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149  structures 2688  species 3  interactions 4823  sequences 7  architectures

Family: P-II (PF00543)

Summary: Nitrogen regulatory protein P-II

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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 9 members:

CutA1 DUF190 DUF2007 DUF3240 DUF3582 DUF970 HisG_C Nit_Regul_Hom P-II

Alignments

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(93)
Full
(4823)
Representative proteomes NCBI
(2996)
Meta
(1680)
RP15
(486)
RP35
(973)
RP55
(1256)
RP75
(1478)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(93)
Full
(4823)
Representative proteomes NCBI
(2996)
Meta
(1680)
RP15
(486)
RP35
(973)
RP55
(1256)
RP75
(1478)
Alignment:
Format:
Order:
Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(93)
Full
(4823)
Representative proteomes NCBI
(2996)
Meta
(1680)
RP15
(486)
RP35
(973)
RP55
(1256)
RP75
(1478)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

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

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

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...

Trees

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.

Note: You can also download the data file for the tree.

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.

Curation View help on the curation process

Seed source: SCOP
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 93
Number in full: 4823
Average length of the domain: 101.60 aa
Average identity of full alignment: 53 %
Average coverage of the sequence by the domain: 82.59 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.4 21.4
Trusted cut-off 21.4 21.4
Noise cut-off 21.3 21.3
Model length: 102
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 3 interactions for this family. More...

P-II AA_kinase Ammonium_transp

Structures

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 149 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 seqence.

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