1LEH,1HRD,1B26,1V9L,1C1X


Conserved Protein Domain Family
NAD_bind_Glu_Leu_Phe_Val

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cd05211: NAD_bind_Glu_Leu_Phe_Val 
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NAD(P) binding domain of glutamate dehydrogenase, leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase
Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NAD(P)+. This subfamily includes glutamate, leucine, phenylalanine, and valine DHs. Glutamate DH is a multi-domain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia assimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. As in other NAD+-dependent DHs, monomers in this family have 2 domains separated by a deep cleft. Here the c-terminal domain contains a modified NAD-binding Rossmann fold with 7 rather than the usual 6 beta strands and one strand anti-parrallel to the others. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts.
Statistics
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PSSM-Id: 133450
View PSSM: cd05211
Aligned: 5 rows
Threshold Bit Score: 223.197
Threshold Setting Gi: 10120619
Created: 8-Nov-2004
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
NAD(P) binding
Conserved site includes 9 residues -Click on image for an interactive view with Cn3D
Feature 1:NAD(P) binding site [chemical binding site]
Evidence:
  • Structure:1CIX_B: Rhodococcus Phe DH binds NAD, contacts determined at 3.5A
    View structure with Cn3D
  • Structure:1V9L_F: Pyrobaculum islandicum Glu DH binds NAD, contacts determined at 3.5A
    View structure with Cn3D
  • Comment:GxGxxG NAD(P) binding pocket motif

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                      ###                    ##                      
1LEH_B    149 VTAYGVYRGMKAAAKeafgsdsLEGLAVSVQGLGNVAKALCKKLNTe--GAKLVVTDVnk-----------aAVSAAVAE 215 Bacillus sphaericus
1HRD_A    208 ATGYGSVYYVEAVMKhen--dtLVGKTVALAGFGNVAWGAAKKLAEl-gAKAVTLSGPdgyiydpegitteeKINYMLEM 284 Clostridium symbiosum
1B26_F    188 ATGRGVKVCAGLAMDvlg--idPKKATVAVQGFGNVGQFAALLISQelgSKVVAVSDSrggiynpegfdveeLIRYKKEH 265 Thermotoga maritima
1V9L_F    188 ATGFGVAVATREMAKklw--ggIEGKTVAIQGMGNVGRWTAYWLEKm-gAKVIAVSDIngvayrk-eglnveLIQKNKGL 263 Pyrobaculum island...
1C1X_B    152 TTAVGVFEAMKATVAhrg-lgsLDGLTVLVQGLGAVGGSLASLAAEa--GAQLLVADTdt-----------eRVAHAVAL 217 Rhodococcus sp.
Feature 1                                         ##                      # #                 
1LEH_B    216 egadavap--------------naiygvtcDIFAPCALGaVLNDFTIPQLk---AKVIAGSADNQLKdpRHGKYLHELg- 277 Bacillus sphaericus
1HRD_A    285 rasgrnkvqdyadkfgvqffpgekpwgqkvDIIMPCATQnDVDLEQAKKIvannVKYYIEVANMPTTn-EALRFLMQQpn 363 Clostridium symbiosum
1B26_F    266 gtvvtypkger--------itneelleldvDILVPAALEgAIHAGNAERIk---AKAVVEGANGPTTp-EADEILSRRg- 332 Thermotoga maritima
1V9L_F    264 tgpalvelfttkdna-efvknpdaifkldvDIFVPAAIEnVIRGDNAGLVk---ARLVVEGANGPTTp-EAERILYERg- 337 Pyrobaculum island...
1C1X_B    218 ghtavale---------------dvlstpcDVFAPCAMGgVITTEVARTLd---CSVVAGAANNVIAdeAASDILHARg- 278 Rhodococcus sp.
Feature 1                                                                                 
1LEH_B    278 IVYAPDYVINAGGVINVADELygyn-------rtraMKRVDGIYDSIEKIFAIskrd--gvpSYVAADRMAEERIA 344 Bacillus sphaericus
1HRD_A    364 MVVAPSKAVNAGGVLVSGFEMsqnserlswtaeevdSKLHQVMTDIHDGSAAAaeryglgynLVAGANIVGFQKIA 439 Clostridium symbiosum
1B26_F    333 ILVVPDILANAGGVTVSYFEWvqdlqsffwdldqvrNALEKMMKGAFNDVMKVkeky--nvdMRTAAYILAIDRVA 406 Thermotoga maritima
1V9L_F    338 VVVVPDILANAGGVIMSYLEWvenlqwyiwdeeetrKRLENIMVNNVERVYKRwqre-kgwtMRDAAIVTALERIY 412 Pyrobaculum islandicum
1C1X_B    279 ILYAPDFVANAGGAIHLVGREvlgws------esvvHERAVAIGDTLNQVFEIsdnd--gvtPDEAARTLAGRRAR 346 Rhodococcus sp.

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