2O1S,1TKA,2OZL,2O1X,1TRK,1AY0,1ITZ,1R9J,2E6K,1QGD


Conserved Protein Domain Family
TPP_PYR_DXS_TK_like

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cd07033: TPP_PYR_DXS_TK_like 
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Pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and related proteins.
Thiamine pyrophosphate (TPP) family, pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and the beta subunits of the E1 component of the human pyruvate dehydrogenase complex (E1- PDHc), subfamily. The PYR domain is found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. A polar interaction between the conserved glutamate of the PYR domain and the N1' of the TPP aminopyrimidine ring is shared by most TPP-dependent enzymes, and participates in the activation of TPP. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this sub-family. Like many TPP-dependent enzymes DXS and TK are homodimers having a PYR and a PP domain on the same subunit. TK has two active sites per dimer which lie between PYR and PP domains of different subunits. For DXS each active site is located at the interface of a PYR and a PP domain from the same subunit. E1-PDHc is an alpha2beta2 dimer-of-heterodimers having two active sites but having the PYR and PP domains arranged on separate subunits, the PYR domains on the beta subunits, the PP domains on the alpha subunits. DXS is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis, it catalyzes a transketolase-type condensation of pyruvate with D-glyceraldehyde-3-phosphate to form 1-deoxy-D-xylulose-5-phosphate (DXP) and carbon dioxide. TK catalyzes the transfer of a two-carbon unit from ketose phosphates to aldose phosphates. In heterotrophic organisms, TK provides a link between glycolysis and the pentose phosphate pathway and provides precursors for nucleotide, aromatic amino acid and vitamin biosynthesis. TK also plays a central role in the Calvin cycle in plants. PDHc catalyzes the irreversible oxidative decarboxylation of pyruvate to produce acetyl-CoA in the bridging step between glycolysis and the citric acid cycle. This subfamily includes the beta subunits of the E1 component of the acetoin dehydrogenase complex (ADC) and the branched chain alpha-keto acid dehydrogenase/2-oxoisovalerate dehydrogenase complex (BCADC). ADC participates in the breakdown of acetoin. BCADC catalyzes the oxidative decarboxylation of 4-methyl-2-oxopentanoate, 3-methyl-2-oxopentanoate and 3-methyl-2-oxobutanoate during the breakdown of branched chain amino acids.
Statistics
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PSSM-Id: 132916
View PSSM: cd07033
Aligned: 302 rows
Threshold Bit Score: 92.8901
Threshold Setting Gi: 149242794
Created: 3-Dec-2008
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 4 residues -Click on image for an interactive view with Cn3D
Feature 1:TPP binding site [chemical binding site]
Evidence:
  • Structure:2OZL_D/A; human E1-PDHc (S264e variant) heterodimer contacts TPP and divalent metal ion; contacts at 3.5A.
    View structure with Cn3D
  • Comment:E1-PDHc is an alpha2beta2 dimer-of-heterodimers. One TPP is bound per heterodimer.
  • Structure:2OIX_A/B; Deinococcus radiodurans DXS monomer binds TPP and divalent metal ion; contacts at 3.5A.
    View structure with Cn3D
  • Comment:DXS is a homodimer, each monomer binds one TPP.
  • Structure:1ITZ_A/B; Zea mays TK homodimer binds TPP and divalent metal ion; contacts at 3.5A.
    View structure with Cn3D
  • Comment:TK has two active sites per dimer which lie between PYR and PP domains of different subunits.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                          # #                          #
2O1S_A       323 KIFGDWLCETAAKDNkLXAITPAxr----egSGXVEfsrk-fpdRYFDVAIAEQHAVTFAAGLAIGG-YKPIVAIY-STF 395
gi 148985016   3 KTFIDELINKNIEEQnIVVLTGDvg----rsTYASKfkei-fpeNYLNLGICEANIVGISAGIAGTLeFVPFVMLFsKHL 77
gi 197924858   7 DAYRDELTRLAADDGsIVCLEADl------gGKGHPfqaa-hpeRFFNLGIAEGAMVDMAAGLAAGG-YKPFASTFaPFA 78
gi 33240730    3 NSFATTLTEIARNDPkVILLAGDig-----fRIFDKfiee-fpdRFINCGIAEQNMVSVAAGMASAG-RRPIVYTIiPFL 75
gi 172061330   3 DAFSDAIVGAARQDPkVLLLTGDhg-----yALFDAfrka-cpdQYINCGIAEQNMVGVAAGLAKAG-FKPIVYGLaAFV 75
gi 167769554   3 NAFVNTLIDCARQDPaVALLMAEvg-----fSVVEPfeke-fpsRFYNTGIAEQNLVLTAAGMALEG-MRPVAYSMsAFL 75
2OZL_D        19 DAINQGMDEELERDEkVFLLGEEvaqydgayKVSRGlwkkygdkRIIDTPISEMGFAGIAVGAAMAG-LRPICEFMtFNF 97
gi 33861792    3 DAFANEIKRLSEANKnVVLLSGDig-----nRMFDKyksv-speRFFNCGIAEANMMSLASGMALCG-LKPVIYTItPFT 75
gi 166363845   3 NAFSDALVKFALGDErVLLLTGDhg-----yALFDDfrqa-cpkQYINAGVAEQNMVGVAAGLAKSG-FFPVVYGLsSFL 75
gi 170691034   9 DGAVSALGRLTAEGRdIVVMVADst----stSKISPflet-ypeRVINVGIAEQNMVGMAAGLALGG-HVVFTANAaPFL 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1          #                                                                             
2O1S_A       396 LQRAYDQVLhDVAIQk--------LPVLFAIdRAGIVg-aDGQTHqgafDLSYLRCIPEXVIXTPSDeNECRQXLYTGYH 466
gi 148985016  78 ILRALEQIN-DSILMn-------kKKVILVGgYSGYSaskEGETHqllnDISILSSFPDISIYCPYDqSSIQTAINESIN 149
gi 197924858  79 ALRAAESLKlTLGYLs--------AGVTVMApYAGVSgawFGTTHhcleDLAILRSVPGVTIAAPYGeAEMRAVVRAAVR 150
gi 33240730   76 IMRSFEQIRvDIGINq--------QGVVLVGvGGGLAydkLGSTHhayeDIALMRTIPSMKIFTPIDpEDVSNCFIQSYN 147
gi 172061330  76 PIRVLEQIKiDVCYEn--------LPVTFIGdGAGVVyaqLGTSHqsteDIAALRAIPQLSIYSPADrFELTACMQDIST 147
gi 167769554  76 ASRAFELIKvSVCYQd--------LPVVLASiGTGLSyseLGATHhateESALMRVLPNLNVFFPADgAELSEALRFALR 147
2OZL_D        98 SMQAIDQVInSAAKTyymsgglqpVPIVFRG-PNGASa-gVAAQHsq-cFAAWYGHCPGLKVVSPWNsEDAKGLIKSAIR 174
gi 33861792   76 TTRCLEQIRiGVAYHn--------APVVIVGtGSGLSyseLGPTHhsleDIAILRAVPNINILTPSDkQELTTQLQEAIS 147
gi 166363845  76 PIRVLEQIKlDICYEq--------LKVLLIGdGAGVVyssLGSSHqsteDIAALRALPNISILSPADaSEMTQCLNWAFN 147
gi 170691034  83 VARANEQVKnDVCYSa--------TNVKMLGlNAGVAygpLASTHhaidDISIMSGFGNVQILAPCDgIEVVQMIEYAAA 154
                        170
                 ....*....|....
Feature 1                      
2O1S_A       467 YNd--gPSAVRYPR 478
gi 148985016 150 NDy---SSYIRINK 160
gi 197924858 151 SGt---PHYIRTGR 161
gi 33240730  148 LAksdiPSYIRLSK 161
gi 172061330 148 RQt---PAYLRMGK 158
gi 167769554 148 AEh---PSYISFPK 158
2OZL_D       175 DNn---PVVVLENE 185
gi 33861792  148 MNt---PSYMRIGK 158
gi 166363845 148 SDr---PVYLRMGK 158
gi 170691034 155 VEg---PVYIRLDN 165

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