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Conserved domains on  [gi|2277417927|ref|XP_040225980|]
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uncharacterized protein LOC120951371 [Anopheles coluzzii]

Protein Classification

type 2 periplasmic-binding domain-containing protein( domain architecture ID 229383)

type 2 periplasmic-binding protein (PBP2) is typically comprised of two globular subdomains connected by a flexible hinge; it binds its ligand in the cleft between these domains in a manner resembling a Venus flytrap; similar to the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Periplasmic_Binding_Protein_Type_2 super family cl21456
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
 223-343 1.21e-03

Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1 (PBP1), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The origin of PBP module can be traced across the distant phyla, including eukaryotes, archebacteria, and prokaryotes. The majority of PBP2 proteins are involved in the uptake of a variety of soluble substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. The substrate binding domain of the LysR transcriptional regulators and the oligopeptide-like transport systems also contain the type 2 periplasmic binding fold and thus they are significantly homologous to that of the PBP2; however, these two families are grouped into a separate hierarchy of the PBP2 superfamily due to the large number of protein sequences.


The actual alignment was detected with superfamily member cd13685:

Pssm-ID: 473866 [Multi-domain]  Cd Length: 252  Bit Score: 41.02  E-value: 1.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277417927 223 LVIGTIHIIPCSIIERDGPGGSTTHKGIEVSQVDDLSRRFNFTPEYRISNGsTRWGFARAVNS-TGLMGWIQRGEVDFGL 301
Cdd:cd13685     4 LRVTTILEPPFVMKKRDSLSGNPRFEGYCIDLLEELAKILGFDYEIYLVPD-GKYGSRDENGNwNGMIGELVRGEADIAV 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2277417927 302 GSIGISLSR---VQHLRPgiasrFGQLAMAIPPKRPDS--SVEKLIK 343
Cdd:cd13685    83 APLTITAEReevVDFTKP-----FMDTGISILMRKPTPieSLEDLAK 124
 
Name Accession Description Interval E-value
PBP2_iGluR_non_NMDA_like cd13685
The ligand-binding domain of non-NMDA (N-methyl-D-aspartate) type ionotropic glutamate ...
 223-343 1.21e-03

The ligand-binding domain of non-NMDA (N-methyl-D-aspartate) type ionotropic glutamate receptors, a member of the type 2 periplasmic-binding fold protein superfamily; This subfamily represents the ligand-binding domain of non-NMDA (N-methyl-D-aspartate) type ionotropic glutamate receptors including AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid) receptors (GluR1-4), kainate receptors (GluR5-7 and KA1/2), and orphan receptors delta 1/2. iGluRs form tetrameric ligand-gated ion channels, which are concentrated at postsynaptic sites in excitatory synapses where they fulfill a variety of different functions. While this ligand-binding domain of iGluRs is structurally homologous to the periplasmic binding fold type II superfamily, the N-terminal leucine/isoleucine/valine#binding protein (LIVBP)-like domain belongs to the periplasmic-binding fold type I.


Pssm-ID: 270403 [Multi-domain]  Cd Length: 252  Bit Score: 41.02  E-value: 1.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277417927 223 LVIGTIHIIPCSIIERDGPGGSTTHKGIEVSQVDDLSRRFNFTPEYRISNGsTRWGFARAVNS-TGLMGWIQRGEVDFGL 301
Cdd:cd13685     4 LRVTTILEPPFVMKKRDSLSGNPRFEGYCIDLLEELAKILGFDYEIYLVPD-GKYGSRDENGNwNGMIGELVRGEADIAV 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2277417927 302 GSIGISLSR---VQHLRPgiasrFGQLAMAIPPKRPDS--SVEKLIK 343
Cdd:cd13685    83 APLTITAEReevVDFTKP-----FMDTGISILMRKPTPieSLEDLAK 124
 
Name Accession Description Interval E-value
PBP2_iGluR_non_NMDA_like cd13685
The ligand-binding domain of non-NMDA (N-methyl-D-aspartate) type ionotropic glutamate ...
 223-343 1.21e-03

The ligand-binding domain of non-NMDA (N-methyl-D-aspartate) type ionotropic glutamate receptors, a member of the type 2 periplasmic-binding fold protein superfamily; This subfamily represents the ligand-binding domain of non-NMDA (N-methyl-D-aspartate) type ionotropic glutamate receptors including AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid) receptors (GluR1-4), kainate receptors (GluR5-7 and KA1/2), and orphan receptors delta 1/2. iGluRs form tetrameric ligand-gated ion channels, which are concentrated at postsynaptic sites in excitatory synapses where they fulfill a variety of different functions. While this ligand-binding domain of iGluRs is structurally homologous to the periplasmic binding fold type II superfamily, the N-terminal leucine/isoleucine/valine#binding protein (LIVBP)-like domain belongs to the periplasmic-binding fold type I.


Pssm-ID: 270403 [Multi-domain]  Cd Length: 252  Bit Score: 41.02  E-value: 1.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277417927 223 LVIGTIHIIPCSIIERDGPGGSTTHKGIEVSQVDDLSRRFNFTPEYRISNGsTRWGFARAVNS-TGLMGWIQRGEVDFGL 301
Cdd:cd13685     4 LRVTTILEPPFVMKKRDSLSGNPRFEGYCIDLLEELAKILGFDYEIYLVPD-GKYGSRDENGNwNGMIGELVRGEADIAV 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2277417927 302 GSIGISLSR---VQHLRPgiasrFGQLAMAIPPKRPDS--SVEKLIK 343
Cdd:cd13685    83 APLTITAEReevVDFTKP-----FMDTGISILMRKPTPieSLEDLAK 124
PBP2_iGluR_ligand_binding cd00998
The ligand-binding domain of ionotropic glutamate receptor family, a member of the periplasmic ...
 223-310 9.62e-03

The ligand-binding domain of ionotropic glutamate receptor family, a member of the periplasmic binding protein type II superfamily; This subfamily represents the ligand binding of ionotropic glutamate receptors. iGluRs are heterotetrameric ion channels that comprises of three functionally distinct subtypes based on their pharmacology and structural similarities: AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid), NMDA (N-methyl-D-aspartate), and kainate receptors. All three types of channels are also activated by the physiological neurotransmitter, glutamate. iGluRs are concentrated at postsynaptic sites, where they exert a variety of different functions. While this ligand-binding domain of iGluRs is structurally homologous to the periplasmic binding fold type II superfamily, the N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain belongs to the periplasmic-binding fold type I.


Pssm-ID: 270219 [Multi-domain]  Cd Length: 243  Bit Score: 38.12  E-value: 9.62e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277417927 223 LVIGTIHIIPCSIIER--DGPGGSTTHKGIEVSQVDDLSRRFNFTPEYRISNGSTrWGFARAVNSTGLMGWIQRGEVDFG 300
Cdd:cd00998     3 LKVVVPLEPPFVMFVTgsNAVTGNGRFEGYCIDLLKELSQSLGFTYEYYLVPDGK-FGAPVNGSWNGMVGEVVRGEADLA 81

                          90
                  ....*....|
gi 2277417927 301 LGSIGISLSR 310
Cdd:cd00998    82 VGPITITSER 91
 
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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