PROSITE documentation PDOC00439
P-II protein family signatures and profile


P-II family proteins are regulators of nitrogen metabolism, with a length of ~110 amino acid residues, found throughout the bacteria and most archaea. P-II proteins sense cellular 2-oxoglutarate as an indicator for nitrogen limitation and bind and respond to ATP. The family is named after the P-II protein (gene glnB), a bacterial protein important for the control of glutamine synthetase [1,2,3]. In nitrogen-limiting conditions, when the ratio of glutamine to 2-ketoglutarate decreases, P-II is uridylylated on a tyrosine residue to form P-II-UMP. P-II-UMP allows the deadenylation of glutamine synthetase (GS), thus activating the enzyme. Conversely, in nitrogen excess, P-II-UMP is deuridylated and then promotes the adenylation of GS. P-II also indirectly controls the transcription of the GS gene (glnA) by preventing NR-II (ntrB) to phosphorylate NR-I (ntrC) which is the transcriptional activator of glnA. Once P-II is uridylylated, these events are reversed. The tyrosine which is uridylated is located in the T-loop in the central part of the protein.

Not all P-II family proteins have this site for sensing cellular glutamine [4]. In cyanobacteria, P-II seems to be phosphorylated on a serine residue rather than being uridylated. It has a different set of interacting proteins.

In methanogenic archaebacteria, the nitrogenase iron protein gene (nifH) is followed by two open reading frames highly similar to the eubacterial P-II protein [5]. These proteins could be involved in the regulation of nitrogen fixation.

In the red alga, Porphyra purpurea, there is a glnB homolog encoded in the chloroplast genome.

Other proteins highly similar to glnB are:

  • Bacillus subtilis protein nrgB [6].
  • Escherichia coli glnK [7].
  • Plant P-II protein, which is localized to the chloroplast [8].

We developed two signature patterns for P-II protein. The first one is a conserved stretch (in eubacteria) of six residues which contains the uridylated tyrosine, the other is derived from a conserved region in the C-terminal part of the P-II protein. We also developed a profile that covers the whole P-II protein.

Last update:

December 2007 / Text revised; profile added.


Technical section

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

PII_GLNB_DOM, PS51343; P-II protein family profile  (MATRIX)

PII_GLNB_CTER, PS00638; P-II protein C-terminal region signature  (PATTERN)

PII_GLNB_UMP, PS00496; P-II protein uridylation site  (PATTERN)


1AuthorsMagasanik B.
TitleRegulation of transcription of the glnALG operon of Escherichia coli by protein phosphorylation.
SourceBiochimie 71:1005-1012(1989).
PubMed ID2574599

2AuthorsHoltel A. Merrick M.
TitleIdentification of the Klebsiella pneumoniae glnB gene: nucleotide sequence of wild-type and mutant alleles.
SourceMol. Gen. Genet. 215:134-138(1988).
PubMed ID2907369

3AuthorsCheah E. Carr P.D. Suffolk P.M. Vasudevan S.G. Dixon N.E. Ollis D.L.
TitleStructure of the Escherichia coli signal transducing protein PII.
SourceStructure 2:981-990(1994).
PubMed ID7866749

4AuthorsLeigh J.A. Dodsworth J.A.
TitleNitrogen regulation in bacteria and archaea.
SourceAnnu. Rev. Microbiol. 61:349-377(2007).
PubMed ID17506680

5AuthorsSibold L. Henriquet M. Possot O. Aubert J.-P.
TitleNucleotide sequence of nifH regions from Methanobacterium ivanovii and Methanosarcina barkeri 227 and characterization of glnB-like genes.
SourceRes. Microbiol. 142:5-12(1991).
PubMed ID2068380

6AuthorsWray L.V. Jr. Atkinson M.R. Fisher S.H.
TitleThe nitrogen-regulated Bacillus subtilis nrgAB operon encodes a membrane protein and a protein highly similar to the Escherichia coli glnB-encoded PII protein.
SourceJ. Bacteriol. 176:108-114(1994).
PubMed ID8282685

7AuthorsAllikmets R. Gerrard B.C. Court D. Dean M.
TitleCloning and organization of the abc and mdl genes of Escherichia coli: relationship to eukaryotic multidrug resistance.
SourceGene 136:231-236(1993).
PubMed ID7904973

8AuthorsMizuno Y. Berenger B. Moorhead G.B. Ng K.K.
TitleCrystal structure of Arabidopsis PII reveals novel structural elements unique to plants.
SourceBiochemistry 46:1477-1483(2007).
PubMed ID17279613

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