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	PROSITE documentation PDOC00439 [for PROSITE entry PS51343]

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.

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

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

• Sequences in UniProtKB/Swiss-Prot known to belong to this class: 55
  • detected by PS51343: 55 (true positives)
  • undetected by PS51343: 0 (false negative or 'partial')
• Other sequence(s) in UniProtKB/Swiss-Prot detected by PS51343:
  NONE.
• Domain architecture view of Swiss-Prot proteins matching PS51343
  
• Retrieve an alignment of UniProtKB/Swiss-Prot true positive hits:
  Clustal format, color, condensed view  /  Clustal format, color  /  Clustal format, plain text  /  Fasta format
• Retrieve the sequence logo from the alignment
• Taxonomic distribution of all UniProtKB (Swiss-Prot + TrEMBL) entries matching PS51343
• Retrieve a list of all UniProtKB (Swiss-Prot + TrEMBL) entries matching PS51343
• Scan UniProtKB (Swiss-Prot and/or TrEMBL) entries against PS51343
• View ligand binding statistics of PS51343
• Matching PDB structures: 1GNK 1PIL 1QY7 1UL3 ... [ALL]

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

• Consensus pattern:
  [ST]-x(3)-G-[DY]-G-[KR]-[IV]-[FW]-[LIVM]-x(2)-[LIVM]
• Sequences in UniProtKB/Swiss-Prot known to belong to this class: 55
  • detected by PS00638: 55 (true positives)
  • undetected by PS00638: 0 (false negative or 'partial')
• Other sequence(s) in UniProtKB/Swiss-Prot detected by PS00638:
  NONE.
• Retrieve an alignment of UniProtKB/Swiss-Prot true positive hits:
  Clustal format, color, condensed view  /  Clustal format, color  /  Clustal format, plain text  /  Fasta format
• Retrieve the sequence logo from the alignment
• Taxonomic distribution of all UniProtKB (Swiss-Prot + TrEMBL) entries matching PS00638
• Retrieve a list of all UniProtKB (Swiss-Prot + TrEMBL) entries matching PS00638
• Scan UniProtKB (Swiss-Prot and/or TrEMBL) entries against PS00638
• View ligand binding statistics of PS00638
• Matching PDB structures: 1GNK 1PIL 1QY7 1UL3 ... [ALL]

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

• Consensus pattern:
  Y-[KR]-G-[AS]-[AE]-Y
  The second Y is uridylated
• Sequences in UniProtKB/Swiss-Prot known to belong to this class: 34
  • detected by PS00496: 31 (true positives)
  • undetected by PS00496: 3 (3 false negatives and 0 'partial')
• Other sequence(s) in UniProtKB/Swiss-Prot detected by PS00496:
  12 false positives.
• Retrieve an alignment of UniProtKB/Swiss-Prot true positive hits:
  Clustal format, color, condensed view  /  Clustal format, color  /  Clustal format, plain text  /  Fasta format
• Retrieve the sequence logo from the alignment
• Taxonomic distribution of all UniProtKB (Swiss-Prot + TrEMBL) entries matching PS00496
• Retrieve a list of all UniProtKB (Swiss-Prot + TrEMBL) entries matching PS00496
• Scan UniProtKB (Swiss-Prot and/or TrEMBL) entries against PS00496
• View ligand binding statistics of PS00496
• Matching PDB structures: 1GNK 1PIL 1QY7 2JJ4 ... [ALL]

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

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