Conserved Protein Domain Family
TPP_PYR_E1-PDHc-beta_like

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cd07036: TPP_PYR_E1-PDHc-beta_like 
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Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins.
Thiamine pyrophosphate (TPP) family, pyrimidine (PYR) binding domain of the beta subunits of the E1 components of: human pyruvate dehydrogenase complex (E1- PDHc), the acetoin dehydrogenase complex (ADC), and the branched chain alpha-keto acid dehydrogenase/2-oxoisovalerate dehydrogenase complex (BCADC), 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. E1-PDHc is an alpha2beta2 dimer-of-heterodimers having two active sites lying between PYR and PP domains of separate subunits, the PYR domains are arranged on the beta subunit, the PP domains on the alpha subunits. PDHc catalyzes the irreversible oxidative decarboxylation of pyruvate to produce acetyl-CoA in the bridging step between glycolysis and the citric acid cycle. 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: 132919
View PSSM: cd07036
Aligned: 75 rows
Threshold Bit Score: 210.798
Threshold Setting Gi: 206685894
Created: 22-Dec-2008
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
Hierarchy
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Display:
 
Conserved site includes 5 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.

cd07036 is part of a hierarchy of related CD models.
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cd07036 is a member of the superfamily cl11410.
cd06586:TPP_enzyme_PYRcd07033:TPP_PYR_DXS_TK_likecd07034:TPP_PYR_PFOR_IOR-alpha_likecd07035:TPP_PYR_POX_likecd07036:TPP_PYR_E1-PDHc-beta_likecd07037:TPP_PYR_MenDcd07038:TPP_PYR_PDC_IPDC_likecd07039:TPP_PYR_POX89890474949688131166220512066858945645928815612777159899111108805281298309062983092011667111188812835110004303162448150774596868990231720668441411593548915912839972546724146015501455914073993698315386872069933921196234479198259316148553961811770168885485884686489118579459119717992206895878146303981206895850206900583179885601179560761798840537526685890957262OZL D16806614708592350754481115720316212505950170578686171429191130644577190017009184072386697170945411678880216806311615948230219826656154299978888026981824146611892190171341021251638475331599011471088051273386148790994457923995311680316351956395021938104833999753116378382889890474949688131166220512066858945645928815612777159899111108805281298309062983092011667111188812835110004303162448150774596868990231720668441411593548915912839972546724146015501455914073993698315386872069933921196234479198259316148553961811770168885485884686489118579459119717992206895878146303981206895850206900583179885601179560761798840537526685890957262OZL D168066147085923507544811157203162125059501705786861714291911306445771900170091840723866971709454116788802168063116159482302198266561542999788880269818241466118921901713410212516384753315990114710880512733861487909944579239953116803163519563950219381048339997531163783828
cd07036 Sequence Cluster
cd07036 Sequence Cluster
Sub-family Hierarchy
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 cd07036 Branch
 Whole Hierarchy
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CD Hierarchy
Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                             #                                          # #             
2OZL_D        19 DAINQGMDEELERDEkVFLLGEEvaqy--------------dgayKVSRGLWKKYGdkRIIDTPISEMGFAGIAVGAAMA 84
gi 77459686   23 QALRSAMDVMLERDDnVVVFGQDvgyf--------------ggvfRCTEGLQTKYGtsRVFDAPISESGIVGVAVGMGAY 88
gi 89890474  360 DCALFAIEELMKKHPeCLLYGQDvggrl-------------ggvfREAATLAQKFGdnRVFNTPIQEAFIVGSTVGMSAA 426
gi 89902317   16 QALRSAMDVMLARDSnVVVYGQDvgyf--------------ggvfRCTEGLQQKYGnqRVFDAPISEGGIVGTAVGMAAY 81
gi 94968813  400 DLINACLKDEMKRDPrIVIFGEDvadcsreeylkqkqvkgkggvfKLTSGLQMEYGadRVFNSPLAEANIVGRATGMAVR 479
gi 115935489   9 QALNNAMDVALTSDStAVIFGEDvafg---------------gvfRCTVGLADKHGkdRVFNTPLCEQGIVGFGIGMAAV 73
gi 116622051  77 DAINHGLREEMERNPkIVMWGEDiadpk-------------ggvfGVTRGLSSALPg-RVFNAPLAEASIAGVAAGMAIA 142
gi 159128399  68 QAINSALRTALATDNrVMLFGEDvafg---------------gvfRCSMDLQTEFGseRVFNTPLTEQGIVGFAIGAAAQ 132
gi 206684414   8 EAIREAHDVAMAADErVVVFGEDvgff--------------ggvfRCTAGLQQKYGksRCFDAPINESGIVGTAIGMAAY 73
gi 206685894 398 RLINWALTDLMLEHReIVVMGEDvgrk--------------ggvyGVSQKLQQRFGpdRVIDTLLDEQSILGLAIGMGHN 463
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                    #  #                                                                
2OZL_D        85 GLRPICEFMtFNFSMQAIDQVINSAAKTYYm--sGGLQPVPIVFRGPNGASa--gVAAQHSqcFAAWYGHCPGLKVVSPW 160
gi 77459686   89 GLRPVAEIQfADYVYPASDQIISEAARLRYr--sAGEFTAPMTLRMPCGGGi--yGGQTHSqsIEAMFTQVCGLRTVMPS 164
gi 89890474  427 GLKPIVEVQfADYIWPGLNQLFTEVSRSCYl--sNGKWPVSMVLRVPIGAYg--sGGPYHSssMESVVSNIRGLKIAYPS 502
gi 89902317   82 GLRPVVEIQfADYVYPATDQIVSEAARLRYr--sAGDFTCPMTIRMPCGGGi--yGGQTHSqsPEAMFTQVCGLRTVMPS 157
gi 94968813  480 GLKPVVEIQfFDYIWPAMHQLRNELPVVRWr--sNGAFSSPAVIRVAIGGYlt-gGAIYHSqcGESIFTHTPGMRVIFPS 556
gi 115935489  74 GATAIAEIQfADYIYPAFDQIINEAAKFRYrs-gNMFDVGGLTIRAPWGAVg--hGALYHSqsPEAFFAHIPGVKVVIPR 150
gi 116622051 143 GYKPIIEIQfADYTWPAFMQLRNEIATVRWr--sQGTWNCPVVVRIAAGAYi--kGGPWHSacVEGVFAHIPGWRVLFPS 218
gi 159128399 133 GMKPVAEIQfADYVFPAFDQIVNEAAKFRYreggTGVNVGGMVVRMPCGAVg--hGALYHTqsPEALFAHVPGVQVVMPR 210
gi 206684414  74 GLKPVIEIQfADYVYPAYDQIVSEAARLRHr--sNADFTCPLVIRMPTGGGi--fGGQTHSqsPEALFTHVSGLKVVVPS 149
gi 206685894 464 GFLPIPEIQfLAYLHNAEDQLRGEAATLPFf--sNGQFANPMVLRIAGLGYqkgfGGHFHNdnSLAVLRDIPGLVIACPS 541
                        170       180
                 ....*....|....*....|....*....
Feature 1                                     
2OZL_D       161 NsEDAKGLIKSAIRDN----NPVVVLENE 185
gi 77459686  165 NpYDAKGLLIASIEND----DPVIFLEPK 189
gi 89890474  503 NgADLKGLMKAAYYDP----NPVVIFEHK 527
gi 89902317  158 NpYDAKGLLIASIEND----DPVIFLEPK 182
gi 94968813  557 NaLDANGLLRTAIRCD----DPVLFLEHK 581
gi 115935489 151 SpIQAKGLLLLILRIDs--tCYWVHTRMV 177
gi 116622051 219 CaEDAKGLIKMAARLE----DPVIFLEHK 243
gi 159128399 211 SpSQAKGLLLSAILQSn---NPVIFMEPK 236
gi 206684414 150 NpRDAKGLLLAAIEDP----DPVIFLEPK 174
gi 206685894 542 DgAEAAMMMREAVRLAreeqRVVVFVEPI 570

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