1PVD,2VBF,2G1I,1QPB,1OVM,2VBG,2VBI,1ZPD,2NXW


Conserved Protein Domain Family
TPP_PYR_PDC_IPDC_like

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cd07038: TPP_PYR_PDC_IPDC_like 
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Pyrimidine (PYR) binding domain of pyruvate decarboxylase (PDC), indolepyruvate decarboxylase (IPDC) and related proteins.
Thiamine pyrophosphate (TPP family), pyrimidine (PYR) binding domain of pyruvate decarboxylase (PDC) and indolepyruvate decarboxylase (IPDC) 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. 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. 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. Also belonging to this group is Mycobacterium tuberculosis alpha-keto acid decarboxylase (MtKDC) which participates in amino acid degradation via the Ehrlich pathway, and Lactococcus lactis branched-chain keto acid decarboxylase (KdcA) an enzyme identified as being involved in cheese ripening, which exhibits a very broad substrate range in the decarboxylation and carboligation reactions.
Statistics
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PSSM-Id: 132921
View PSSM: cd07038
Aligned: 81 rows
Threshold Bit Score: 170.753
Threshold Setting Gi: 127514563
Created: 22-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:2G1I_A, Kluyveromyces lactis, PDC homodimer binds TPP and divalent metal ion; contacts at 3.5A.
    View structure with Cn3D
  • Structure:2VBF_A; Lactococcus lactis branched-chain keto acid decarboxylase (KdcA) homodimer binds TPP and divalent metal ion; contacts at 3.5A.
    View structure with Cn3D
  • Comment:Kluyveromyces lactis PDC is a tetramer (dimer-of-homodimers), Lactococcus lactis KdcA is a homodimer. 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                          #                        #                        #           
1PVD_A         7 KYLFERLKQVNvNTVFGLPGDFNLSLLDKIYEvegMRWAGNANELNAAYAADGYARIKGMSCIITTFGVGELSALNGIAG 86  baker's yeast
2G1I_B         8 RYLFERLKQVEvQTIFGLPGDFNLSLLDNIYEvpgMRWAGNANELNAAYAADGYARLKGMSCIITTFGVGELSALNGIAG 87  Kluyveromyces l...
YP_002128150  27 DVMADILTLFGcKTVFGVGGDFADNIISAFEGk--LETTPSSNEMHAGYAACAQAQISGLGATLTTFTVGSLPCSSPAAL 104 Alteromonas mac...
ZP_01854712   41 SYLVQRLQDYGvTDLFGIPGDFVLQFYGMLEEs-pIRVVGTTREDNAGYAADGYARVHGLGAVCVTYCVGGLSLCNSIAG 119 Planctomyces ma...
YP_001095760  22 DSIAELLAFFGvKRVYGVGGDFVANLINTLDKr--VAVLPSSNEMHAGFSACAQAELNPLGVCMTTYTVGSLPCTSAAAL 99  Shewanella loih...
YP_433239     11 DYLLTRLRQLGlRKVFQVPGDYVSEFMEALEKfdgVEAVGDINELGAGYAADGYARFAGIGAVSVQYGVGTFSVLNAVAG 90  Hahella chejuen...
YP_001940848   5 QFLAQQLLAHNvKHLFCVPGDYSLKILDGFAKe-gIRIINTCDEQGAGFAADAYGRLNGLGAVCITYCVGGLKVTNPVAE 83  Methylokorus in...
NP_925003     10 EYLIERLYSHGvHHIFGVPGDYVLGFFKQLCDs-pIKVINTCDEQGAGFAADAYARVRGLGAVCVTYCVGGLKVANTTAQ 88  Gloeobacter vio...
CAO88944       6 EYLFQRLHNLGvNHIFGVPGDYVLDLMDVLVEs-pIELVCTCNELNAGYAADAYARVKGMGAVCVTYGVGGFSLVNAVVG 84  Microcystis aer...
YP_001952626   9 TYLLQRLKELGvNHLFGVPGDYVLDFLDQVIEs-pLAWVGTCNELNAGYAADGYARLNGLGGAVVTYGVGGFSILNAVAG 87  Geobacter lovle...
Feature 1                                       #                                                
1PVD_A        87 SYAEHVGVLHVVGVPSISsqak----qlllHHTLg-----nGDFTVFHRMSANISETTAMITdi------atAPAEIDRC 151 baker's yeast
2G1I_B        88 SYAEHVGVLHVVGVPSVSsqak----qlllHHTLg-----nGDFTVFHRMSSNISETTAMITdi------ntAPAEIDRC 152 Kluyveromyces l...
YP_002128150 105 AVAEKLPVVFISGAPGEQeisd-----tllHHSVasssewmLKYDCALESFRALGMRAERLQgarskgqpnmAAERFFQL 179 Alteromonas mac...
ZP_01854712  120 AYAEKSPVIVISGAPGMSerat----dpllHHRV-------KDFHTQRDVFEKITVATALLDdp------mtAFLEIDRC 182 Planctomyces ma...
YP_001095760 100 ARTEGLPVVFISGAPGEAeins-----qalHHSVhphtawhTDLDAALNAFKALGLRAERLQgqrhsgqpnvAAEQFLQL 174 Shewanella loih...
YP_433239     91 SYVERNPVVVISASPSAQdrliirdkgvlfHHST-------GNLSADKKVFEQVTVAAEILSna------aeAPLQIDRA 157 Hahella chejuen...
YP_001940848  84 AFAEKSPVVVISGAPGLRerqk----dpllHHKV-------KDFDTQLNVFKALTVFATILEnp------rdIGAQILQA 146 Methylokorus in...
NP_925003     89 AYAEKSPVVVISGAPGTNerhk----npllHHKV-------REFDTQLKVFEQLTVAATVLDdp------qtAFCEIDRV 151 Gloeobacter vio...
CAO88944      85 AYAERVPLVVISGASDRSirrd----nlllHHTT-------GDYNLQFSIMEKVTVASVILTns------aqAASQIDQA 147 Microcystis aer...
YP_001952626  88 AFAEMVPLVLISGAPPTGrrka----galvHHLV-------ADYNRQLEIFQKVTVDAALLDnp------etAPALIDRL 150 Geobacter lovle...
Feature 1                         
1PVD_A       152 IRTTYVTQRPVYLGLPA 168 baker's yeast
2G1I_B       153 IRTTYVSQRPVYLGLPA 169 Kluyveromyces lactis
YP_002128150 180 VAHAYANKQPVFIEIPR 196 Alteromonas macleodii 'Deep ecotype'
ZP_01854712  183 LEACVRFKRPVYLELPR 199 Planctomyces maris DSM 8797
YP_001095760 175 LTHAYVNRQPVYIEVPR 191 Shewanella loihica PV-4
YP_433239    158 LTAAISKRRPIYLEAWR 174 Hahella chejuensis KCTC 2396
YP_001940848 147 VELALQYKRPVYLEIPR 163 Methylokorus infernorum V4
NP_925003    152 FEAALRYRRPVYIELPR 168 Gloeobacter violaceus PCC 7421
CAO88944     148 LAACLHHKRPVYIEIPR 164 Microcystis aeruginosa PCC 7806
YP_001952626 151 LATCISRKLPVYLELPA 167 Geobacter lovleyi SZ

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