1OZH,1N0H,1PVD,2G1I,2O1X,2O1S,2VBI,1POW,1Y9D,2OZL,2JLC,2PDA,2JLA


Conserved Protein Domain Family
TPP_enzyme_PYR

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cd06586: TPP_enzyme_PYR 
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Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes.
Thiamine pyrophosphate (TPP) family, pyrimidine (PYR) binding domain; 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 group. Most TPP-dependent enzymes have the PYR and PP domains on the same subunit although these domains can be alternatively arranged in the primary structure. In the case of 2-oxoisovalerate dehydrogenase (2OXO), sulfopyruvate decarboxylase (ComDE), and the E1 component of human pyruvate dehydrogenase complex (E1- PDHc) the PYR and PP domains appear on different subunits. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites. For many of these enzymes the active sites lie between PP and PYR domains on different subunits. However, for the homodimeric enzymes 1-deoxy-D-xylulose 5-phosphate synthase (DXS) and Desulfovibrio africanus pyruvate:ferredoxin oxidoreductase (PFOR), each active site lies at the interface of the PYR and PP domains from the same subunit.
Statistics
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PSSM-Id: 132915
View PSSM: cd06586
Aligned: 13 rows
Threshold Bit Score: 121.683
Threshold Setting Gi: 4558221
Created: 8-Jan-2008
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 3 residues -Click on image for an interactive view with Cn3D
Feature 1:TPP binding site [chemical binding site]
Evidence:
  • Structure:2JLA_A/B; Escherichia coli MenD homodimer binds TPP and divalent metal ion; contacts at 3.5A
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  • Structure:1Y9D_A/C; Lactobacillus plantarum pyruvate oxidase (POX) variant V265a homodimer binds TPP and divalent metal ion; contacts at 3.5A.
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  • Structure:1N0H_A/B; Saccharomyces cerevisiae acetohydroxyacid synthase (AHAS) homodimer binds TPP and divalent metal ion; contacts at 3.5A.
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  • Structure:2PDA_A/B; Desulfovibrio africanus PFOR monomer binds TPP and divalent metal ion; contacts at 3.5A
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  • Structure:2OIX_A/B; Deinococcus radiodurans DXS monomer binds TPP and divalent metal ion; contacts at 3.5A.
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  • 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:many proteins in this group are either homotetramers (dimer-of-homodimers), e.g. E. coli MenD, and L. plantarum POX, or homodimers, e.g. S. cerevisiae AHAS, D. africanus PFOR, and D. radiodurans DXS, and have two TPP-binding sites per homodimer. E1-PDHc is an alpha2beta2 dimer-of-heterodimers, having one TPP bound per heterodimer.
  • Comment:for some the TPP binds in a site lying between a PYR domain and a PP domain from different subunits. For others it lies between a PYR and a PP domain from the same subunit.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                            #                                      #                  
1OZH_B      15 DLVVSQLEAqg----vrQVFGIPgak----idKVFDsll-----------dssIRIIPvrHEANAAFMAAAVGRITgkaG 75   Klebsiella pneum...
1N0H_A      86 QIFNEMMSRqn----vdTVFGYPgga----ilPVYDaihn----------sdkFNFVLpkHEQGAGHMAEGYARASgkpG 147  baker's yeast
1PVD_A       7 KYLFERLKQvn----vnTVFGLPgdf----nlSLLDkiye----------vegMRWAGnaNELNAAYAADGYARIKg-mS 67   baker's yeast
2G1I_B       8 RYLFERLKQve----vqTIFGLPgdf----nlSLLDniye----------vpgMRWAGnaNELNAAYAADGYARLKg-mS 68   Kluyveromyces la...
2O1X_A     326 AAFGEAVTEwaktdprtFVVTPAmre----gsGLVEfsrv----------hphRYLDVgiAEEVAVTTAAGMALQGm-rP 390  Deinococcus radi...
2O1S_A     323 KIFGDWLCEtaakdnklXAITPAxre----gsGXVEfsrk----------fpdRYFDVaiAEQHAVTFAAGLAIGGy-kP 387  Escherichia coli
2VBI_A       7 MYLAERLVQig----lkHHFAVAgdy----nlVLLDqlll----------nkdMKQIYccNELNCGFSAEGYARSNg-aA 67   Acetobacter past...
1POW_A       7 AAVIKVLEAwg----vdHLYGIPggs----inSIMDalsa---------erdrIHYIQvrHEEVGAMAAAADAKLTgkiG 69   Lactobacillus pl...
1Y9D_A      15 AAVIKVLEAwg----vdHLYGIPggs----inSIMDalsa---------erdrIHYIQvrHEEVGAMAAAADAKLTgkiG 77   Lactobacillus pl...
2OZL_D      19 DAINQGMDEelerdekvFLLGEEvaqydgaykVSRGlwkk---------ygdkRIIDTpiSEMGFAGIAVGAAMAGl-rP 88   human
2JLC_A      33 AVILEALTRhg----vrHICIAPgsr----stPLTLaaae----------nsaFIHHThfDERGLGHLALGLAKVSkqpV 94   Escherichia coli
2PDA_A      11 TATAHVAYAms-----eVAAIYPitp----ssTMGEeaddwaaqgrknifgqtLTIREmqSEAGAAGAVHGALAAGa-lT 80   Desulfovibrio af...
2JLA_A      14 AVILEALTRhg----vrHICIAPgsr----stPLTLaaae----------nsaFIHHThfDERGLGHLALGLAKVSkqpV 75   Escherichia coli
Feature 1                 #                                                                    
1OZH_B      76 VALVtsGPGCSNLITGMA-TANSEg--------DPVVALGgAVKRAdkakqv--------hqsmdTVAMFSpvtKYAIEV 138  Klebsiella pneum...
1N0H_A     148 VVLVtsGPGATNVVTPMA-DAFADg--------IPMVVFTgQVPTSaigtda--------fqeadVVGISRsctKWNVMV 210  baker's yeast
1PVD_A      68 CIITtfGVGELSALNGIA-GSYAEh--------VGVLHVVgVPSISsqakqlllhhtlgngdftvFHRMSAnisETTAMI 138  baker's yeast
2G1I_B      69 CIITtfGVGELSALNGIA-GSYAEh--------VGVLHVVgVPSVSsqakqlllhhtlgngdftvFHRMSSnisETTAMI 139  Kluyveromyces la...
2O1X_A     391 VVAIy-STFLQRAYDQVLhDVAIEh--------LNVTFCIdRAGIVgadgat--------hngvfDLSFLRsipGVRIGL 453  Deinococcus radi...
2O1S_A     388 IVAIy-STFLQRAYDQVLhDVAIQk--------LPVLFAIdRAGIVgadgqt--------hqgafDLSYLRcipEXVIXT 450  Escherichia coli
2VBI_A      68 AAVVtfSVGAISAMNALG-GAYAEn--------LPVILISgAPNSNdqgtghilhhtigktdysyQLEMARqvtCAAESI 138  Acetobacter past...
1POW_A      70 VCFGsaGPGGTHLMNGLY-DAREDh--------VPVLALIgQFGTTgmnmdt--------fqemnENPIYAdvaDYNVTA 132  Lactobacillus pl...
1Y9D_A      78 VCFGsaGPGGTHLMNGLY-DAREDh--------VPVLALIgQFGTTgmnmdt--------fqemnENPIYAdvaDYNVTA 140  Lactobacillus pl...
2OZL_D      89 ICEFmtFNFSMQAIDQVInSAAKTyymsgglqpVPIVFRG-PNGASagvaa---------qhsqcFAAWYGhcpGLKVVS 158  human
2JLC_A      95 AVIVtsGTAVANLYPALI-EAGLTg--------EKLILLTaDRPPElidcga--------nqairQPGMFAshpTHSISL 157  Escherichia coli
2PDA_A      81 TTFTa-SQGLLLMIPNMY-KISGEl--------LPGVFHVtARAIAahalsi--------fgdhqDIYAARqtgFAMLAS 142  Desulfovibrio af...
2JLA_A      76 AVIVtsGTAVANLYPALI-EAGLTg--------EKLILLTaDRPPElidcga--------nqairQPGXFAshpTHSISL 138  Escherichia coli
Feature 1                                           
1OZH_B     139 Tap------daLAEVVSNAFRAAEqgrpgSAFVSLPQ 169  Klebsiella pneumoniae
1N0H_A     211 Ksv------eeLPLRINEAFEIATsgrpgPVLVDLPK 241  baker's yeast
1PVD_A     139 Tdi------atAPAEIDRCIRTTYvt-qrPVYLGLPA 168  baker's yeast
2G1I_B     140 Tdi------ntAPAEIDRCIRTTYvs-qrPVYLGLPA 169  Kluyveromyces lactis
2O1X_A     454 Pkd------aaELRGMLKYAQTHDg----PFAIRYPR 480  Deinococcus radiodurans
2O1S_A     451 Psd------enECRQXLYTGYHYNd---gPSAVRYPR 478  Escherichia coli
2VBI_A     139 Tda------hsAPAKIDHVIRTALre-rkPAYLDIAC 168  Acetobacter pasteurianus
1POW_A     133 Vna------atLPHVIDEAIRRAYah-qgVAVVQIPV 162  Lactobacillus plantarum
1Y9D_A     141 Vna------atLPHVIDEAIRRAYah-qgVAVVQIPV 170  Lactobacillus plantarum
2OZL_D     159 Pwn------seDAKGLIKSAIRDNn----PVVVLENE 185  human
2JLC_A     158 PrptqdiparwLVSTIDHALGTLHa---gGVHINCPF 191  Escherichia coli
2PDA_A     143 Ssv------qeAHDMALVAHLAAIes-nvPFMHFFDG 172  Desulfovibrio africanus
2JLA_A     139 PrptqdiparwLVSTIDHALGTLHa---gGVHINCPF 172  Escherichia coli

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