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15  structures 3044  species 3  interactions 3372  sequences 34  architectures

Family: Glu_syn_central (PF04898)

Summary: Glutamate synthase central domain

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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.

Glutamate synthase central domain Provide feedback

The central domain of glutamate synthase connects the amino terminal amidotransferase domain with the FMN-binding domain and has an alpha / beta overall topology [1]. This domain appears to be a rudimentary form of the FMN-binding TIM barrel according to SCOP.

Literature references

  1. van den Heuvel RH, Ferrari D, Bossi RT, Ravasio S, Curti B, Vanoni MA, Florencio FJ, Mattevi A; , J Biol Chem 2002;277:24579-24583.: Structural studies on the synchronization of catalytic centers in glutamate synthase. PUBMED:11967268 EPMC:11967268


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006982

Glutamate synthase (GltS)1 is a key enzyme in the early stages of the assimilation of ammonia in bacteria, yeasts, and plants. In bacteria, L-glutamate is involved in osmoregulation, is the precursor for other amino acids, and can be the precursor for haem biosynthesis. In plants, GltS is especially essential in the reassimilation of ammonia released by photorespiration. On the basis of the amino acid sequence and the nature of the electron donor, three different classes of GltS can de defined as follows: 1) ferredoxin-dependent GltS (Fd-GltS), 2) NADPH-dependent GltS (NADPH-GltS), and 3) NADH-dependent GltS (properties of the three classes have been reviewed extensively [PUBMED:10357231]). The enzyme is a complex iron-sulphur flavoprotein catalysing the reductive transfer of the amido nitrogen from L-glutamine to 2-oxoglutarate to form two molecules of L-glutamate via intramolecular channelling of ammonia from the amidotransferase domain to the FMN-binding domain.

Reaction of amidotransferase domain:

L-glutamine + H2O = L-glutamate + NH3

Reactions of FMN-binding domain:

2-oxoglutarate + NH3 = 2-iminoglutarate + H2O 2e + FMNox = FMNred 2-iminoglutarate + FMNred = L-glutamate + FMNox The central domain of glutamate synthase connects the N-terminal amidotransferase domain with the FMN-binding domain and has an alpha/beta overall topology [PUBMED:11967268].

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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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
(37)
Full
(3372)
Representative proteomes NCBI
(2992)
Meta
(3369)
RP15
(289)
RP35
(615)
RP55
(816)
RP75
(950)
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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
(37)
Full
(3372)
Representative proteomes NCBI
(2992)
Meta
(3369)
RP15
(289)
RP35
(615)
RP55
(816)
RP75
(950)
Alignment:
Format:
Order:
Sequence:
Gaps:
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Download options

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
(37)
Full
(3372)
Representative proteomes NCBI
(2992)
Meta
(3369)
RP15
(289)
RP35
(615)
RP55
(816)
RP75
(950)
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.

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: Pfam-B_455 (release 7.6)
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 37
Number in full: 3372
Average length of the domain: 283.90 aa
Average identity of full alignment: 42 %
Average coverage of the sequence by the domain: 18.60 %

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 21.5 21.5
Trusted cut-off 21.6 21.5
Noise cut-off 21.3 21.4
Model length: 288
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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Interactions

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

GATase_2 GXGXG Glu_synthase

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 Glu_syn_central domain has been found. There are 15 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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