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3  structures 2142  species 0  interactions 5858  sequences 24  architectures

Family: GlnD_UR_UTase (PF08335)

Summary: GlnD PII-uridylyltransferase

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GlnD PII-uridylyltransferase Provide feedback

This is a family of bifunctional uridylyl-removing enzymes/uridylyltransferases (UR/UTases, GlnD) that are responsible for the modification ( EC:2.7.7.59) of the regulatory protein P-II, or GlnB (e.g. P05826 PF00543). In response to nitrogen limitation, these transferases (e.g. P27249) catalyse the uridylylation of the PII protein, which in turn stimulates deadenylylation of glutamine synthetase (GlnA). Deadenylylated glutamine synthetase is the more active form of the enzyme [1]. Moreover, uridylylated PII can act together with NtrB and NtrC to increase transcription of genes in the sigma54 regulon, which include glnA and other nitrogen-level controlled genes [2]. It has also been suggested that the product of the glnD gene is involved in other physiological functions such as control of iron metabolism in certain species [2]. The region described in this family is found in many of its members to be C-terminal to a nucleotidyltransferase domain (PF01909), and N-terminal to an HD domain (PF01966) and two ACT domains (PF01842) [3].

Literature references

  1. van Heeswijk WC, Rabenberg M, Westerhoff HV, Kahn D; , Mol Microbiol 1993;9:443-457.: The genes of the glutamine synthetase adenylylation cascade are not regulated by nitrogen in Escherichia coli. PUBMED:8412694 EPMC:8412694

  2. Graf J, Ruby EG; , Mol Microbiol 2000;37:168-179.: Novel effects of a transposon insertion in the Vibrio fischeri glnD gene: defects in iron uptake and symbiotic persistence in addition to nitrogen utilization. PUBMED:10931314 EPMC:10931314

  3. Perlova O, Nawroth R, Zellermann EM, Meletzus D; , Gene 2002;297:159-168.: Isolation and characterization of the glnD gene of Gluconacetobacter diazotrophicus, encoding a putative uridylyltransferase/uridylyl-removing enzyme. PUBMED:12384297 EPMC:12384297


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013546

This entry represents a region found in a family of nucleotide transferases that includes bifunctional uridylyl-removing enzymes/uridylyltransferases (UR/UTases, GlnD; EC) and glutamine-synthetase adenylyltransferases (GlnE; EC). The region described in this family is found in many of its members to be C-terminal to a nucleotidyltransferase domain, and N-terminal to an HD domain and two ACT domains [PUBMED:8412694].

Bifunctional uridylyl-removing enzymes/uridylyltransferases are responsible for the modification of the regulatory protein PII, or GlnB, thereby acting as the sensory component of the nitrogen regulation (ntr) system [PUBMED:11810255]. The ntr system modulates nitrogen metabolism in response to the prevailing nitrogen source and the requirements of the cell. During nitrogen fixation, ammonia and 2-oxoglutarate can be used to produce glutamate. In response to nitrogen limitation, these transferases catalyse the uridylylation of the PII protein, which in turn stimulates deadenylylation of glutamine synthetase (GlnA), leading to the activation of glutamate synthetase and to the stimulation of NtrC-dependent promoters [PUBMED:12384297]. Uridylylated PII can act together with NtrB and NtrC to increase transcription of genes in the sigma54 regulon, which include glnA and other nitrogen-level controlled genes [PUBMED:10931314]. Under high concentrations of fixed nitrogen, PII is de-uridylylated leading to the inactivation of the glutamate synthetase pathway and switching off NtrC-dependent promoters [PUBMED:11065377]. It has also been suggested that the product of the glnD gene is involved in other physiological functions such as control of iron metabolism in certain species [PUBMED:10931314].

Glutamine-synthetase adenylyltransferase is an adenylyl transferase comprised of an adenylylating domain and a deadenylylating domain which modulate glutamine synthetase (GS) activity, where GS plays an important role in nitrogen assimilation [PUBMED:18469098].

Gene Ontology

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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 KNTase_C (CL0291), which contains the following 8 members:

DUF294_C DUF4145 DUF86 GlnD_UR_UTase HEPN KNTase_C NTase_sub_bind PaREP1

Alignments

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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
(122)
Full
(5858)
Representative proteomes NCBI
(4628)
Meta
(1176)
RP15
(366)
RP35
(832)
RP55
(1128)
RP75
(1374)
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Format an alignment

  Seed
(122)
Full
(5858)
Representative proteomes NCBI
(4628)
Meta
(1176)
RP15
(366)
RP35
(832)
RP55
(1128)
RP75
(1374)
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
(122)
Full
(5858)
Representative proteomes NCBI
(4628)
Meta
(1176)
RP15
(366)
RP35
(832)
RP55
(1128)
RP75
(1374)
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:

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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.

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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.

Curation View help on the curation process

Seed source: Pfam-B_2147 (release 18.0)
Previous IDs: none
Type: Family
Author: Fenech M
Number in seed: 122
Number in full: 5858
Average length of the domain: 134.10 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 21.87 %

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 20.5 20.5
Trusted cut-off 20.5 20.5
Noise cut-off 20.2 20.4
Model length: 142
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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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 GlnD_UR_UTase domain has been found. There are 3 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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