3DXI


Conserved Protein Domain Family
DRE_TIM_HOA_like

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cd07944: DRE_TIM_HOA_like 
Click on image for an interactive view with Cn3D
4-hydroxy-2-oxovalerate aldolase-like, N-terminal catalytic TIM barrel domain
This family of bacterial enzymes is sequence-similar to 4-hydroxy-2-oxovalerate aldolase (HOA) but its exact function is unknown. This family includes the Bacteroides vulgatus Bvu_2661 protein and 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: 163682
View PSSM: cd07944
Aligned: 39 rows
Threshold Bit Score: 265.966
Threshold Setting Gi: 213969851
Created: 14-Sep-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 10 residues -Click on image for an interactive view with Cn3D
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              ##  #                          #                                         #
3DXI_A         5 ILDCTLRDGGYYTNWDFNSKIVDAYILAXNELPIDYLEVGYRnkps-keyxGKFGYTPVSVLKHLRNis----tkKIAIX 79  Bacteroides vul...
ZP_03461320    6 ILDCTLRDGGRVINCEFSDDEIRDISRRLSDSNIDIVEVGFLrdskkvhfeGNSTFFTDVNQIAPYLdkss-gncMYVAF 84  Bacteroides pec...
ZP_03730297    6 VLDCTLRDGGRIINCAFPDTEIKDISVRLARAKIDIVEVGFLrdwrkvkyeGNSTFFTNVDQIRPFIdkrq-kgtMFVAF 84  Clostridium sp....
ZP_04542735    1 MLDCTLRDGGYVNDWDFGHSTITGIYKRLEAAGADYIEVGFLddrr-efdiNRSIMPSTEAINKIFGsvkk-gkaIPVAM 78  Bacteroides sp....
ZP_02423842    6 ILDCTLRDGGYINNWKFGYENIKDTVRRLIQAGIDIIEAGYLsskg-dfsaDESQYSSVDAIKRILPadr--kntLIAVM 82  Eubacterium sir...
ZP_05348510   19 ILDCTLRDGGYINNWKFGGRTIKSIISNLEDAGVDIIECGFIrked--hssDSSVFSSMEQVADIIApkk--aniSYAIM 94  Bryantella form...
YP_001301260   6 LLDCTLRDGGYINNFRFGKYAIRKILQQLTHAGLDIVECGFLedge--ydeDTSIFNAAEQIASLLPneh--grtMFVAM 81  Bacteroides vul...
ZP_02080945    5 LLDCTLRDGGYINDWKFGYRTAKSIIQKLVDSNADYVEVGFLrncs--ydkNATLFNNIAELKKILPreq--kntKFTVM 80  Clostridium lep...
YP_001951033   6 ILDCTLRDGGFVNDWNFGLGSMKSIISRLDKAGVDMVEIGFIderr-sydpNRAIQPDTQSFQAVLQgldi-rnsLILGM 83  Geobacter lovle...
ZP_03775585    6 LLDCTLRDGGYINDWRWGFGSARRIIQSLTRAGTDLVEVGFLrnve-gydpDVTVCNTIEELNRLLPdegqrghtLYSGM 84  Subdoligranulum...
Feature 1         #                                                           #                  
3DXI_A        80 LNeknttpedlnHLLLPIIGlv--dXIRIAIDpq----niDRAIVLAKAIKTXGFEVGFNVXyxskwaexNGFLSKLKAI 153 Bacteroides vul...
ZP_03461320   85 IDygm----fdfDTLGQCDGts-vdGIRVGFTkkdyyssrDDIIRCLNIVKARGYKLFVQGVnsls-ysdKEMLDLVDLV 158 Bacteroides pec...
ZP_03730297   85 IDygm----fdfESLTPYDGts-idGIRFGFTkkdytehcDDILKCIERIKNLGYKLFIQGVnsln-ysdKELLELVELV 158 Clostridium sp....
ZP_04542735   79 IDfgt----cslDSIGSCDStf-idGIRVIFKke----kiDQALPFCKAIKEKGYKLFIQAIsita-ysdIEMLEYVNRI 148 Bacteroides sp....
ZP_02423842   83 INcgd-----ydAELLPQYDgtgpdCIRVCFHks----qaLQAVELCRKIKEKGYKVYFQPMvals-ysdAEYLGLIGMA 152 Eubacterium sir...
ZP_05348510   95 IEqhn-----hvDKLIPENDgngadIIRITFRrk----ewEEAKVAIKHLICKGYKVCVQPVgtvt-yddESLLKLIKDV 164 Bryantella form...
YP_001301260  82 VCyge----ydlSQLSPCTRns-idGIRVTFHyd----evEGALEYCREIKEKGYKVFVQPVgtss-ytdIQLLHLIEKV 151 Bacteroides vul...
ZP_02080945   81 ALhnk----ydiTKLEPNDGtv--eAVRVTFHdy----diDEGLEFVKKVMEKGYKCFCNPInimg-ysdQEILNLIQKI 149 Clostridium lep...
YP_001951033  84 VDygt----cdiDKIAPKEHsy-idGIRVIFKkk----dqDAALRYLQQIKAKGYKIYVNPVsitg-ysdEEICSLIGKI 153 Geobacter lovle...
ZP_03775585   85 AMrsn----ydiSKLSPYDGhg-ieLIRITAHdy----diRDGMDFAREVKARGYKLSINPInimg-yndKDLLWIFDQV 154 Subdoligranulum...
Feature 1                  #                              # #                                    
3DXI_A       154 Dki-aDLFCXVDSFGGITPKEVKNLLKEVRKYth--vpVGFHGHDNLQLGLINSITAIDDGi----DFIDATITGXGRGA 226 Bacteroides vul...
ZP_03461320  159 NevhpYSFGIVDTYGAMYEDDLQRIYALINNNmhkdicIDFHSHNNYQLSFSLAQSIIRLSdsvrhIIIDATLNGMGKVA 238 Bacteroides pec...
ZP_03730297  159 NrakpYSFGIVDTYGAMYADDVERIYRLIDHNmdpdicINFHSHNNYQLSFSFAQEVIKLSrgirnVIIDSTLSGMGKVA 238 Clostridium sp....
ZP_04542735  149 NeikpYAFSIVDTYGLLDNSSMARYFYLIDNNldpsikMGYHEHNNFQLGFSNTIKFLEKStk-rtLVADSTVYGMGKSA 227 Bacteroides sp....
ZP_02423842  153 NkfrpDGFYIVDSHGSMKQKDVARFFYLIENNldkeiaVGFHSHNNLQLSYSNAQYLTALHtd-hnLIIDSSIMGMGRGA 231 Eubacterium sir...
ZP_05348510  165 NqikpYAFYLVDTLGVMYRHDMRRFFYLIDNNlskeicLGFHSHNNLQMSFANAQEMMRLAkq-rsIIVDTSCYGMGRGV 243 Bryantella form...
YP_001301260 152 NelqpYSFYLVDTLGLMHKNDIARFFYLINTNldksinMGFHSHNNLQLSFSNSQEFFEYVgd-rvISLDASIYGMGRGA 230 Bacteroides vul...
ZP_02080945  150 NqikpYAFSIVDTFGSMIKSDLLRIYSLLEHNldksivIGLHLHENLSLSYSLAQEFIGMRnvnrdCVIDGSLMGMGRVP 229 Clostridium lep...
YP_001951033 154 NgldpEGVSIVDTYGLMHRKDLLHYFRLFDKYlsnhitLGYHAHNNFQLVYANSIELCELLge-rnIIIDSSLYGMGKGA 232 Geobacter lovle...
ZP_03775585  155 NaihpWQFSIVDTFGSMRRRDLERIVSLADHNlapdirLGLHLHENMALSFCLAQEFIDKPll-rdKTVDASLMGMGRAP 233 Subdoligranulum...
Feature 1                                                   
3DXI_A       227 GNLKXELLLTYLNkh-hGLNVDFNVLGNIiTTFTPLLEKYQWG 268 Bacteroides vulgatus ATCC 8482
ZP_03461320  239 GNLNTELIVDYMVrklnCNYDFEQILDIIdDYIYPYKEKDFWG 281 Bacteroides pectinophilus ATCC 43243
ZP_03730297  239 GNLNTELLVDYLVrkknYDYEFDEILDLIdDYIVPYSLNYRWG 281 Clostridium sp. M62/1
ZP_04542735  228 GNCASELLAMHLNeyygGHYDLNQLLEIVdTDLMPIYQKHYWG 270 Bacteroides sp. 9_1_42FAA
ZP_02423842  232 GNLNTELFVEYLNetagADYSTEPILCSIdNTIARIYMTTAWG 274 Eubacterium siraeum DSM 15702
ZP_05348510  244 GNLATELFADYVNktieYRYALTPILNIVdKYLMPVYAEQRWG 286 Bryantella formatexigens DSM 14469
YP_001301260 231 GNLNTELIANYVNdregHMYAIEPLLEVVdEFIIHIRQKHEWG 273 Bacteroides vulgatus ATCC 8482
ZP_02080945  230 GNLCLELIMDYMNkydsVKYNVDSVLDAIdDHILAIRKESPWG 272 Clostridium leptum DSM 753
YP_001951033 233 GNANTELIAMYYNeninSKYEVEHLLEAIdVDILKEYAKAPWG 275 Geobacter lovleyi SZ
ZP_03775585  234 GNLPIELVADYRNetgsCHYDLDEIMDAIqDHIAPIKGESEWG 276 Subdoligranulum variabile DSM 15176

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