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: 2-Oct-2020
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:
Feature 1                                                                                     
1GPJ_A      4 LVSVGITHKeae----veeLEKArfes---deaVRDIVESFgl--sGSVLLQTSNRVEVYASGar------dRAEELGDL 68  Methanopyrus kandleri
Q9Y9J2      5 LAMIGVNVKtasre-hvarLEKEwe------khLDTIGYASr----GTVIIATCNRFEVYLDSp-------sRLVEDLAS 66  Aeropyrum pernix
Q8ZYV6      7 LAAVILTYRevd----adtLGRVgee----mkkCIEILGVKr----PMFVLHTCGRVEAYLYNa--------SEEEINSV 66  Pyrobaculum aeroph...
Q60172      1 MIILKADYKky------nvSELEk---------LRMDEEKFyetfdNAILLQTCNRVEIIFDAd-------sLEEIKGIE 58  Methanocaldococcus...
P42809      2 ILNIRLDHKtsd----vktMETAsgri---eeiVGELEALGav--tEKVPLMTCNRVEYYLHVtg-----vpPEFDFNGF 67  Methanothermobacte...
Q976H4     11 YIAIVYTYKtvgi---sklYEHYvk------dqELLLLKGLik--gEISVLQTCNRAETYLYTyn-----keEFKDFLQK 74  Sulfolobus tokodaii
Q8D2K8      3 LLVFGISYKtap----islRERVifspeniniaLNNLLKKSdi--lGGVILSTCNRTEVYLSIknfy-kakkIIILWLYK 75  Wigglesworthia glo...
Q980U7     11 YCSILFTYKtig----isnLHLYyfr----eteIKSLKQLIn---aEFAILQTCNRVEIYLYSdtntlkevnKIIQYLNN 79  Sulfolobus solfata...
Q9HKR0      4 LTLISWDFKrnnnffnqavLNPYe--------yWADILEKNgi--sRYVILLTCNRVEIYLRAg--------FPEDLEAM 65  Thermoplasma acido...
Q8R687      7 IIVIGVSHEnl------slLEREnfmrtrpkyiIERLYTEKki--nAYINLSTCLRTEFYIELnsni--kakEIKNLFSV 76  Fusobacterium nucl...
Feature 1                                                                                     
1GPJ_A     69 ih----------ddAWVKRgsEAVRHLFRVASGLESMMVGEQEILRQVKKAYDRAARLGtLDEALKIVFRRAINLGKRAR 138 Methanopyrus kandleri
Q9Y9J2     67 siasp-----ggegLVRLQgiDAARHLFRVASGLESQIIGDHEVLGQVRRAWLKSREKGfTTPLLDEVFHRALKTGARVR 141 Aeropyrum pernix
Q8ZYV6     67 tlryr----ryaesIRVVRgvEAARHLFRVAAGLESMLIGETDILGQVEEAFDRQVKAGfTKGLLKTIVERAIRAGKRVR 142 Pyrobaculum aeroph...
Q60172     59 nidl------ekfdILFGD--KAIEHLFRVACGLESMIVGEDQILGQLKNAYLKAKEKGrISKKLEKIILKAIHTGQRAR 130 Methanocaldococcus...
P42809     68 --------------TVEKDe-DALLHLLRLASGLESMIIGEDQILGQIKAARLQALREGtCGPLLDMVFTKAVHVGQTVR 132 Methanothermobacte...
Q976H4     75 ldeihgkqiskdamILKGE--DAVKHLFEVASGLDSLAIGEYEILRQLKESIEKSKKLGlSSEKLEFLFKNAIKVGRKIR 152 Sulfolobus tokodaii
Q8D2K8     76 ffndlki-keiknnFYSYIdnYAVSHLMRVTSGLDSMILGEHQILSQVKSAFFRSLKNKnISIDLQKLFESAFSVAKKIR 154 Wigglesworthia glo...
Q980U7     80 ihnepi---gnqarVLCGK--DAAKHLFLVASGADSLSIGEYEILSQIRSTIDMFKKLGfSGKYLQIFFERAIKVGRKVR 154 Sulfolobus solfata...
Q9HKR0     66 k------------pNVLHDe-EAIKHLMEVSSGLDSMSLGENEILKQVKEAYELSVRNGkVDKVLSLIFQKAIFVGKKVR 132 Thermoplasma acido...
Q8R687     77 d------------mIVKSRv-EAIEYLFKVGCGFYSVIKGEDQILAQVKGAYAEALENEhSSKFLNIIFNKSIELGKKFR 143 Fusobacterium nucl...
Feature 1                                         # #  #                                      
1GPJ_A    139 EETRISEGAVSIGSAAVELAERELgs-lhDKTVLVVGAGEMGKTVAKSLVd-rGVRAVLVANRTyERAVELARDLGG--- 213 Methanopyrus kandleri
Q9Y9J2    142 SESAISSGGVGYSSAAVSLAASLLgggldGARVGIVGAGMAAVGIARALCtrwRPRVVAVFNRTpERGWEVAGKCRGves 221 Aeropyrum pernix
Q8ZYV6    143 AETGISRGPAGLGSLSIIYVSQLLdl--tKSKVAVLGAGAVGAGLAKELAe-rGVAKLYILNRTlEKAVEIANKLGA--- 216 Pyrobaculum aeroph...
Q60172    131 VETKINEGGVSIGSAAVELAEKIFgl--eGKNVLLIGAGEMANLVIKALKe-kNIKAIIVANRTyEKAEKLAKELGG--- 204 Methanocaldococcus...
P42809    133 RKTKINRGSVSIGSAAVDLAESIHgd-lkCKKVLVIGAGKMGTLVARALAe-kHLKAIMVANRTyERAYQLACELGG--- 207 Methanothermobacte...
Q976H4    153 QQTEISKGKTGIYALAVEYAKHVSnnnigNVKIAIVGAGEIGNKLALMLKn-eGAQNVTIFNRTyEKALEVANKYGF--- 228 Sulfolobus tokodaii
Q8D2K8    155 SETKIGSYSISIPYIICVLLKKIFis-ftEIKVMLIGSGTINELIAKQLFk-yKIKDLFISNRTiDHAKNLAIKVNG--- 229 Wigglesworthia glo...
Q980U7    155 EETSISKGKVGIYSLAIDEAKKRFnd-fyDRRILVIGAGEMAQKITSMLHn-eGAKDVTIMNRTiEKAKQLALKFGY--- 229 Sulfolobus solfata...
Q9HKR0    133 SETEISRGKVSVPSIVYDILSSRV-----VQKVLIIGNGMIAGEIAPYLS---GKFEVTIAGRNiDHVKDLASKYNY--- 201 Thermoplasma acido...
Q8R687    144 TKSMIAHNALSLEAISLKFIKSKFpn-ieDKNIFILGIGELAQDILTLLTk-eQLKNIYIANRTyHKAEQIKKEFDIv-- 219 Fusobacterium nucl...
Feature 1                                                                                     
1GPJ_A    214 EAVRFd--eLVDHLARsDVVVSATAAphp---vihVDDVREALrkrdrrsPILIIDIANPRd-VEEGVEniedVEVRTID 287 Methanopyrus kandleri
Q9Y9J2    222 LVLPLd--eLAKLINElDALFVAIAGstn----ilERGRVERGv-----sPRVIVDISNPP--VTPKVA----GRVFHMP 284 Aeropyrum pernix
Q8ZYV6    217 EARPLtreeVQKCLMEcDVVFSSVHS---------LEYVIDRVpdg--avVKIIVDLGVPQt-VAPGLP----VRVVRLS 280 Pyrobaculum aeroph...
Q60172    205 MAIKFd--kLEEALRYaDIVISATGAp--------HPILNKERlkn--agKTIIIDIANPRd-TTDDIRelpdIFLFTID 271 Methanocaldococcus...
P42809    208 DAIHFd--rLNRALRDaDVVISATGSphy---iltRERVMDAVppe-rrsSIVMVDIANPRd-IEESVRel-gVRLFTID 279 Methanothermobacte...
Q976H4    229 KAEPL----DFYKINNyDIVFVAIYY---------DKKINLPN-------PKLVIDLSVPQivLGNNVIt--lENLRSIS 286 Sulfolobus tokodaii
Q8D2K8    230 CVVEFn--eIFKNLNKmQVIITSTYSrkliitykiIKSIIEKNkn----kKIIFIDISIPRn-IDKKIKkitgVHLYTLE 302 Wigglesworthia glo...
Q980U7    230 NYEKL----DLDKLGNfDVAFISIYHe--------NLRLENKW-------NTLIVDITVPPlfTGNNVIt--lEELERIS 288 Sulfolobus solfata...
Q9HKR0    202 SYTTIn--dLHELIMRnDAIISATSSkt------pIIRREEMVe------GKLYIDLGNPRn-IEDKPG----ADIITID 262 Thermoplasma acido...
Q8R687    220 NIVDYr--eKYPKMIEaDVIISATSAphivveydkFVAQMKENk------DYLFIDLAVPRd-VDERLAnfknIEIYNLD 290 Fusobacterium nucl...
Feature 1                      
1GPJ_A    288 DLRVIARENLERRRKEI 304 Methanopyrus kandleri
Q9Y9J2    285 EVEEEAKRMMEERLRWI 301 Aeropyrum pernix
Q8ZYV6    281 DLKQLAEKYSEARKQEA 297 Pyrobaculum aerophilum
Q60172    272 DLRLVAEENLKKRKEEI 288 Methanocaldococcus jannaschii
P42809    280 DLRGVAEENRKRREAEA 296 Methanothermobacter marburgensis str. Marburg
Q976H4    287 DKIMETKILSLQKAEEL 303 Sulfolobus tokodaii
Q8D2K8    303 DLKDLITNNLEKRKNAA 319 Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis
Q980U7    289 NLNFKAREEELAKINKL 305 Sulfolobus solfataricus
Q9HKR0    263 DIYSVSNRNGSARMESV 279 Thermoplasma acidophilum
Q8R687    291 DIWEVYHLNSMNRDKLL 307 Fusobacterium nucleatum subsp. nucleatum

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