PROSITE documentation PDOC00795
PTS EIIB domain profiles and cysteine phosphorylation site signature


The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [1,2] is a major carbohydrate transport system in bacteria. The PTS catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred to enzyme I (EI) of PTS which in turn transfers it to a phosphoryl carrier protein (HPr) (see <PDOC00318>). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease which consists of at least three structurally distinct domains (IIA, IIB, and IIC), [3] which can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII).

The first domain (IIA) (see <PDOC00528>), carries the first permease-specific phosphorylation site, an histidine which is phosphorylated by phospho-HPr. The second domain (IIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain (see <PDOC51103>). The IIC domain forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID (see <PDOC51108>), homologous to IIC, can be found in some PTSs, e.g. for mannose [1,3,4,5,6].

According to structural and sequence analyses, the PTS EIIB domain (EC can be divided in five groups [7,8,9,10].

  • The PTS EIIB type 1 domain, which is found in the Glucose class of PTS, has an average length of about 80 amino acids. It forms a split α/β sandwich composed of an antiparallel sheet (β 1 to β 4) and three α helices superimposed onto one side of the sheet (see <PDB:1IBA>). The phosphorylation site (Cys) is located at the end of the first β strand on a protrusion formed by the edge of β 1 and the reverse turn between β 1 and β 2 [7].
  • The PTS EIIB type 2 domain, which is found in the Mannitol class of PTS, has an average length of about 100 amino acids. It consists of a four stranded parallel β sheet flanked by two α helices (α 1 and 3) on one face and helix α 2 on the opposite face, with a characteristic Rossmann fold comprising two right-handed β-α-β motifs (see <PDB:1VKR>). The phosphorylation site (Cys) is located at the N-terminus of the domain, in the first β strand [8].
  • The PTS EIIB type 3 domain, which is found in the Lactose class of PTS, has an average length of about 100 amino acids. It is composed of a central four-stranded parallel open twisted β sheet, which is flanked by three α helices on the concave side and two on the convex side of the β sheet (see <PDB:1IIB>). The phosphorylation site (Cys) is located in the C-terminal end of the first β strand [9].
  • The PTS EIIB type 4 domain, which is found in the Mannose class of PTS, has an average length of about 160 amino acids. It has a central core of seven parallel β strands surrounded by a total of six α-helices. Three helices cover the front face, one the back face with the remaining two capping the central β sheet at the top and bottom (see <PDB:1NRZ>). The phosphorylation site (His) is located at the suface exposed loop between strand 1 and helix 1 [10].
  • The PTS EIIB type 5 domain, which is found in the Sorbitol class of PTS, has an average length of about 190 amino acids. The phosphorylation site (Cys) is located in the N-terminus of the domain.

The region around the phosphorylated cysteine of some PTS components is well conserved and can be used [11] as a signature pattern for the following IIB domains:

  • Arbutin-, cellobiose- and salicin-specific; IIB(Asc).
  • β-glucosides-specific; IIB(Bgl).
  • Glucose-specific; IIB(Glc).
  • N-acetylglucosamine-specific; IIB(Nag).
  • Sucrose-specific; IIB(Scr).
  • Maltose and glucose-specific (gene malX).
  • Trehalose-specific (gene treB).
  • Escherichia coli arbutin-like (gene glvB).
  • Bacillus subtilis sacX.

A EIIB-like type 2 domain can be found in bacterial transcriptional regulatory proteins [5]. In these cases, the EIIB-like domain is found in association with other domains like the DeoR-type HTH domain (see <PDOC00696>) or the PTS regulatory domain (a transcriptional antiterminator). It may possess a regulatory function, through its phosphorylation activity, or act as a simple phosphoryl donor.

We have developed a signature pattern for the phosphorylation site of EIIB domains. We also developed five profiles that cover the entire PTS EIIB domains. These profiles are directed respectively against Glucose class of PTS, Mannitol class of PTS, Lactose class of PTS, Mannose class of PTS, and Sorbitol class of PTS.

Last update:

May 2005 / Revision to a profile


Technical section

PROSITE methods (with tools and information) covered by this documentation:

PTS_EIIB_TYPE_1, PS51098; PTS_EIIB type-1 domain profile  (MATRIX)

PTS_EIIB_TYPE_2, PS51099; PTS_EIIB type-2 domain profile  (MATRIX)

PTS_EIIB_TYPE_3, PS51100; PTS_EIIB type-3 domain profile  (MATRIX)

PTS_EIIB_TYPE_4, PS51101; PTS_EIIB type-4 domain profile  (MATRIX)

PTS_EIIB_TYPE_5, PS51102; PTS_EIIB type-5 domain profile  (MATRIX)

PTS_EIIB_TYPE_1_CYS, PS01035; PTS EIIB domains cysteine phosphorylation site signature  (PATTERN)


1AuthorsPostma P.W. Lengeler J.W. Jacobson G.R.
TitlePhosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria.
SourceMicrobiol. Rev. 57:543-594(1993).
PubMed ID8246840

2AuthorsMeadow N.D. Fox D.K. Roseman S.
TitleThe bacterial phosphoenolpyruvate: glycose phosphotransferase system.
SourceAnnu. Rev. Biochem. 59:497-542(1990).
PubMed ID2197982

3AuthorsSaier M.H. Jr. Reizer J.
TitleProposed uniform nomenclature for the proteins and protein domains of the bacterial phosphoenolpyruvate: sugar phosphotransferase system.
SourceJ. Bacteriol. 174:1433-1438(1992).
PubMed ID1537788

4AuthorsSaier M.H. Jr. Reizer J.
TitleThe bacterial phosphotransferase system: new frontiers 30 years later.
SourceMol. Microbiol. 13:755-764(1994).
PubMed ID7815935

5AuthorsTchieu J.H. Norris V. Edwards J.S. Saier M.H. Jr.
TitleThe complete phosphotranferase system in Escherichia coli.
SourceJ. Mol. Microbiol. Biotechnol. 3:329-346(2001).
PubMed ID11361063

6AuthorsSaier M.H. Hvorup R.N. Barabote R.D.
TitleEvolution of the bacterial phosphotransferase system: from carriers and enzymes to group translocators.
SourceBiochem. Soc. Trans. 33:220-224(2005).
PubMed ID15667312

7AuthorsEberstadt M. Grdadolnik S.G. Gemmecker G. Kessler H. Buhr A. Erni B.
TitleSolution structure of the IIB domain of the glucose transporter of Escherichia coli.
SourceBiochemistry 35:11286-11292(1996).
PubMed ID8784182

8AuthorsLegler P.M. Cai M. Peterkofsky A. Clore G.M.
TitleThree-dimensional solution structure of the cytoplasmic B domain of the mannitol transporter IImannitol of the Escherichia coli phosphotransferase system.
SourceJ. Biol. Chem. 279:39115-39121(2004).
PubMed ID15258141

9Authorsvan Montfort R.L.M. Pijning T. Kalk K.H. Reizer J. Saier M.H. Jr. Thunnissen M.M.G.M. Robillard G.T. Dijkstra B.W.
SourceStructure 5:217-225(1997).

10AuthorsOrriss G.L. Erni B. Schirmer T.
SourceJ. Mol. Biol. 327:1111-1119(2003).

11AuthorsReizer J. Michotey V. Reizer A. Saier M.H. Jr.
TitleNovel phosphotransferase system genes revealed by bacterial genome analysis: unique, putative fructose- and glucoside-specific systems.
SourceProtein Sci. 3:440-450(1994).
PubMed ID8019415

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