2VBI,1POW,1PVD,2JLC,1Y9D,2VBF,2C31,2JLA,2G1I,2AG1,2PGN,2FN3,1MCZ,1PO7,1YBH,1UPB,1OZG,1JSC,2Q27,1N0H,1OZH,2PAN,1YNO,1PI3,2V3W


Conserved Protein Domain Family
TPP_PYR_POX_like

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cd07035: TPP_PYR_POX_like 
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Pyrimidine (PYR) binding domain of POX and related proteins.
Thiamine pyrophosphate (TPP family), pyrimidine (PYR) binding domain of pyruvate oxidase (POX) and related protiens 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. For glyoxylate carboligase, which belongs to this subfamily, but lacks this conserved glutamate, the rate of the initial TPP activation step is reduced but the ensuing steps of the enzymic reaction proceed efficiently. 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. 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. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites, for many the active sites lie between PP and PYR domains on different subunits. POX decarboxylates pyruvate, producing hydrogen peroxide and the energy-storage metabolite acetylphosphate. This subfamily includes pyruvate decarboxylase (PDC) and indolepyruvate decarboxylase (IPDC). PDC catalyzes the conversion of pyruvate to acetaldehyde and CO2 in alcoholic fermentation. IPDC plays a role in the indole-3-pyruvic acid (IPA) pathway in plants and various plant-associated bacteria, it catalyzes the decarboxylation of IPA to IAA. This subfamily also includes the large catalytic subunit of acetohydroxyacid synthase (AHAS). AHAS catalyzes the condensation of two molecules of pyruvate to give the acetohydroxyacid, 2-acetolactate, a precursor of the branched chain amino acids, valine and leucine. AHAS also catalyzes the condensation of pyruvate and 2-ketobutyrate to form 2-aceto-2-hydroxybutyrate in isoleucine biosynthesis. Methanococcus jannaschii sulfopyruvate decarboxylase (MjComDE) and phosphonopyruvate decarboxylase (PpyrDc) also belong to this subfamily. PpyrDc is a homotrimeric enzyme having the PP and PYR domains tandemly arranged on the same subunit. It functions in the biosynthesis of C-P compounds such as bialaphos tripeptide in Streptomyces hygroscopicus. MjComDE is a dodecamer having the PYR and PP domains on different subunits, it has six alpha (PYR/ComD) subunits and six beta (PP/ComE) subunits. MjComDE catalyzes the decarboxylation of sulfopyruvic acid to sulfoacetaldehyde in the coenzyme M pathway.
Statistics
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PSSM-Id: 132918
View PSSM: cd07035
Aligned: 507 rows
Threshold Bit Score: 45.6004
Threshold Setting Gi: 168702736
Created: 4-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: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 POX (variant V265a) homodimer binds TPP and divalent metal ion; contacts at 3.5A.
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  • Structure:2G1I_A/B, Kluyveromyces lactis, PDC homodimer binds TPP and divalent metal ion; contacts at 3.5A.
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  • Structure:2AG1_A/B; Pseudomonas fluorescens benzaldehyde lyase (BAL) homodimer binds TPP and divalent metal ion; contacts at 3.5A.
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  • Structure:2VBF_A/B; Lactococcus lactis branched-chain keto acid decarboxylase (KdcA) homodimer binds TPP and divalent metal ion; contacts at 3.5A.
    View structure with Cn3D
  • Structure:1N0H_A/B; Saccharomyces cerevisiae AHAS homodimer binds TPP and divalent metal ion; contacts at 3.5A.
    View structure with Cn3D
  • Comment:proteins in this group are either homotetramers (dimer-of-homodimers) (e.g. E. coli MenD, L. plantarum POX, K. lactis PDC, P. fluorescens BAL,), or homodimers (e.g. L. lactis KdcA, S. cerevisiae AHAS). There are two TPP-binding sites per homodimer.
  • Comment:each TPP binds in a site lying between a PYR domain and a PP domain from different subunits.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                          #                            #                         #   #  
2VBI_A         7 MYLAERLVQiglkHHFAVAG----DYNLVLLDqlllnkdMKQIYCCNELNCGFSAEGYARSNg-aAAAVVtfSVGAISAM 81  Acetobacter pas...
2JLA_A        14 AVILEALTRhgvrHICIAPG----SRSTPLTLaaaensaFIHHTHFDERGLGHLALGLAKVSkqpVAVIVtsGTAVANLY 89  Escherichia coli
Q54271         5 SDMLAGLTGlgvtTVAGVPCsyltPLINRVISdr----aTRYLTVTQEGEAAAVAAGSWLGGg-lGCAITq-NSGLGNMT 78  Streptomyces hy...
CAB45023       5 DEFAAALLDqdyqFFSGVPCsrlaGVTSILSSh-----eGRYVPAANEGAALAIAAGARMAGt-rAAVLIq-NSGLGNMV 77  Amycolatopsis o...
ZP_01998558    5 ENFVQIAKKkgfgLYAGVPCsflkPFINYVIDsp----dIQYVGAANEGEAVAIAAGAELAGm-rSVAMFq-NSGLGNAV 78  Beggiatoa sp. PS
YP_343344      5 HEFIDSAREggfgCYGGVPCsfltPFINYVIErn----dLTYVSSANEGDAVALAAGAYLGGq-pAIAMMq-NSGLGNAV 78  Nitrosococcus o...
YP_001117109   5 AQFVEAARErgfdWYAGVPCsyltPFINYVLQdp----tLHYLSAANEGDAVALIAGATLGGk-rGIAMMq-NSGLGNAV 78  Burkholderia vi...
YP_001819858   5 QLFLDACRErdvrFFTGTPCsymkPFMNAVINdp----aLTFRDATNEGDAVALAAGVHVATgatTVVMFq-NSGLGNAV 79  Opitutus terrae...
ZP_01128073    5 ESFVEAGRRrgfnRYIGVPCsfitPFINYVIGae----gLQYISHANEGDAVATAAGLEIAGq-rTVVMMq-NSGLGNAV 78  Nitrococcus mob...
NP_733715      5 QEFCDLLADggftFASGVPCshfgGPIAHLSTe-----pGRYVPAPNEGSALAVAAGAALGGq-rAYVMLq-NSGLGNLI 77  Streptomyces co...
Feature 1                                                                                        
2VBI_A        82 NALGGAYAE-NLPVILISGAPNSNdqgtghilhhtigktdysyQLEMARQVT---CAAESITda--------hsAPAKID 149 Acetobacter pas...
2JLA_A        90 PALIEAGLT-GEKLILLTADRPPElidcga--------nqairQPGXFASHP---THSISLPrptqd--iparwLVSTID 155 Escherichia coli
Q54271        79 NPLTSLLHPaRIPAVVISTWRGRPgek-------------depQHHLMGRVTgdlFGLCDMEwsl------lpdTPDALR 139 Streptomyces hy...
CAB45023      78 NPLTSLVLPyEIPVLVVVSLRGWPvgt-------------depQHNVMGKATkpmADLCGMPsmv------lepSLGSLA 138 Amycolatopsis o...
ZP_01998558   79 NPLTSLHQIfNIPILLIVTWRGEPegap------------depQHKLMGAITpqlLELMQIPwayfp--teteqIESTLN 144 Beggiatoa sp. PS
YP_343344     79 NPLTSLTHTfHIPILLIITLRGDPtlr-------------depQHELMGQITgslLEAMEIPweyfp--leskqIHSALE 143 Nitrosococcus o...
YP_001117109  79 SPLTSLTWTfRLPQLLIVTWRGQPgvp-------------depQHALMGPITpamLDTMEIPwetfp--tdpeqVGPALD 143 Burkholderia vi...
YP_001819858  80 NALTSLNVPfQIPALLIITHRAQPggvp------------depQHQFMGEVTiplLEALQIPwapfp--ktaaeIAPLLD 145 Opitutus terrae...
ZP_01128073   79 SPLTSLSNIfRLPVLLICTHRGAAgve-------------depQHSKMGAITgalFETMGIPwrafp--aeldrIEAALD 143 Nitrococcus mob...
NP_733715     78 NPLTSLVMTyQLPILTFASLRGWPdpat------------depQHAVMGPAThglLDSVDTPhhtlyaqdgveeFAAVLE 145 Streptomyces co...
Feature 1                               
2VBI_A       150 HVIRTALre----rkPAYLDIAC 168 Acetobacter pasteurianus
2JLA_A       156 HALGTLHa------gGVHINCPF 172 Escherichia coli
Q54271       140 GEFDVCRealarrelPYGFLLPQ 162 Streptomyces hygroscopicus
CAB45023     139 EALASSQkaem-dgkPFCLLVPK 160 Amycolatopsis orientalis
ZP_01998558  145 HAVEFMAkh----qkPYALIMKK 163 Beggiatoa sp. PS
YP_343344    144 RAHQYMQqa----erPYAFIMRK 162 Nitrosococcus oceani ATCC 19707
YP_001117109 144 RAVAHMDat----grPYALVMQK 162 Burkholderia vietnamiensis G4
YP_001819858 146 RALTHLRer----slPFAIVMPW 164 Opitutus terrae PB90-1
ZP_01128073  144 EADNYLQre----qqPFALVMQK 162 Nitrococcus mobilis Nb-231
NP_733715    146 KAEKDLAeq----raPFVLVERG 164 Streptomyces coelicolor A3(2)

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