins operating from Escherichia coli to human: Traffic ATPases." FEMS Microbiol Rev 6(4);429-46. PMID: 2147378

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

Boos98a: Boos W (1998). "Binding protein-dependent ABC transport system for glycerol 3-phosphate of Escherichia coli." Methods Enzymol 1998;292;40-51. PMID: 9711545

Brzoska88: Brzoska P, Boos W (1988). "Characteristics of a ugp-encoded and phoB-dependent glycerophosphoryl diester phosphodiesterase which is physically dependent on the ugp transport system of Escherichia coli." J Bacteriol 1988;170(9);4125-35. PMID: 2842304

Brzoska89: Brzoska P, Boos W (1989). "The ugp-encoded glycerophosphoryldiester phosphodiesterase, a transport-related enzyme of Escherichia coli." FEMS Microbiol Rev 5(1-2);115-24. PMID: 2561262

Brzoska94: Brzoska P, Rimmele M, Brzostek K, Boos W (1994). "The pho regulon-dependent Ugp uptake system for glycerol-3-phosphate in Escherichia coli is trans inhibited by Pi." J Bacteriol 1994;176(1);15-20. PMID: 8282692

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

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

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Hekstra93: Hekstra D, Tommassen J (1993). "Functional exchangeability of the ABC proteins of the periplasmic binding protein-dependent transport systems Ugp and Mal of Escherichia coli." J Bacteriol 1993;175(20);6546-52. PMID: 8407831

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

Kasahara91: Kasahara M, Makino K, Amemura M, Nakata A, Shinagawa H (1991). "Dual regulation of the ugp operon by phosphate and carbon starvation at two interspaced promoters." J Bacteriol 1991;173(2);549-58. PMID: 1987150

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

Overduin88: Overduin P, Boos W, Tommassen J (1988). "Nucleotide sequence of the ugp genes of Escherichia coli K-12: homology to the maltose system." Mol Microbiol 2(6);767-75. PMID: 3062310

Saurin99: Saurin W, Hofnung M, Dassa E (1999). "Getting in or out: early segregation between importers and exporters in the evolution of ATP-binding cassette (ABC) transporters." J Mol Evol 1999;48(1);22-41. PMID: 9873074

Schweizer82: Schweizer H, Argast M, Boos W (1982). "Characteristics of a binding protein-dependent transport system for sn-glycerol-3-phosphate in Escherichia coli that is part of the pho regulon." J Bacteriol 150(3);1154-63. PMID: 7042685

Schweizer82a: Schweizer H, Grussenmeyer T, Boos W (1982). "Mapping of two ugp genes coding for the pho regulon-dependent sn-glycerol-3-phosphate transport system of Escherichia coli." J Bacteriol 1982;150(3);1164-71. PMID: 6281238

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

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

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

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

Wuttge12: Wuttge S, Bommer M, Jager F, Martins BM, Jacob S, Licht A, Scheffel F, Dobbek H, Schneider E (2012). "Determinants of substrate specificity and biochemical properties of the sn-glycerol-3-phosphate ATP binding cassette transporter (UgpB-AEC2 ) of Escherichia coli." Mol Microbiol 86(4);908-20. PMID: 23013274

Xavier95: Xavier KB, Kossmann M, Santos H, Boos W (1995). "Kinetic analysis by in vivo 31P nuclear magnetic resonance of internal Pi during the uptake of sn-glycerol-3-phosphate by the pho regulon-dependent Ugp system and the glp regulon-dependent GlpT system." J Bacteriol 177(3);699-704. PMID: 7836304

Yang09a: Yang K, Wang M, Metcalf WW (2009). "Uptake of glycerol-2-phosphate via the ugp-encoded transporter in Escherichia coli K-12." J Bacteriol 191(14);4667-70. PMID: 19429609

Other References Related to Gene Regulation

Marzan13: Marzan LW, Hasan CM, Shimizu K (2013). "Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant." Arch Microbiol 195(3);161-71. PMID: 23274360

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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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