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Conserved domains on  [gi|376319256|ref|NP_001243672|]
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glutamate receptor 3 isoform 3 precursor [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Periplasmic_Binding_Protein_type1 super family cl10011
Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This ...
 35-89 1.03e-35

Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins, the ligands are monosaccharides, including lactose, ribose, fructose, xylose, arabinose, galactose/glucose and other sugars, with a few exceptions. Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has six beta strands while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold.


The actual alignment was detected with superfamily member cd06387:

Pssm-ID: 471960 [Multi-domain]  Cd Length: 375  Bit Score: 126.29  E-value: 1.03e-35
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 376319256  35 SIGGLFMRNTVQEHSAFRFAVQLYNTNQNTTEKPFHLNYHVDHLDSSNSFSVTNA 89
Cdd:cd06387    1 SIGGLFMRNTVQEHSAFRFAVQLYNTNQNTTEKPFHLNYHVDHLDSSNSFSVTNA 55
 
Name Accession Description Interval E-value
PBP1_iGluR_AMPA_GluR3 cd06387
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR3 subunit ...
 35-89 1.03e-35

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR3 subunit of the AMPA receptor; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR3 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).


Pssm-ID: 380610 [Multi-domain]  Cd Length: 375  Bit Score: 126.29  E-value: 1.03e-35
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 376319256  35 SIGGLFMRNTVQEHSAFRFAVQLYNTNQNTTEKPFHLNYHVDHLDSSNSFSVTNA 89
Cdd:cd06387    1 SIGGLFMRNTVQEHSAFRFAVQLYNTNQNTTEKPFHLNYHVDHLDSSNSFSVTNA 55
 
Name Accession Description Interval E-value
PBP1_iGluR_AMPA_GluR3 cd06387
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR3 subunit ...
 35-89 1.03e-35

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR3 subunit of the AMPA receptor; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR3 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).


Pssm-ID: 380610 [Multi-domain]  Cd Length: 375  Bit Score: 126.29  E-value: 1.03e-35
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 376319256  35 SIGGLFMRNTVQEHSAFRFAVQLYNTNQNTTEKPFHLNYHVDHLDSSNSFSVTNA 89
Cdd:cd06387    1 SIGGLFMRNTVQEHSAFRFAVQLYNTNQNTTEKPFHLNYHVDHLDSSNSFSVTNA 55
PBP1_iGluR_N_LIVBP-like cd06351
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the NMDA, AMPA, ...
 35-89 3.17e-21

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the NMDA, AMPA, and kainate receptor subtypes of ionotropic glutamate receptors (iGluRs); N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the NMDA, AMPA, and kainate receptor subtypes of ionotropic glutamate receptors (iGluRs). While this N-terminal domain belongs to the periplasmic-binding fold type 1 superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type 2. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Glutamate mediates the majority of excitatory synaptic transmission in the central nervous system via two broad classes of ionotropic receptors characterized by their response to glutamate agonists: N-methyl-aspartate (NMDA) and non-NMDA receptors. NMDA receptors have intrinsically slow kinetics, are highly permeable to Ca2+, and are blocked by extracellular Mg2+ in a voltage-dependent manner. On the other hand, non-NMDA receptors have faster kinetics, are weakly permeable to Ca2+, and are not blocked by extracellular Mg2+. While non-NMDA receptors typically mediate excitatory synaptic responses at resting membrane potentials, NMDA receptors contribute to several forms of synaptic plasticity and are suggested to play an important role in the development of synaptic pathways.


Pssm-ID: 380574  Cd Length: 348  Bit Score: 87.40  E-value: 3.17e-21
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 376319256  35 SIGGLFMRNTVQEHSAFRFAVQLYNTNQNtTEKPFHLNYHVDHLDSSNSFSVTNA 89
Cdd:cd06351    1 HIGFIFEVNNEPAAKAFEVAVTYLKKNIN-TRYGLSVQYDSIEANKSNAFVLLEA 54
PBP1_iGluR_AMPA_GluR4 cd06388
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR4 subunit ...
 36-89 1.24e-16

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR4 subunit of the AMPA receptor; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR4 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).


Pssm-ID: 380611 [Multi-domain]  Cd Length: 373  Bit Score: 75.06  E-value: 1.24e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 376319256  36 IGGLFMRNTVQEHSAFRFAVQLYNTNQNTTEKPFHLNYHVDHLDSSNSFSVTNA 89
Cdd:cd06388    2 IGGLFIRNTDQEYTAFRLAIFLHNTSPNASEAPFNLVPHVDNIETANSFAVTNA 55
PBP1_iGluR_non_NMDA-like cd06368
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the non-NMDA ...
 35-90 9.07e-14

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the non-NMDA (N-methyl-D-aspartate) subtypes of ionotropic glutamate receptors; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the non-NMDA (N-methyl-D-asparate) subtypes of ionotropic glutamate receptors. While this N-terminal domain belongs to the periplasmic-binding fold type 1 superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type 2. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Glutamate mediates the majority of excitatory synaptic transmission in the central nervous system via two broad classes of ionotropic receptors, characterized by their response to glutamate agonists: N-methyl-D-aspartate (NMDA) and non-NMDA receptors. NMDA receptors have intrinsically slow kinetics, are highly permeable to Ca2+, and are blocked by extracellular Mg2+ in a voltage-dependent manner. Non-NMDA receptors have faster kinetics, are most often only weakly permeable to Ca2+, and are not blocked by extracellular Mg2+. While non-NMDA receptors typically mediate excitatory synaptic responses at resting membrane potentials, NMDA receptors contribute several forms of synaptic plasticity and are thought to play an important role in the development of synaptic pathways. Non-NMDA receptors include alpha-amino-3-hydroxy-5-methyl-4-isoxazole proprionate (AMPA) and kainate receptors.


Pssm-ID: 380591 [Multi-domain]  Cd Length: 339  Bit Score: 66.62  E-value: 9.07e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 376319256  35 SIGGLFM-RNTVQEHSAFRFAVQLYNTNQNtTEKPFHLNYHVDHLDSSNSFSVTN-AC 90
Cdd:cd06368    1 KIGAIFNeVNDAHERAAFRYAVERLNTNIV-KLAYFRITYSIEAIDSNSHFDATDkAC 57
PBP1_iGluR_AMPA cd06380
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the AMPA receptor; ...
 36-89 3.20e-13

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the AMPA receptor; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor, a member of the glutamate-receptor ion channels (iGluRs). AMPA receptors are the major mediators of excitatory synaptic transmission in the central nervous system. While this N-terminal domain belongs to the periplasmic-binding fold type 1 superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type 2. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. AMPA receptors consist of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important roles in mediating the rapid excitatory synaptic current.


Pssm-ID: 380603 [Multi-domain]  Cd Length: 390  Bit Score: 65.38  E-value: 3.20e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 376319256  36 IGGLFMRNTVQEHSAFRFAVQLYNTNQNTTEKPFHLNYHVDHLDsSNSFSVTNA 89
Cdd:cd06380    2 IGAIFDSGEDQVQTAFRYAIDRHNSNNNNRFRLFPLTERIDITN-ADSFSVSRA 54
PBP1_iGluR_AMPA_GluR2 cd06389
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR2 subunit ...
 36-89 4.43e-08

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR2 subunit of the AMPA receptor; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR2 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).


Pssm-ID: 380612 [Multi-domain]  Cd Length: 372  Bit Score: 50.40  E-value: 4.43e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 376319256  36 IGGLFMRNTVQEHSAFRFAVQLYNTNQnttekpFHLNYHVDHLDSSNSFSVTNA 89
Cdd:cd06389    2 IGGLFPRGADQEYSAFRVGMVQFSTSE------FRLTPHIDNLEVANSFAVTNA 49
PBP1_iGluR_AMPA_GluR1 cd06390
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR1 subunit ...
 36-87 3.31e-04

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR1 subunit of the AMPA receptor; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR1 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).


Pssm-ID: 380613 [Multi-domain]  Cd Length: 367  Bit Score: 39.15  E-value: 3.31e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 376319256  36 IGGLFMRNTVQEHSAFRFAVQLYNtnqntteKPFHLNYHVDHLDSSNSFSVT 87
Cdd:cd06390    2 IGGLFPNQQSQEHAAFRFALSQLT-------EPPKLLPQIDIVNISDSFEMT 46
PBP1_iGluR_Kainate cd06382
N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the kainate ...
 36-90 3.55e-04

N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the kainate receptors; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the kainate receptors, non-NMDA ionotropic receptors which respond to the neurotransmitter glutamate. While this N-terminal domain belongs to the periplasmic-binding fold type 1 superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type 2. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Kainate receptors have five subunits, GluR5, GluR6, GluR7, KA1 and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels activated by kainate and glutamate when expressed in heterologous systems. Kainate receptors are involved in excitatory neurotransmission by activating postsynaptic receptors and in inhibitory neurotransmission by modulating release of the inhibitory neurotransmitter GABA through a presynaptic mechanism. Kainate receptors are closely related to AMAP receptors. In contrast of AMPA receptors, kainate receptors play only a minor role in signaling at synapses and their function is not well defined.


Pssm-ID: 380605  Cd Length: 335  Bit Score: 39.13  E-value: 3.55e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 376319256  36 IGGLFMRNTVQEHSAFRFAVqlYNTNQNTTEKPFHLNYHVDHLDSSNSFSVTN-AC 90
Cdd:cd06382    2 IGGIFDEDDEDLEIAFKYAV--DRINRERTLPNTKLVPDIERVPRDDSFEASKkVC 55
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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