2OZL


Conserved Protein Domain Family
TPP_PYR_E1-PDHc-beta_like

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cd07036: TPP_PYR_E1-PDHc-beta_like 
Click on image for an interactive view with Cn3D
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: 210.797
Threshold Setting Gi: 206685894
Created: 22-Dec-2008
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
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.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                             #                                          # #             
2OZL_D        19 DAINQGMDEELERDEkVFLLGEEvaqy--------------dgayKVSRGLWKKYGdkRIIDTPISEMGFAGIAVGAAMA 84  human
YP_349193     23 QALRSAMDVMLERDDnVVVFGQDvgyf--------------ggvfRCTEGLQTKYGtsRVFDAPISESGIVGVAVGMGAY 88  Pseudomonas flu...
ZP_01201984  360 DCALFAIEELMKKHPeCLLYGQDvggrl-------------ggvfREAATLAQKFGdnRVFNTPIQEAFIVGSTVGMSAA 426 Flavobacteria b...
YP_524788     16 QALRSAMDVMLARDSnVVVYGQDvgyf--------------ggvfRCTEGLQQKYGnqRVFDAPISEGGIVGTAVGMAAY 81  Rhodoferax ferr...
YP_590861    400 DLINACLKDEMKRDPrIVIFGEDvadcsreeylkqkqvkgkggvfKLTSGLQMEYGadRVFNSPLAEANIVGRATGMAVR 479 Acidobacteria b...
XP_001190493   9 QALNNAMDVALTSDStAVIFGEDvafg---------------gvfRCTVGLADKHGkdRVFNTPLCEQGIVGFGIGMAAV 73  purple urchin
YP_824207     77 DAINHGLREEMERNPkIVMWGEDiadpk-------------ggvfGVTRGLSSALPg-RVFNAPLAEASIAGVAAGMAIA 142 Solibacter usit...
EDP53514      68 QAINSALRTALATDNrVMLFGEDvafg---------------gvfRCSMDLQTEFGseRVFNTPLTEQGIVGFAIGAAAQ 132 Aspergillus fum...
EDZ44897       8 EAIREAHDVAMAADErVVVFGEDvgff--------------ggvfRCTAGLQQKYGksRCFDAPINESGIVGTAIGMAAY 73  Rhodobacterales...
EDZ46376     398 RLINWALTDLMLEHReIVVMGEDvgrk--------------ggvyGVSQKLQQRFGpdRVIDTLLDEQSILGLAIGMGHN 463 Rhodobacterales...
Feature 1                    #  #                                                                
2OZL_D        85 GLRPICEFMtFNFSMQAIDQVINSAAKTYYm--sGGLQPVPIVFRGPNGASa--gVAAQHSqcFAAWYGHCPGLKVVSPW 160 human
YP_349193     89 GLRPVAEIQfADYVYPASDQIISEAARLRYr--sAGEFTAPMTLRMPCGGGi--yGGQTHSqsIEAMFTQVCGLRTVMPS 164 Pseudomonas flu...
ZP_01201984  427 GLKPIVEVQfADYIWPGLNQLFTEVSRSCYl--sNGKWPVSMVLRVPIGAYg--sGGPYHSssMESVVSNIRGLKIAYPS 502 Flavobacteria b...
YP_524788     82 GLRPVVEIQfADYVYPATDQIVSEAARLRYr--sAGDFTCPMTIRMPCGGGi--yGGQTHSqsPEAMFTQVCGLRTVMPS 157 Rhodoferax ferr...
YP_590861    480 GLKPVVEIQfFDYIWPAMHQLRNELPVVRWr--sNGAFSSPAVIRVAIGGYlt-gGAIYHSqcGESIFTHTPGMRVIFPS 556 Acidobacteria b...
XP_001190493  74 GATAIAEIQfADYIYPAFDQIINEAAKFRYrs-gNMFDVGGLTIRAPWGAVg--hGALYHSqsPEAFFAHIPGVKVVIPR 150 purple urchin
YP_824207    143 GYKPIIEIQfADYTWPAFMQLRNEIATVRWr--sQGTWNCPVVVRIAAGAYi--kGGPWHSacVEGVFAHIPGWRVLFPS 218 Solibacter usit...
EDP53514     133 GMKPVAEIQfADYVFPAFDQIVNEAAKFRYreggTGVNVGGMVVRMPCGAVg--hGALYHTqsPEALFAHVPGVQVVMPR 210 Aspergillus fum...
EDZ44897      74 GLKPVIEIQfADYVYPAYDQIVSEAARLRHr--sNADFTCPLVIRMPTGGGi--fGGQTHSqsPEALFTHVSGLKVVVPS 149 Rhodobacterales...
EDZ46376     464 GFLPIPEIQfLAYLHNAEDQLRGEAATLPFf--sNGQFANPMVLRIAGLGYqkgfGGHFHNdnSLAVLRDIPGLVIACPS 541 Rhodobacterales...
Feature 1                                     
2OZL_D       161 NsEDAKGLIKSAIRDN----NPVVVLENE 185 human
YP_349193    165 NpYDAKGLLIASIEND----DPVIFLEPK 189 Pseudomonas fluorescens PfO-1
ZP_01201984  503 NgADLKGLMKAAYYDP----NPVVIFEHK 527 Flavobacteria bacterium BBFL7
YP_524788    158 NpYDAKGLLIASIEND----DPVIFLEPK 182 Rhodoferax ferrireducens T118
YP_590861    557 NaLDANGLLRTAIRCD----DPVLFLEHK 581 Acidobacteria bacterium Ellin345
XP_001190493 151 SpIQAKGLLLLILRIDs--tCYWVHTRMV 177 purple urchin
YP_824207    219 CaEDAKGLIKMAARLE----DPVIFLEHK 243 Solibacter usitatus Ellin6076
EDP53514     211 SpSQAKGLLLSAILQSn---NPVIFMEPK 236 Aspergillus fumigatus A1163
EDZ44897     150 NpRDAKGLLLAAIEDP----DPVIFLEPK 174 Rhodobacterales bacterium Y4I
EDZ46376     542 DgAEAAMMMREAVRLAreeqRVVVFVEPI 570 Rhodobacterales bacterium Y4I

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