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206  structures 5473  species 0  interactions 11393  sequences 16  architectures

Family: P-II (PF00543)

Summary: Nitrogen regulatory protein P-II

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Pii nitrogen regulatory proteins". More...

Pii nitrogen regulatory proteins Edit Wikipedia article

Nitrogen regulatory protein P-II
GlnB protein from E.coli. PDB 2pii
Pfam clanCL0089

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.

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Nitrogen regulatory protein P-II Provide feedback

P-II modulates the activity of glutamine synthetase.

Literature references

  1. 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

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:

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

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 [1].

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


We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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Representative proteomes UniProt

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...


This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

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Seed source: SCOP
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
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 information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 25.0 25.0
Noise cut-off 24.9 24.9
Model length: 108
Family (HMM) version: 25
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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.

Protein Predicted structure External Information
A0A0H3GKJ1 View 3D Structure Click here
A0A0H3GW77 View 3D Structure Click here
A0A0R0KN50 View 3D Structure Click here
C6TCD9 View 3D Structure Click here
K0F4R5 View 3D Structure Click here
K7MHS7 View 3D Structure Click here
O26758 View 3D Structure Click here
O26760 View 3D Structure Click here
O28524 View 3D Structure Click here
O28527 View 3D Structure Click here
O29284 View 3D Structure Click here
O30794 View 3D Structure Click here
O54053 View 3D Structure Click here
O66513 View 3D Structure Click here
P0A3F4 View 3D Structure Click here
P0A9Z1 View 3D Structure Click here
P0A9Z3 View 3D Structure Click here
P0A9Z4 View 3D Structure Click here
P0A9Z6 View 3D Structure Click here
P0AC55 View 3D Structure Click here
P0AC57 View 3D Structure Click here
P0AC58 View 3D Structure Click here
P0CW45 View 3D Structure Click here
P0CW47 View 3D Structure Click here
P14179 View 3D Structure Click here
P43795 View 3D Structure Click here
P9WN31 View 3D Structure Click here
Q07428 View 3D Structure Click here
Q32D19 View 3D Structure Click here
Q32JA7 View 3D Structure Click here
Q52905 View 3D Structure Click here
Q53044 View 3D Structure Click here
Q55247 View 3D Structure Click here
Q58740 View 3D Structure Click here
Q5F7J5 View 3D Structure Click here
Q60381 View 3D Structure Click here
Q6AUR2 View 3D Structure Click here
Q7CR20 View 3D Structure Click here
Q8PYW7 View 3D Structure Click here
Q9CJK1 View 3D Structure Click here