{PDOC00439}
{PS00496; PII_GLNB_UMP}
{PS00638; PII_GLNB_CTER}
{PS51343; PII_GLNB_DOM}
{BEGIN}
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* 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.

-Consensus pattern: Y-[KR]-G-[AS]-[AE]-Y
                    [The second Y is uridylated]
-Sequences known to belong to this class detected by the pattern: ALL   glnB's
 from eubacteria.
-Other sequence(s) detected in Swiss-Prot: 5.

-Consensus pattern: [ST]-x(3)-G-[DY]-G-[KR]-[IV]-[FW]-[LIVM]-x(2)-[LIVM]
-Sequences known to belong to this class detected by the pattern: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Last update: December 2007 / Text revised; profile added.

[ 1] Magasanik B.
     "Regulation of transcription of the glnALG operon of Escherichia coli
     by protein phosphorylation."
     Biochimie 71:1005-1012(1989).
     PubMed=2574599
[ 2] Holtel A., Merrick M.
     "Identification of the Klebsiella pneumoniae glnB gene: nucleotide
     sequence of wild-type and mutant alleles."
     Mol. Gen. Genet. 215:134-138(1988).
     PubMed=2907369
[ 3] Cheah E., Carr P.D., Suffolk P.M., Vasudevan S.G., Dixon N.E.,
     Ollis D.L.
     "Structure of the Escherichia coli signal transducing protein PII."
     Structure 2:981-990(1994).
     PubMed=7866749
[ 4] Leigh J.A., Dodsworth J.A.
     "Nitrogen regulation in bacteria and archaea."
     Annu. Rev. Microbiol. 61:349-377(2007).
     PubMed=17506680; DOI=10.1146/annurev.micro.61.080706.093409
[ 5] Sibold L., Henriquet M., Possot O., Aubert J.-P.
     "Nucleotide sequence of nifH regions from Methanobacterium ivanovii
     and Methanosarcina barkeri 227 and characterization of glnB-like
     genes."
     Res. Microbiol. 142:5-12(1991).
     PubMed=2068380
[ 6] Wray L.V. Jr., Atkinson M.R., Fisher S.H.
     "The nitrogen-regulated Bacillus subtilis nrgAB operon encodes a
     membrane protein and a protein highly similar to the Escherichia coli
     glnB-encoded PII protein."
     J. Bacteriol. 176:108-114(1994).
     PubMed=8282685
[ 7] Allikmets R., Gerrard B.C., Court D., Dean M.
     "Cloning and organization of the abc and mdl genes of Escherichia
     coli: relationship to eukaryotic multidrug resistance."
     Gene 136:231-236(1993).
     PubMed=7904973
[ 8] Mizuno Y., Berenger B., Moorhead G.B., Ng K.K.
     "Crystal structure of Arabidopsis PII reveals novel structural
     elements unique to plants."
     Biochemistry 46:1477-1483(2007).
     PubMed=17279613; DOI=10.1021/bi062149e

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