PROSITE documentation PDOC00439P-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.
-------------------------------------------------------------------------------
PROSITE methods (with tools and information) covered by this documentation:
1 | Authors | Magasanik B. |
Title | Regulation of transcription of the glnALG operon of Escherichia coli by protein phosphorylation. | |
Source | Biochimie 71:1005-1012(1989). | |
PubMed ID | 2574599 |
2 | Authors | Holtel A. Merrick M. |
Title | Identification of the Klebsiella pneumoniae glnB gene: nucleotide sequence of wild-type and mutant alleles. | |
Source | Mol. Gen. Genet. 215:134-138(1988). | |
PubMed ID | 2907369 |
3 | Authors | Cheah E. Carr P.D. Suffolk P.M. Vasudevan S.G. Dixon N.E. Ollis D.L. |
Title | Structure of the Escherichia coli signal transducing protein PII. | |
Source | Structure 2:981-990(1994). | |
PubMed ID | 7866749 |
4 | Authors | Leigh J.A. Dodsworth J.A. |
Title | Nitrogen regulation in bacteria and archaea. | |
Source | Annu. Rev. Microbiol. 61:349-377(2007). | |
PubMed ID | 17506680 | |
DOI | 10.1146/annurev.micro.61.080706.093409 |
5 | Authors | Sibold L. Henriquet M. Possot O. Aubert J.-P. |
Title | Nucleotide sequence of nifH regions from Methanobacterium ivanovii and Methanosarcina barkeri 227 and characterization of glnB-like genes. | |
Source | Res. Microbiol. 142:5-12(1991). | |
PubMed ID | 2068380 |
6 | Authors | Wray L.V. Jr. Atkinson M.R. Fisher S.H. |
Title | The nitrogen-regulated Bacillus subtilis nrgAB operon encodes a membrane protein and a protein highly similar to the Escherichia coli glnB-encoded PII protein. | |
Source | J. Bacteriol. 176:108-114(1994). | |
PubMed ID | 8282685 |
7 | Authors | Allikmets R. Gerrard B.C. Court D. Dean M. |
Title | Cloning and organization of the abc and mdl genes of Escherichia coli: relationship to eukaryotic multidrug resistance. | |
Source | Gene 136:231-236(1993). | |
PubMed ID | 7904973 |
8 | Authors | Mizuno Y. Berenger B. Moorhead G.B. Ng K.K. |
Title | Crystal structure of Arabidopsis PII reveals novel structural elements unique to plants. | |
Source | Biochemistry 46:1477-1483(2007). | |
PubMed ID | 17279613 | |
DOI | 10.1021/bi062149e |
PROSITE is copyrighted by the SIB Swiss Institute of Bioinformatics and distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives (CC BY-NC-ND 4.0) License, see prosite_license.html.
View entry in original PROSITE document format
View entry in raw text format (no links)