1GPJ


Conserved Protein Domain Family
NAD_bind_Glutamyl_tRNA_reduct

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cd05213: NAD_bind_Glutamyl_tRNA_reduct 
Click on image for an interactive view with Cn3D
NADP-binding domain of glutamyl-tRNA reductase
Glutamyl-tRNA reductase catalyzes the conversion of glutamyl-tRNA to glutamate-1-semialdehyde, initiating the synthesis of tetrapyrrole. Whereas tRNAs are generally associated with peptide bond formation in protein translation, here the tRNA activates glutamate in the initiation of tetrapyrrole biosynthesis in archaea, plants and many bacteria. In the first step, activated glutamate is reduced to glutamate-1-semi-aldehyde via the NADPH dependent glutamyl-tRNA reductase. Glutamyl-tRNA reductase forms a V-shaped dimer. Each monomer has 3 domains: an N-terminal catalytic domain, a classic nucleotide binding domain, and a C-terminal dimerization domain. Although the representative structure 1GPJ lacks a bound NADPH, a theoretical binding pocket has been described. (PMID 11172694). Amino acid dehydrogenase (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: 133452
View PSSM: cd05213
Aligned: 31 rows
Threshold Bit Score: 242.557
Threshold Setting Gi: 16611928
Created: 8-Sep-2005
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
putative NADPputative tRNAtRNA
Conserved site includes 3 residues -Click on image for an interactive view with Cn3D
Feature 1:putative NADP binding site [chemical binding site]
Evidence:
  • Comment:Postulated NADP binding site by analogy to tetrahydrofolate dehydrogenase/cyclohydrolase
  • Comment:GxGxxG NADP binding motif

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                       
1GPJ_A        4 LVSVGITHKeae----veeLEKArfes---deaVRDIVESFgl--sGSVLLQTSNRVEVYASGar------dRAEELGDL 68
gi 7387744    5 LAMIGVNVKtasre-hvarLEKEwe------khLDTIGYASr----GTVIIATCNRFEVYLDSp-------sRLVEDLAS 66
gi 20138246   7 LAAVILTYRevd----adtLGRVgee----mkkCIEILGVKr----PMFVLHTCGRVEAYLYNa--------SEEEINSV 66
gi 2495162    1 MIILKADYKky------nvSELEk---------LRMDEEKFyetfdNAILLQTCNRVEIIFDAd-------sLEEIKGIE 58
gi 1170204    2 ILNIRLDHKtsd----vktMETAsgri---eeiVGELEALGav--tEKVPLMTCNRVEYYLHVtg-----vpPEFDFNGF 67
gi 20138289  11 YIAIVYTYKtvgi---sklYEHYvk------dqELLLLKGLik--gEISVLQTCNRAETYLYTyn-----keEFKDFLQK 74
gi 30173027   3 LLVFGISYKtap----islRERVifspeniniaLNNLLKKSdi--lGGVILSTCNRTEVYLSIknfy-kakkIIILWLYK 75
gi 20138300  11 YCSILFTYKtig----isnLHLYyfr----eteIKSLKQLIn---aEFAILQTCNRVEIYLYSdtntlkevnKIIQYLNN 79
gi 13878528   4 LTLISWDFKrnnnffnqavLNPYe--------yWADILEKNgi--sRYVILLTCNRVEIYLRAg--------FPEDLEAM 65
gi 30315931   7 IIVIGVSHEnl------slLEREnfmrtrpkyiIERLYTEKki--nAYINLSTCLRTEFYIELnsni--kakEIKNLFSV 76
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                       
1GPJ_A       69 ih----------ddAWVKRgsEAVRHLFRVASGLESMMVGEQEILRQVKKAYDRAARLGtLDEALKIVFRRAINLGKRAR 138
gi 7387744   67 siasp-----ggegLVRLQgiDAARHLFRVASGLESQIIGDHEVLGQVRRAWLKSREKGfTTPLLDEVFHRALKTGARVR 141
gi 20138246  67 tlryr----ryaesIRVVRgvEAARHLFRVAAGLESMLIGETDILGQVEEAFDRQVKAGfTKGLLKTIVERAIRAGKRVR 142
gi 2495162   59 nidl------ekfdILFGD--KAIEHLFRVACGLESMIVGEDQILGQLKNAYLKAKEKGrISKKLEKIILKAIHTGQRAR 130
gi 1170204   68 --------------TVEKDe-DALLHLLRLASGLESMIIGEDQILGQIKAARLQALREGtCGPLLDMVFTKAVHVGQTVR 132
gi 20138289  75 ldeihgkqiskdamILKGE--DAVKHLFEVASGLDSLAIGEYEILRQLKESIEKSKKLGlSSEKLEFLFKNAIKVGRKIR 152
gi 30173027  76 ffndlki-keiknnFYSYIdnYAVSHLMRVTSGLDSMILGEHQILSQVKSAFFRSLKNKnISIDLQKLFESAFSVAKKIR 154
gi 20138300  80 ihnepi---gnqarVLCGK--DAAKHLFLVASGADSLSIGEYEILSQIRSTIDMFKKLGfSGKYLQIFFERAIKVGRKVR 154
gi 13878528  66 k------------pNVLHDe-EAIKHLMEVSSGLDSMSLGENEILKQVKEAYELSVRNGkVDKVLSLIFQKAIFVGKKVR 132
gi 30315931  77 d------------mIVKSRv-EAIEYLFKVGCGFYSVIKGEDQILAQVKGAYAEALENEhSSKFLNIIFNKSIELGKKFR 143
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                           # #  #                                      
1GPJ_A      139 EETRISEGAVSIGSAAVELAERELgs-lhDKTVLVVGAGEMGKTVAKSLVd-rGVRAVLVANRTyERAVELARDLGG--- 213
gi 7387744  142 SESAISSGGVGYSSAAVSLAASLLgggldGARVGIVGAGMAAVGIARALCtrwRPRVVAVFNRTpERGWEVAGKCRGves 221
gi 20138246 143 AETGISRGPAGLGSLSIIYVSQLLdl--tKSKVAVLGAGAVGAGLAKELAe-rGVAKLYILNRTlEKAVEIANKLGA--- 216
gi 2495162  131 VETKINEGGVSIGSAAVELAEKIFgl--eGKNVLLIGAGEMANLVIKALKe-kNIKAIIVANRTyEKAEKLAKELGG--- 204
gi 1170204  133 RKTKINRGSVSIGSAAVDLAESIHgd-lkCKKVLVIGAGKMGTLVARALAe-kHLKAIMVANRTyERAYQLACELGG--- 207
gi 20138289 153 QQTEISKGKTGIYALAVEYAKHVSnnnigNVKIAIVGAGEIGNKLALMLKn-eGAQNVTIFNRTyEKALEVANKYGF--- 228
gi 30173027 155 SETKIGSYSISIPYIICVLLKKIFis-ftEIKVMLIGSGTINELIAKQLFk-yKIKDLFISNRTiDHAKNLAIKVNG--- 229
gi 20138300 155 EETSISKGKVGIYSLAIDEAKKRFnd-fyDRRILVIGAGEMAQKITSMLHn-eGAKDVTIMNRTiEKAKQLALKFGY--- 229
gi 13878528 133 SETEISRGKVSVPSIVYDILSSRV-----VQKVLIIGNGMIAGEIAPYLS---GKFEVTIAGRNiDHVKDLASKYNY--- 201
gi 30315931 144 TKSMIAHNALSLEAISLKFIKSKFpn-ieDKNIFILGIGELAQDILTLLTk-eQLKNIYIANRTyHKAEQIKKEFDIv-- 219
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                       
1GPJ_A      214 EAVRFd--eLVDHLARsDVVVSATAAphp---vihVDDVREALrkrdrrsPILIIDIANPRd-VEEGVEniedVEVRTID 287
gi 7387744  222 LVLPLd--eLAKLINElDALFVAIAGstn----ilERGRVERGv-----sPRVIVDISNPP--VTPKVA----GRVFHMP 284
gi 20138246 217 EARPLtreeVQKCLMEcDVVFSSVHS---------LEYVIDRVpdg--avVKIIVDLGVPQt-VAPGLP----VRVVRLS 280
gi 2495162  205 MAIKFd--kLEEALRYaDIVISATGAp--------HPILNKERlkn--agKTIIIDIANPRd-TTDDIRelpdIFLFTID 271
gi 1170204  208 DAIHFd--rLNRALRDaDVVISATGSphy---iltRERVMDAVppe-rrsSIVMVDIANPRd-IEESVRel-gVRLFTID 279
gi 20138289 229 KAEPL----DFYKINNyDIVFVAIYY---------DKKINLPN-------PKLVIDLSVPQivLGNNVIt--lENLRSIS 286
gi 30173027 230 CVVEFn--eIFKNLNKmQVIITSTYSrkliitykiIKSIIEKNkn----kKIIFIDISIPRn-IDKKIKkitgVHLYTLE 302
gi 20138300 230 NYEKL----DLDKLGNfDVAFISIYHe--------NLRLENKW-------NTLIVDITVPPlfTGNNVIt--lEELERIS 288
gi 13878528 202 SYTTIn--dLHELIMRnDAIISATSSkt------pIIRREEMVe------GKLYIDLGNPRn-IEDKPG----ADIITID 262
gi 30315931 220 NIVDYr--eKYPKMIEaDVIISATSAphivveydkFVAQMKENk------DYLFIDLAVPRd-VDERLAnfknIEIYNLD 290
                       330
                ....*....|....*..
Feature 1                        
1GPJ_A      288 DLRVIARENLERRRKEI 304
gi 7387744  285 EVEEEAKRMMEERLRWI 301
gi 20138246 281 DLKQLAEKYSEARKQEA 297
gi 2495162  272 DLRLVAEENLKKRKEEI 288
gi 1170204  280 DLRGVAEENRKRREAEA 296
gi 20138289 287 DKIMETKILSLQKAEEL 303
gi 30173027 303 DLKDLITNNLEKRKNAA 319
gi 20138300 289 NLNFKAREEELAKINKL 305
gi 13878528 263 DIYSVSNRNGSARMESV 279
gi 30315931 291 DIWEVYHLNSMNRDKLL 307

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