Conserved Protein Domain Family
PBP1_iGluR_NMDA

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cd06367: PBP1_iGluR_NMDA 
N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors
N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. 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. The function of the NMDA subtype receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer comprising two NR1 and two NR2 (A, B, C, and D) or NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in the treatment of chronic pain.
Statistics
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PSSM-Id: 107362
View PSSM: cd06367
Aligned: 31 rows
Threshold Bit Score: 227.568
Threshold Setting Gi: 47216887
Created: 18-Dec-2006
Updated: 17-Jan-2013
Structure
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Aligned Rows:
 
putative
Feature 1:putative dimerization interface [polypeptide binding site]
Evidence:
  • Comment:based on sequence similarity to mGluR

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
gi 548377      25 KIVNIGAVLstr---------------khEQMFREAVNQANKrh----------------------gsWKIQLNATSvt- 66
gi 68164778    25 KIVNIGAVLstk---------------khEQIFREAVNQANKrh----------------------gtWKLQLNATSvt- 66
gi 24644257    37 STYNIGGVLsns---------------dsEEHFSTTIKHLNFdqq--------------------yvpRKVTYYDKTir- 80
gi 33243903    27 QVITIGASLsse---------------kmEFEFKQAVNALNRrh----------------------lkSRILFNSTTil- 68
gi 67043573    25 KIVNIGAVLstk---------------khEQIFREAVNQANKrh----------------------ftRKIQLNATSvt- 66
gi 94732623    22 KTVNIGAVLsqk---------------ryEQVFKDAVTQANNiy----------------------gkDKFKMNAISvt- 63
gi 25147808    21 YKVSVLIVSepn--------------qetFKELKVSVTAAFVevf---------------------gsTSYHLGNDTisa 65
gi 110758353   40 ETITIGLIVp------------------hTNFGRREYTKAVNrtvgalhksygknksksysfldkynfTQHAVQLRMms- 100
gi 62473388    99 EQLNIGLIAphtnfgkre--ylrsinnavTGLTKTRGAKLTFlkd--------------------ysfEQKNIHFDMms- 155
gi 118104429   46 GVAAAPRGEvaagardqrpvgvgerrpgpAPSPRDAILLAVAnlngv----------------agmlpYNLSLEVVMaie 109
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                               # ##  ##                                     #            
gi 548377      67 -----------------hKPNAIQMALSVCEDLISs-qVYAILVSHPptpndh--ftptpVSYTAGFYRIPVLGLTTrms 126
gi 68164778    67 -----------------hKPNAIQMALSVCEDLISs-qVYAILVSHPpapndh--ltptpVSYTAGFYRIPVIGLTTrms 126
gi 24644257    81 -----------------mDKNPIKTVFNVCDKLIEn-rVYAVVVSHEqtsgd---lspaaVSYTSGFYSIPVIGISSrda 139
gi 33243903    69 -----------------mDSNPIRSALDICDKLLAq-hVYTVVASHPnstdh----spisVSYTCGYYNIPVVGISArds 126
gi 67043573    67 -----------------hRPNAIQMALSVCEDLISs-qVYAILVSHPpaptdh--ltptpISYTAGFYRIPVIGLTTrms 126
gi 94732623    64 -----------------hKPNAIQMALSVCEDLISn-qVYAILVSHPpqsndh--ltptpVSYTAGFYRIPVVGLTTrms 123
gi 25147808    66 afv----------daksgDNRLELTQDIVCSQMLNh-sLASVIFSPLltsssrfidlvtsSAYTLSFYKLPVVGVMVrda 134
gi 110758353  101 -----------------lTPSPSEILKSLCNDFLPk-nVSAILYLMNyek--------ygRSTASAQYFLQLAGYLGipv 154
gi 62473388   156 -----------------lTPSPTAILSTLCKEFLRv-nVSAILYMMNneq--------fgHSTASAQYFLQLAGYLGipv 209
gi 118104429  110 agladlplfpfsspsaswSNDPVSFLQSLCHTVVVqgvSAILAFPQTrge-------mleLDFVSAALRIPVVSIVLgef 182
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                         #  #            
gi 548377     127 iy---------sdksiHLSFLRTVPPYSHQSSVWFEMMRvYSWNHIILLVSDDhegraaQKRLETLLEEREsk------- 190
gi 68164778   127 iy---------sdksiHLSFLRTVPPYSHQANVWFEMMRvFNWNHVILIVSDDhegraaQKKLETLLEEREskskkrnye 197
gi 24644257   140 af---------sdkniHVSFLRTVPPYYHQADVWLEMLShFAYTKVIIIHSSDtdgraiLGRFQTTSQTYYddvdv---- 206
gi 33243903   127 af---------sdvnvHKMFLRTVPPFAHQADVWLELLVnLTWHKVIFVYSADeegrsvLSRFQTLAEEHNir------- 190
gi 67043573   127 iy---------sdksiHLSFLRTVPPYSHQALVWFEMMRlFNWNHVILIVSDDhegraaQKKLETLLEEKEsk------- 190
gi 94732623   124 iy---------sdksiHLSFLRTVPPYSHQAQVWFDMMReFQWNHIILIVSDDhegraaQKRLETLLEEREtksknrnye 194
gi 25147808   135 ef---------skkniYPTFVRPTAPLSDEAFVFLHMLLsLKYRQVVVLSVKRdi---nADQFVEEFEKRRvefk----- 197
gi 110758353  155 iawnadnsglerrasqSNLQLQLAPSLEHQTAAMLSILErYKWHQFSVVTSQIaghddfVQAVRERISEMQdtf------ 228
gi 62473388   210 iswnadnsglerrasqSTLQLQLAPSIEHQSAAMLSILErYKWHQFSVVTSQIaghddfVQAVRERVAEMQehf------ 283
gi 118104429  183 pr---------rspnpLHLQMSLENSLSSDADITFSILAmNNWYNFSLMVCQEe----wNITDFLFLTQQSsk------- 242
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                             # #                                                         
gi 548377     191 --------------aEKVLQFDPGtk------nvTALLMEAKELEAR---VIILSAseddAATVYRAAAMLnmtgsgYVW 247
gi 68164778   198 nldqlsydnkrgpkaEKVLQFDPGtk------nvTSLLLEAKELEAR---VIILSAseddAATVYRSAAMLnmtgsgYVW 268
gi 24644257   207 -----------ratvELIVEFEPKle------sfTEHLIDMKTAQSR---VYLMYAstedAQVIFRDAGEYnmtgegHVW 266
gi 33243903   191 --------------iEPSVKYAPGek------nyTSVLAPILKHTSR---VILLSAstedAEVIYRDADVLgmtgegWAW 247
gi 67043573   191 --------------aDKVLQFEPGtk------nlTALLLEAKELEAR---VIILSAseddATAVYKSAAMLdmtgagYVW 247
gi 94732623   195 nldqlsfdnkrgpkaEKVLLFSQDtn-------lTALLQEAKELEAR---VIILSAsedeAAAIYKVARQLnmtgsgYVW 264
gi 25147808   198 ------------iivQRYIEVELNen------lnDTLAESFEEVTSN---IIVLFAkkddAVRIFANAGDLtg--kgKVW 254
gi 110758353  229 -------------kfTILNAILVTd---------PRDLMELVNSESR---VMLLYStreeAIRILGAAHDYkitgenYVW 283
gi 62473388   284 -------------kfTILNSIVVTr---------TSDLMELVNSEAR---VMLLYAtqteAITILRAAEEMkltgenYVW 338
gi 118104429  243 --------------fHLGSIINITanltstndllNYLQFYLESIKDTtstMVMFGCdmekTRRIFEITTRFgvmppeLHW 308
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
gi 548377     248 LVGERei-sgNALRYAPDGILGLQLing-knESAHISDAVGVVAQAVHElle-----kenITDPPRGCVGntni-----w 315
gi 68164778   269 LVGERei-sgNALRYAPDGVIGLQLing-knESAHISDAVAVVAQAVHDlfe-----kenITDPPRGCVGntni-----w 336
gi 24644257   267 IVTEQa----LFSNNTPDGVLGLQLeha-hsDKGHIRDSVYVLASAIKEmis-----netIAEAPKDCGDsavn-----w 331
gi 33243903   248 IVSEQa----FDAYNIPVGFLGVHLvng-tnEVNHIKDAVQVIGHAFWSlld-----tenISNPPTECKDidsw------ 311
gi 67043573   248 LVGERei-sgSALRYAPDGIIGLQLing-knESAHISDAVAVVAQAIHElfe-----menITDPPRGCVGntni-----w 315
gi 94732623   265 LVGERem-sgKALSEAPDGLLGLQLing-knESAHIYDAVAVVAQSIQElfe-----kenITEPPRGCVGntni-----w 332
gi 25147808   255 IVSESa----GEAHNVPNGSLGCRLgq---tAFSVLRDSFSILKSAMETifre----skiDIFPPVECDRdsvd-----a 318
gi 110758353  284 VVTQSvienlQTPSQFPIGMLGVHFdtstesLVNEITTAVKVYANGAEDflndp-ankdyTLNTKLSCEGresrwn-tgd 361
gi 62473388   339 VVSQSviekkDAHSQFPVGMLGVHFdtssaaLMNEISNAIKIYSYGVEAyltdpanrdrrLTTQSLSCEDegrgrwdnge 418
gi 118104429  309 IIGDSqnveeLRTEGLPLGLIAHGKttq-svFEHYVQDAMELVARAVAAatmiq--pelaLIPSTMNCMDtdekn----i 381
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
gi 548377     316 ktgPLFKRVLMsskyadgvTGRVEFNe-dGDRKFANYSIMnlq------nrkLVQVGIYngt------hviPNDRKIIWP 382
gi 68164778   337 ktgPLFKRVLMsskysegvTGRVEFNe-dGDRKFANYSIMnlq------nrkLVQVGIYngs------nvlTNDRKIIWP 403
gi 24644257   332 esgKRLFQYLKsrni-tgeTGQVAFDd-nGDRIYAGYDVInire-----qqkKHVVGKFsydsmrakmrmrINDSEIIWP 404
gi 33243903   312 tdgEKVYNELIktql-ngeTGQVSFNs-eGDRLNPMYDIMning-----nrrSMSVGLYghqek--vlglrMMGRNITWP 382
gi 67043573   316 ktgPLFKRVLMsskypdgvTGRIEFNe-dGDRKFANYSIMnlq------nrkLVQVGIFngs------yiiQNDRKIIWP 382
gi 94732623   333 ktgPLFKRVLMsskypdglTGRVEFNd-dGDRRFAHYSILnyq------ktrLVQVGVYngsq-----vvmNAQRKIIWP 400
gi 25147808   319 ewnSLQAPALLneic-gtsTSRVHFNd-kCERIGVEYDIInfh-------meRKQVGNMvgd------ilrLDEDSIEWA 383
gi 110758353  362 lffKYLKNVSVegd---qgKPNVEFTq-dGVLKSAELKIMnlrpgl-skqlvWEEIGVWkswe-----kegLDIKDIVWP 431
gi 62473388   419 iffKYLRNVSIegd---lnKPNIEFTa-dGDLRSAELKIMnlrpsannknlvWEEIGVWkswe-----tqkLDIRDIAWP 489
gi 118104429  382 tsgQYLSKFLAntsf-dglSGHIKVKgssVVSSENNFFIWnlqhdp-vgnpmWTRLGSWqe--------gkIVMDYGIWP 451

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