Summary: Nitrogen regulatory protein P-II
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Pii nitrogen regulatory proteins Edit Wikipedia article
|Nitrogen regulatory protein P-II|
|SCOP2||1pil / SCOPe / SUPFAM|
The Nitrogen regulatory protein P-II family contains a series of homologous prokaryotic signalling proteins which are involved in the regulation of nitrogen metabolism. The proteins are post translationally modified via addition of a uridylyl group by the enzyme Uridylyltransferase. The presence or absence of this group modulates the behaviour of the protein. In turn, uridylation is controlled by cellular levels of alphaletoglutarate and ATP.
PII proteins exist in trimers in vivo and bind ATP in a cleft between the subunits. There are two flexible loops call the B-loop and T-loop which are involved in regulation of the protein. The T-loop contains a conserved tyrosine which is the site of uridyl attachment.
Following nitrogen starvation, increased intra-cellular concentrations of ammonia cause the de-uridylylation of GlnK. This then binds directly to the ammonia channel AmtB to block ammonia conduction.
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Nitrogen regulatory protein P-II Provide feedback
P-II modulates the activity of glutamine synthetase.
Cheah E, Carr PD, Suffolk PM, Vasudevan SG, Dixon NE, Ollis DL; , Structure 1994;2:981-990.: Structure of the Escherichia coli signal transducing protein P-II. PUBMED:7866749 EPMC:7866749
Internal database links
|SCOOP:||CdAMP_rec DUF190 DUF3240|
|Similarity to PfamA using HHSearch:||CdAMP_rec|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR002187
In Gram-negative bacteria, the activity and concentration of glutamine synthetase (GS) is regulated in response to nitrogen source availability. PII, a tetrameric protein encoded by the glnB gene, is a component of the adenylation cascade involved in the regulation of GS activity [ PUBMED:1702507 ]. 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 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.
P-II is a protein of about 110 amino acid residues extremely well conserved. The tyrosine which is uridylated is located in the central part of the protein. In cyanobacteria, P-II seems to be phosphorylated on a serine residue rather than being uridylated. In methanogenic archaebacteria, the nitrogenase iron protein gene (nifH) is followed by two open reading frames highly similar to the eubacterial P-II protein [ PUBMED:2068380 ]. These proteins could be involved in the regulation of nitrogen fixation. In the red alga, Porphyra purpurea, there is a glnB homologue encoded in the chloroplast genome.
Other proteins highly similar to glnB are:
- Bacillus subtilis protein nrgB [ PUBMED:8282685 ].
- Escherichia coli hypothetical protein ybaI [ PUBMED:7904973 ].
- GlnK from Archaea and bacteria, an homologue of GlnB protein, which regulates ammonium transport (Amt) proteins [ PUBMED:22039461 , PUBMED:17203075 ]
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||enzyme regulator activity (GO:0030234)|
|Biological process||regulation of nitrogen utilization (GO:0006808)|
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This family is a member of clan GlnB-like (CL0089), which has the following description:
The members of this clan are characterised by the fact the domains, each comprised of four beta-strand and two alpha helices, tend to form tetrameric structures .
The clan contains the following 12 members:CBD_PlyG CdAMP_rec CutA1 DUF190 DUF2007 DUF2179 DUF3240 HisG_C Nit_Regul_Hom NRho P-II Rhomboid_N
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|Number in seed:||75|
|Number in full:||11393|
|Average length of the domain:||107.3 aa|
|Average identity of full alignment:||47 %|
|Average coverage of the sequence by the domain:||81.09 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||25|
|Download:||download the raw HMM for this family|
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the P-II domain has been found. There are 206 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.