1RQE,3BG3,3BG9,1S3H,3HB9,3BG5,3HBL,3HO8,2QF7,2NX9


Conserved Protein Domain Family
DRE_TIM_PC_TC_5S

?
cd07937: DRE_TIM_PC_TC_5S 
Click on image for an interactive view with Cn3D
Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain
This family includes the carboxyltransferase domains of pyruvate carboxylase (PC) and the transcarboxylase (TC) 5S subunit. Transcarboxylase 5S is a cobalt-dependent metalloenzyme subunit of the biotin-dependent transcarboxylase multienzyme complex. Transcarboxylase 5S transfers carbon dioxide from the 1.3S biotin to pyruvate in the second of two carboxylation reactions catalyzed by TC. The first reaction involves the transfer of carbon dioxide from methylmalonyl-CoA to the 1.3S biotin, and is catalyzed by the 12S subunit. These two steps allow a carboxylate group to be transferred from oxaloacetate to propionyl-CoA to yield pyruvate and methylmalonyl-CoA. The catalytic domain of transcarboxylase 5S has a canonical TIM-barrel fold with a large C-terminal extension that forms a funnel leading to the active site. Transcarboxylase 5S forms a homodimer and there are six dimers per complex. In addition to the catalytic domain, transcarboxylase 5S has several other domains including a carbamoyl-phosphate synthase domain, a biotin carboxylase domain, a carboxyltransferase domain, and an ATP-grasp domain. Pyruvate carboxylase, like TC, is a biotin-dependent enzyme that catalyzes the carboxylation of pyruvate to produce oxaloacetate. In mammals, PC has critical roles in gluconeogenesis, lipogenesis, glyceroneogenesis, and insulin secretion. Inherited PC deficiencies are linked to serious diseases in humans such as lactic acidemia, hypoglycemia, psychomotor retardation, and death. PC is a single-chain enzyme and is active only in its homotetrameric form. PC has three domains, an N-terminal biotin carboxylase domain, a carboxyltransferase domain (this alignment model), and a C-terminal biotin-carboxyl carrier protein domain. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name "DRE-TIM".
Statistics
?
PSSM-Id: 163675
View PSSM: cd07937
Aligned: 201 rows
Threshold Bit Score: 258.13
Threshold Setting Gi: 237747106
Created: 11-Sep-2009
Updated: 2-Oct-2020
Structure
?
Program:
Drawing:
Aligned Rows:
 
Conserved site includes 12 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Structure:1RQE_A; Propionibacterium freudenreichii transcarboxylase 5S binds Co2+ and oxaloacetate, contacts at 4A.
    View structure with Cn3D
  • Comment:The active site contains a carbamylated lysine.

Sequence Alignment
?
Format: Row Display: Color Bits: Type Selection:
Feature 1              ##  #                            #   #                                 # #
1RQE_A        27 ITELVLRDAHQSLMATRMAMEDMVGACADIDAag-yWSVECWGGATYDSCIRFLNEDPWERLRTFRKl-mPNSRLQMLLR 104 Propionibacteri...
NP_661728      6 FMDVSFRDGFQSCYGARVKTEDFLPVLEAAVEag-tDNFEIGGGARFQSLYFYCQEDAFEMMDACRRvvgPDINLQTLSR 84  Chlorobium tepi...
YP_379167      6 FMDVSFRDGFQSCYGARVRTEDFLPVLEAAVAag-tDNFEIGGGARFQSLYFYCEEDAFEMMDRAREvvgPDINLQTLSR 84  Chlorobium chlo...
YP_001130534   6 FMDVSFRDGFQSCYGARVKTADFIPALEAAVAag-tDNFEIGGGARFQSLYFYCQEDAFEMMDAARKvvgPDINLQTLSR 84  Prosthecochlori...
YP_497133      6 LVDVTMRDGNQSLWGATGLNTAHMLQAAALTEacgfRAIDFTSSSHMAVAVRYFQNNPWERLRRMAAa-mPTTPLQFITT 84  Novosphingobium...
YP_160306      6 LVDVSLRDGNQSLWGAVGVKTRTIERVCPAIDrvgyRALELLSSTQVAVAVRFHREDPWARIDAASRa-aPRTPLGFLTT 84  Azoarcus sp. EbN1
ZP_03933203   33 IIDTTLRDAHQSIWATRMTTSHILSLLDDITNag-fEHVDLVAPIQFDVSVRYLKEDPWERVRLVHEnaaPGTKFRALIR 111 Corynebacterium...
ZP_04495938    7 LIDVTLRDGNQSLWSATGIDTETVLAVAPLLDqvgfKALDFTTSTHMAISVRYHQEDPFERIRLTSQl-mPNTPLIFMTT 85  Sphaerobacter t...
ZP_01904236    7 FIDVTLRDAHQCLWATRMTTGMMKDIAPFLDRag-fEAIDLVGGAVFDVCVRFLREDPWERMRILNTw-iTETPLIIHTR 84  Roseobacter sp....
NP_879691      7 IIDTTLRDAQQCLWATRMTAGMMDPIAQALDEag-fDMIDFMAPVQFDVCVRYLREDPFEKARHFRKr-fRNTPMRSYCR 84  Bordetella pert...
Feature 1                                                                     #                  
1RQE_A       105 GQNllgyrhyndevvdRFVDKSAEngmdVFRVFDAMNDPRNMAHAMAAVKKAg-kHAQGTICYtis-------pvHTVEG 176 Propionibacteri...
NP_661728     85 GANvvglvsqsrdiidLHAKMFKKhgvsTIRNFDALMDVRNLAWSGQCIVNAg-lKHQVVIALmglppglnepycHTPQF 163 Chlorobium tepi...
YP_379167     85 GANvvglisqsrdiidLHARLFKKhgisTIRNFDALMDVRNLAYSGQCIHNAg-lKHQVVIALmglapglketycHTPQF 163 Chlorobium chlo...
YP_001130534  85 GANvvglvsqsrdiidLHARMFKKhgitTIRNFDALMDVRNIAYSGQCIHNAg-lKHQVVIALmglppglsekycHTPQF 163 Prosthecochlori...
YP_497133     85 GLRfiawqqadpefmrLVYRALQAngvgRFVLLDPMHEVPAVIEAAKLVKEEgnaEVMAALTFtls-------eiHTDQF 157 Novosphingobium...
YP_160306     85 GKRfisfsrtpanlfqLAFDLLRRhgvtRMWIIDPMHDMASARETARMARRAgfdEVVAGICYtis-------pvHTDDY 157 Azoarcus sp. EbN1
ZP_03933203  112 SKNlasfdflpddailNWTERLYAngfrVIGSFDGLNDIDNIDQGLKLAKELg-aETFGALSYcls-------pvHTDDL 183 Corynebacterium...
ZP_04495938   86 GMRfitwepapraiirLAMQLVIKhgirRIQIVEPMNNMPALLEAAKIAREEgaeQVVAGLVYsis-------pvHTDEF 158 Sphaerobacter t...
ZP_01904236   85 GQSlftfeffpddiveLAAERFAAngmrYHTPYDPLNDIRNLRIPVQAARKLg-iHTVPGLVYtys-------pvHTDEY 156 Roseobacter sp....
NP_879691     85 SKSlvgfsmvpddmveLWIDCLAAngfsAVGTLDSLLDVDNMKVSVRRAKKIg-iKSIGALVFces-------plHTDAL 156 Bordetella pert...
Feature 1                            #                              # #                          
1RQE_A       177 YVKLAGQLLdmg--adSIALKDMAALLKPQPAYDIIKAIKDTygqktqINLHCHSTTGVTEVSLMKAIEAGVDVVDTAIS 254 Propionibacteri...
NP_661728    164 YLDKLKEILdagipfdSVAFKDASGTTTPAVIYETIKGARKMlpegtvLQFHTHDTAGMGVACNFAAIEAGIDIIDLAMA 243 Chlorobium tepi...
YP_379167    164 YLDKLQEILdtgipfdSVAFKDASGTTTPATVYETVKGARKMlpsetvIEFHTHDTAGMGVACNFAAIEAGADIIDLSMA 243 Chlorobium chlo...
YP_001130534 164 YLDKLREILdagipfdSVAFKDASGVTTPAVVFESIKGARKMlpegtiIEFHTHDTAGMGVACNFAAIEGGADIIDLAMA 243 Prosthecochlori...
YP_497133    158 YADFARAVGqsp-nidLFYIKDPAGLLSVDRARTLVPAVKAVign-rpLEIHAHTTVGQGMMASLEAAKLGISAIHVGVG 235 Novosphingobium...
YP_160306    158 FADRVAELDdce-aidSVYLKDPAGLLTPARLESLVPHMRQRlkrlriDELHTHCNTGLAPITLLTAADLGIGTLHCALP 236 Azoarcus sp. EbN1
ZP_03933203  184 YKRKATELLert-dvdRIMLKDAGGLLTPDRLKTLIPAIRSSigd-vpLEVHTHSLTGLSPLTYLYAAELGVDSIHTSIA 261 Corynebacterium...
ZP_04495938  159 YVGCAAALAgatdlidTVYIKDPSGLLTPERVETIVPAMRKAlgs-mpLEIHSHCNAGMAPLCYLRAAELGVETVHTAIP 237 Sphaerobacter t...
ZP_01904236  157 YRKKALELVeig--vdGIFIKDPSGLLTPERVATLVPAIKSAigd-lpLQLHSHCLSGLSPYVALQAVEHGIDVLHTATS 233 Roseobacter sp....
NP_879691    157 YAGTAAELVrcg--vdGIMLKDSGALLTIERIRTLIPALRAAvgd-ipIEVHSHSNTGLVQRVYLDAADLGIDQLHTSIA 233 Bordetella pert...
Feature 1               #                                           
1RQE_A       255 SMSLGPGHNPTESVAEMLEgtgyTTNLDY--DRLHKIRDHFKAIRPKYKKF 303 Propionibacterium freudenreichii
NP_661728    244 PVSGGTAEVDILTMWHRLRg--tDYTLDIdqEKYLEVERMFIEHMDKYYMP 292 Chlorobium tepidum TLS
YP_379167    244 PVSGGTAEVDILTMWQRLRg--tDYTLDIdqEKYLEVESFFTEQMYKYYMP 292 Chlorobium chlorochromatii CaD3
YP_001130534 244 PVSGGTAEVDILTMWHRMRg--tDYTLDIdpEKYIEVEALFAERMEKYYMP 292 Prosthecochloris vibrioformis DSM 265
YP_497133    236 PGGDGSSLPEANRMVANLEeagfSVGVDK--AALKRLTTYWERVALAEGLP 284 Novosphingobium aromaticivorans DSM 12444
YP_160306    237 PLANGSSHAPAAQLVANLRarghRVDVDL--DAMEEASAILRREAMLRRLP 285 Azoarcus sp. EbN1
ZP_03933203  262 PLANGPGQPATQAVVRDLRalgyTVDVDD--ERIDSASERIQEIADTEDKP 310 Corynebacterium accolens ATCC 49725
ZP_04495938  238 PLAEGTSLPSITRTVANLRelgfDVDIDL--EPIERISQHLFELARRKGYR 286 Sphaerobacter thermophilus DSM 20745
ZP_01904236  234 TLAHGASHPPTERVVENLRrrghSAALDL--DAIREVAERLDYIAKVEGKP 282 Roseobacter sp. AzwK-3b
NP_879691    234 PLAGGVAQPSIQNMTRNLAqrgyRTDVDM--ARVEEISAYLHRLAARYDFP 282 Bordetella pertussis Tohama I

| Disclaimer | Privacy statement | Accessibility |
NCBI Home NCBI Search NCBI SiteMap