Conserved Protein Domain Family
DRE_TIM_Re_CS

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cd07947: DRE_TIM_Re_CS 
Clostridium kluyveri Re-citrate synthase and related proteins, catalytic TIM barrel domain
Re-citrate synthase (Re-CS) is a Clostridium kluyveri enzyme that converts acetyl-CoA and oxaloacetate to citrate. In most organisms, this reaction is catalyzed by Si-citrate synthase which is Si-face stereospecific with respect to C-2 of oxaloacetate, and phylogenetically unrelated to Re-citrate synthase. Re-citrate synthase is also found in a few other strictly anaerobic organisms. 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
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PSSM-Id: 163684
View PSSM: cd07947
Aligned: 14 rows
Threshold Bit Score: 413.641
Threshold Setting Gi: 52352366
Created: 16-Sep-2009
Updated: 2-Oct-2020
Structure
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Aligned Rows:
 
Feature 1:active site [active site]
Evidence:
  • Comment:Based on the active sites of other DRE-TIM superfamily members such as 3-hydroxy-3-methylglutaryl-CoA lyase.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                ##  #                               #                           # #     
BAH05928      49 IYITDTTFRDGQQSMppy-tsrEIVRIFDYLHELdnnsgiIKQTEFFLYTKKDRKAAEVCMERGyefPEVTSWIRAdkED 127 Clostridium klu...
NP_619128     21 IFISDSTIRDGSQMPgivlsreHKIQIYEYLHEIg-----IEKLEAFVFNKRDRDAVELMFDRGyecPEITGWARAsrAD 95  Methanosarcina ...
YP_001179534  54 LYITDTTFRDGQQSRspy-tveQICRIYDYLHELdngsgvILHTEFFVYSKQDKEAVLKCLEKGydfPKVTAWIRAkkED 132 Caldicellulosir...
CAJ71194      56 IWITDTTFRDGQQSMppy-tvkQIVDLFDMIHKLggkrglIRQCEFFLYNEKDKEAVRKCMERGykyPEITGWIRAvkSD 134 Candidatus Kuen...
ZP_05497866   56 FWITDTTFRDGQQSRvpy-tvdQILKLYDFLHLLggekgiIRQTEFFLYSDKDKEAALGCMERGykfPEVTGWIRPlsKD 134 Clostridium pap...
YP_461521     64 IFITDTTFRDGQQARppy-ttqQIVDLYQMMSRLggyngiIRQTEFFLYSNRDKEAVRMCQDLGlqyPEITGWIRAarED 142 Syntrophus acid...
YP_002435965  51 MFITDTTFRDGQQARppy-tvkQIVHIFDMLHRLggrsglIQASEFFMYSEKDRKAIDACRAKGykfPRVTGWIRAnvND 129 Desulfovibrio v...
YP_001541724  20 LYITDTTFRDGQQAFyay-spsDVKGLFKLLSELdngsgrLSRSEFFLYTERDRRIVNAVKGLGlkyPKVIGWGRArvED 98  Caldivirga maqu...
YP_001737402  25 LLITDTTLRDGQQGSrpf-skeECIKIYSILSELdggsgvIRDIELFPYTSKDREVIKALRDFGt-tPNPIGWIRAriED 102 Candidatus Kora...
YP_001181224  47 LYVTDSTFREGQQAIsyi-gkeNVAKIFEYLHYVdngtgtIKYSEFFLYTNYHKQCVQECLKKRfkfPKVVGWVRSkkDE 125 Caldicellulosir...
Feature 1                                                                  #                     
BAH05928     128 LKLVKDm-GIKETGMLMSCSDYHIFKKlk-mtRKETMDMYLDLAREALNNGIRPRCHLEDITRADFYGFVVPFVNELMkm 205 Clostridium klu...
NP_619128     96 IDKILEvdGLEETGILMSVSDTHIYSKmrlsgREEAEEKYLDALQYAVDHGLRTRAHLEDMTRADNYGFVFPLVKKIMei 175 Methanosarcina ...
YP_001179534 133 FEIVKSl-GIKETGILVSCSDYHIFKKlk-mtRSQAMKQYLEIVSAALEAGIIPRCHFEDITRADFYGFVLPFINELMkl 210 Caldicellulosir...
CAJ71194     135 FKLAKEm-GLKETGILCSSSDYHIYLKlk-ktRKQALEMYLDIVRAALEEGMIPRCHFEDITRADLYGFVIPFAKELMkl 212 Candidatus Kuen...
ZP_05497866  135 LELVKDf-GLKEVGFLVSSSDYHIFKKln-ktRQQAMEDYMSIIRKAVELEIKPRCHFEDITRSDFYGFVLPFANELQkl 212 Clostridium pap...
YP_461521    143 IPLVKEa-GLKETGILTSVSDYHIFLKln-mtRSQALEEYLGIVKAILDAGIVPRCHFEDITRADIYGFCIPFAIELMkl 220 Syntrophus acid...
YP_002435965 130 LKIARDm-EFEEVGLLTSVSDYHLYLKlg-ldREKAMDNYLRVVEQALEWGITPRCHFEDITRADIHGFCLPFARKLMdl 207 Desulfovibrio v...
YP_001541724  99 VRLVKEs-GLDEMVMLMSISDIHIKAKfn-ttRARVVEKYLEAAEEAMRSGIALRCSLEDVTRADVLGFVVPFVNKLLrl 176 Caldivirga maqu...
YP_001737402 103 LKLVKEc-GLDTTVLLTSVSDYHIHYKlr-msRTEAREKFLSAIREGLRMGLKLKVAMEDITRSDIYGFVLPFIEDILri 180 Candidatus Kora...
YP_001181224 126 LKLAKEf-GLDEVGILMSCSDYHIYKKfq-ktRSEIAARYIDIIQEAFSLGITPRVHLEDITRSDIENFVIPLILAIEem 203 Caldicellulosir...
Feature 1                    #                                      # #                          
BAH05928     206 skeanipiKIRACDTLGLGVPyngvEIPRSVQGIIHGLRNIcevpsesIEWHGHNDFYGVVTNSSTAWLYGASSINTSFL 285 Clostridium klu...
NP_619128    176 d----pdcIIRVCDTVGYGMPfmniDEPYGIPKIVQYLKKDigv--knIETHIHDDYGFGAASSIAGFWHGANWTSVTFL 249 Methanosarcina ...
YP_001179534 211 skeanmpvKIRACDTLGLGSPipgvALPRSVPQIIYGIVNYgevpsewLEWHGHNDFYKAVINSTMAWLYGASMVNTSLL 290 Caldicellulosir...
CAJ71194     213 sresgipiKIRACDTMGVGVSypgaAPPRSVPGIIYGLTHFadvpsecLEWHGHNDLYLAMSNATASWLYGCSAINGALL 292 Candidatus Kuen...
ZP_05497866  213 mvesgtpvKIRLCDTMGYGVSypgaSLPRSVPEIIYSLRTLagfdselLEWHGHNDFYRSVSNAATAWLYGCSGVNCSLL 292 Clostridium pap...
YP_461521    221 reesgvdiKIRLCDTMGYGVTypgaSLPRGVDKLVRAFIDDadvpgrlLEWHGHNDFHKALINATTAWLYGCSAANSTLL 300 Syntrophus acid...
YP_002435965 208 skqsgqpvKIRMCDTMGYGVPypgaTLPRSVPRIVRALTDEggvpgqwLEWHGHNDFHKVLINGATAWLYGCSGVNCTLL 287 Desulfovibrio v...
YP_001541724 177 rdkygaslVIKLPDTTGVGVPyptaSLPYSIPKLIWVMRSLlkipsnaLEFHGHGDYHMAVANAVAAWVYGAGINNGTLL 256 Caldivirga maqu...
YP_001737402 181 sereggevSFKISDTLGLALPfpesPLPRGVPRLIRSLIEEmglrseqIEFHGHNDFHLVVANHLAAWLYGASISNCTLM 260 Candidatus Kora...
YP_001181224 204 akkcdkkvYFKLCDTLGFGVPyeyaSLPRSVPKLIYTISKStdvpperLEWHGHNDFYKAQSNAVCAWLYGASMVNCSIR 283 Caldicellulosir...
Feature 1                                                   
BAH05928     286 GIGERTGNCPLEAMIFEYAqik-gnTKNMKLHVITELAQYFEK 327 Clostridium kluyveri NBRC 12016
NP_619128    250 GIGERAGNSEMEKILLFLAdrv-egFDKYNLEPVTRFAKFMEK 291 Methanosarcina acetivorans C2A
YP_001179534 291 GIGERTGNTPLEAMVMEYIqir-gsADGMNVAVISEIAEYFKK 332 Caldicellulosiruptor saccharolyticus DSM 8903
CAJ71194     293 GLGERTGNTPLEALVIEYLalr-gnDDEIDTTVITDIADYYRN 334 Candidatus Kuenenia stuttgartiensis
ZP_05497866  293 GIGERTGNTPLEAMVIEYAqlr-gtLDGMEVSVITDIARYFEK 334 Clostridium papyrosolvens DSM 2782
YP_461521    301 GLGERTGNPPIEGLIIEYIglm-gkTNGIDTTVITDIANYFKN 342 Syntrophus aciditrophicus SB
YP_002435965 288 GFGERTGNTPLEALVIEYVslt-gdDDAADTRVINEIAEYFEK 329 Desulfovibrio vulgaris str. 'Miyazaki F'
YP_001541724 257 GIGERAGNVPIEALVVWYSrlk-gsFDGMEPRVISRIVEYFKG 298 Caldivirga maquilingensis IC-167
YP_001737402 261 GIGERAGNCPLEAMAIMHSql--sgERKLNLKALSKIIDVFSE 301 Candidatus Korarchaeum cryptofilum OPF8
YP_001181224 284 GIGERTGIAALEVAILDLVqikdenAPNLNFEALDELLEFTSR 326 Caldicellulosiruptor saccharolyticus DSM 8903

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