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: 2-Oct-2020
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:
Feature 1                                                          # #                          #
2O1S_A       323 KIFGDWLCETAAKDNkLXAITPAxr----egSGXVEfsrk-fpdRYFDVAIAEQHAVTFAAGLAIGG-YKPIVAIY-STF 395 Escherichia coli
ZP_01818259    3 KTFIDELINKNIEEQnIVVLTGDvg----rsTYASKfkei-fpeNYLNLGICEANIVGISAGIAGTLeFVPFVMLFsKHL 77  Streptococcus p...
ZP_03189804    7 DAYRDELTRLAADDGsIVCLEADl------gGKGHPfqaa-hpeRFFNLGIAEGAMVDMAAGLAAGG-YKPFASTFaPFA 78  Streptomyces pr...
NP_875672      3 NSFATTLTEIARNDPkVILLAGDig-----fRIFDKfiee-fpdRFINCGIAEQNMVSVAAGMASAG-RRPIVYTIiPFL 75  Prochlorococcus...
YP_001808982   3 DAFSDAIVGAARQDPkVLLLTGDhg-----yALFDAfrka-cpdQYINCGIAEQNMVGVAAGLAKAG-FKPIVYGLaAFV 75  Burkholderia am...
ZP_02441607    3 NAFVNTLIDCARQDPaVALLMAEvg-----fSVVEPfeke-fpsRFYNTGIAEQNLVLTAAGMALEG-MRPVAYSMsAFL 75  Anaerotruncus c...
2OZL_D        19 DAINQGMDEELERDEkVFLLGEEvaqydgayKVSRGlwkkygdkRIIDTPISEMGFAGIAVGAAMAG-LRPICEFMtFNF 97  human
NP_893353      3 DAFANEIKRLSEANKnVVLLSGDig-----nRMFDKyksv-speRFFNCGIAEANMMSLASGMALCG-LKPVIYTItPFT 75  Prochlorococcus...
YP_001656118   3 NAFSDALVKFALGDErVLLLTGDhg-----yALFDDfrqa-cpkQYINAGVAEQNMVGVAAGLAKSG-FFPVVYGLsSFL 75  Microcystis aer...
ZP_02882200    9 DGAVSALGRLTAEGRdIVVMVADst----stSKISPflet-ypeRVINVGIAEQNMVGMAAGLALGG-HVVFTANAaPFL 82  Burkholderia gr...
Feature 1          #                                                                             
2O1S_A       396 LQRAYDQVLhDVAIQk--------LPVLFAIdRAGIVg-aDGQTHqgafDLSYLRCIPEXVIXTPSDeNECRQXLYTGYH 466 Escherichia coli
ZP_01818259   78 ILRALEQIN-DSILMn-------kKKVILVGgYSGYSaskEGETHqllnDISILSSFPDISIYCPYDqSSIQTAINESIN 149 Streptococcus p...
ZP_03189804   79 ALRAAESLKlTLGYLs--------AGVTVMApYAGVSgawFGTTHhcleDLAILRSVPGVTIAAPYGeAEMRAVVRAAVR 150 Streptomyces pr...
NP_875672     76 IMRSFEQIRvDIGINq--------QGVVLVGvGGGLAydkLGSTHhayeDIALMRTIPSMKIFTPIDpEDVSNCFIQSYN 147 Prochlorococcus...
YP_001808982  76 PIRVLEQIKiDVCYEn--------LPVTFIGdGAGVVyaqLGTSHqsteDIAALRAIPQLSIYSPADrFELTACMQDIST 147 Burkholderia am...
ZP_02441607   76 ASRAFELIKvSVCYQd--------LPVVLASiGTGLSyseLGATHhateESALMRVLPNLNVFFPADgAELSEALRFALR 147 Anaerotruncus c...
2OZL_D        98 SMQAIDQVInSAAKTyymsgglqpVPIVFRG-PNGASa-gVAAQHsq-cFAAWYGHCPGLKVVSPWNsEDAKGLIKSAIR 174 human
NP_893353     76 TTRCLEQIRiGVAYHn--------APVVIVGtGSGLSyseLGPTHhsleDIAILRAVPNINILTPSDkQELTTQLQEAIS 147 Prochlorococcus...
YP_001656118  76 PIRVLEQIKlDICYEq--------LKVLLIGdGAGVVyssLGSSHqsteDIAALRALPNISILSPADaSEMTQCLNWAFN 147 Microcystis aer...
ZP_02882200   83 VARANEQVKnDVCYSa--------TNVKMLGlNAGVAygpLASTHhaidDISIMSGFGNVQILAPCDgIEVVQMIEYAAA 154 Burkholderia gr...
Feature 1                      
2O1S_A       467 YNd--gPSAVRYPR 478 Escherichia coli
ZP_01818259  150 NDy---SSYIRINK 160 Streptococcus pneumoniae SP3-BS71
ZP_03189804  151 SGt---PHYIRTGR 161 Streptomyces pristinaespiralis ATCC 25486
NP_875672    148 LAksdiPSYIRLSK 161 Prochlorococcus marinus subsp. marinus str. CCMP1375
YP_001808982 148 RQt---PAYLRMGK 158 Burkholderia ambifaria MC40-6
ZP_02441607  148 AEh---PSYISFPK 158 Anaerotruncus colihominis DSM 17241
2OZL_D       175 DNn---PVVVLENE 185 human
NP_893353    148 MNt---PSYMRIGK 158 Prochlorococcus marinus subsp. pastoris str. CCMP1986
YP_001656118 148 SDr---PVYLRMGK 158 Microcystis aeruginosa NIES-843
ZP_02882200  155 VEg---PVYIRLDN 165 Burkholderia graminis C4D1M

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