Summary: Ligated ion channel L-glutamate- and glycine-binding site
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Ligated ion channel L-glutamate- and glycine-binding site Provide feedback
This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine [2]. It is found in association with Lig_chan, PF00060.
Literature references
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Ishii T, Moriyoshi K, Sugihara H, Sakurada K, Kadotani H, Yokoi M, Akazawa C, Shigemoto R, Mizuno N, Masu M, et al.; , J Biol Chem. 1993;268:2836-2843.: Molecular characterization of the family of the N-methyl-D-aspartate receptor subunits. PUBMED:8428958 EPMC:8428958
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Yamakura T, Shimoji K; , Prog Neurobiol. 1999;59:279-298.: Subunit- and site-specific pharmacology of the NMDA receptor channel. PUBMED:10465381 EPMC:10465381
Internal database links
SCOOP: | ANF_receptor Lig_chan NMT1 OpuAC Phosphonate-bd SBP_bac_3 |
Similarity to PfamA using HHSearch: | SBP_bac_3 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR019594
This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and binds L-glutamate and glycine in the ionotropic glutamate receptor NMDA [PUBMED:10465381, PUBMED:8428958]. It is found in association with INTERPRO.
Ionotropic Receptors (IRs) are a variant subfamily of the Ionotropic glutamate receptors (iGluRs). In IRs, the ligand binding domain lacks one or more residues that directly contact the glutamate ligand in iGluRs [PUBMED:20808886].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Cellular component | membrane (GO:0016020) |
Molecular function | ionotropic glutamate receptor activity (GO:0004970) |
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 PBP (CL0177), which has the following description:
Periplasmic binding proteins (PBPs) consist of two large lobes that close around the bound ligand. This architecture is reiterated in transcriptional regulators, such as the lac repressors. In the process of evolution, genes encoding the PBPs have fused with genes for integral membrane proteins. Thus, diverse mammalian receptors contain extracellular ligand binding domains that are homologous to the PBPs; these include glutamate/glycine-gated ion channels such as the NMDA receptor, G protein-coupled receptors, including metabotropic glutamate, GABA-B, calcium sensing, and pheromone receptors, and atrial natriuretic peptide-guanylate cyclase receptors [2].
The clan contains the following 27 members:
DctP DUF3834 HisG Lig_chan-Glu_bd Lipoprotein_8 Lipoprotein_9 LysR_substrate Mycoplasma_p37 NMT1 NMT1_2 NMT1_3 OpuAC PBP_like PBP_like_2 PDT Phosphonate-bd Porphobil_deam SBP_bac_1 SBP_bac_11 SBP_bac_3 SBP_bac_5 SBP_bac_6 SBP_bac_8 TctC Transferrin VitK2_biosynth YhfZ_CAlignments
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, the UniProtKB sequence database, 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 (108) |
Full (8489) |
Representative proteomes | UniProt (14089) |
NCBI (69233) |
Meta (793) |
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RP15 (1489) |
RP35 (2980) |
RP55 (6012) |
RP75 (8874) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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not generated,
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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 (108) |
Full (8489) |
Representative proteomes | UniProt (14089) |
NCBI (69233) |
Meta (793) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (1489) |
RP35 (2980) |
RP55 (6012) |
RP75 (8874) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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
Seed source: | Pfam-B_203 (release 22.0) |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Coggill P |
Number in seed: | 108 |
Number in full: | 8489 |
Average length of the domain: | 112.90 aa |
Average identity of full alignment: | 39 % |
Average coverage of the sequence by the domain: | 13.08 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 116 | ||||||||||||
Family (HMM) version: | 10 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
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 Lig_chan-Glu_bd domain has been found. There are 1169 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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