3BLE


Conserved Protein Domain Family
DRE_TIM_CMS

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cd07945: DRE_TIM_CMS 
Click on image for an interactive view with Cn3D
Leptospira interrogans citramalate synthase (CMS) and related proteins, N-terminal catalytic TIM barrel domain
Citramalate synthase (CMS) catalyzes the conversion of pyruvate and acetyl-CoA to (R)-citramalate in the first dedicated step of the citramalate pathway. Citramalate is only found in Leptospira interrogans and a few other microorganisms. 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: 163683
View PSSM: cd07945
Aligned: 10 rows
Threshold Bit Score: 515.773
Threshold Setting Gi: 241776134
Created: 16-Sep-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 11 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Structure:3BLE_A; Leptospira interrogans citramalate synthase binds Zn2+ and malonate, contacts at 4A.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1             ##  #                           #                                  #       
3BLE_A        23 LDVTLRDGEQTRGVSFSTSEKLNIAKFLLQklnVDRVEIASARVSKGELETVQKIMEWAateqlteRIEILGFVDGNKTV 102 Leptospira inte...
YP_001838677  11 LDVTLRDGEQTNGVSFSWQQKLNITKHLLKdlkTDRVEIASARVSPGEFEAVQKIIEWAkvegltdRIEILGFVDFDKTV 90  Leptospira bifl...
ZP_01721225    1 MDTTLRDGEQTSGVSFLPSEKLQIAKLLLEelrVDRIEVASARVSDGELEGVQKITHWAaekgyldRVEVLGFVDTPSSV 80  Algoriphagus sp...
YP_003088042   9 MDTTLRDGEQTSGVSFSASEKLTIAQILLQevkVDRIEVASARVSEGEFQAVKKITDWAgangfldKIEVLTFVDGDASI 88  Dyadobacter fer...
NP_810771      1 MDTTLRDGEQTSGVSFVPHEKLMIARLLLEdlkVDRVEVASARVSEGEFEAVKMICDWAarrnllqKVEVLGFVDGHTSV 80  Bacteroides the...
YP_002309266   6 LDTTLRDGEQTSGVSFASSEKLHIARILLVdlnIDRIEIASAKVSEGEYETVKRIVRWAiannyidRIEVLGFVDNTISL 85  Candidatus Azob...
ZP_02033774    5 MDTTLRDGEQTSGVSFAAHEKLSIAQALLDl-gVNRLEIASARVSDGEFEAVKRVASWAertgniqKLEVLGFVDGDVSL 83  Parabacteroides...
ZP_04773415   26 MDTTLRDGEQTQGVSFAPAEKLNLAKVLLEqvrVDRIEVASARVSSGEASAVAQIIDWArerglveRVEVLGFVDGGASV 105 Allochromatium ...
ZP_01898551   11 MDTTLRDGEQTQGVSFTPDEKVSIAKALLQslnVDRIEVASARVSLGEKQAVSSLMQWAeqeqvadRIEILGFVDHTKSV 90  Moritella sp. PE36
ZP_01999460   11 MDTTLRDGEQMQGVSYTPEEKLTISKMLLTevkVDRLEVTSARVSEGEKKSLQKMLDWAkevnlvdKFEVLSFVDKNKSI 90  Beggiatoa sp. PS
Feature 1                                                             # #                        
3BLE_A       103 DWIKDSGAKVLNLLTKGSLHHLEKQLGKTPKEFFTDVSFVIEYAIKSGLKINVYLEDWSNGFRNSPDYVKSLVEHLSkeh 182 Leptospira inte...
YP_001838677  91 EWMKGTGVKVLNLLTKGSLNHLTNQLRKTPEEHFNDIKQTVEVAVKAGITVNVYLEDWSNGYLHSRDYVIQYLKTVSefp 170 Leptospira bifl...
ZP_01721225   81 NWLLKAGAKVMNLLTKGSLNHLTHQLRKTKEEHFSDIAKSIAHAQENGIDVNIYLEDWSNGMRNSPEYTMDLIQFLSekp 160 Algoriphagus sp...
YP_003088042  89 NWMVQAGARVMNLLTKGSLNHLTHQLKKSPEAHFEDIRNVVELAEKNGIQCNVYLEDWSNGMRSSKEYVFQSLDFLStlp 168 Dyadobacter fer...
NP_810771     81 DWIQRTGCRVINLLCKGSLKHCTQQLKKTPEEHIADIINVVHYADEQDIGVNVYLEDWSNGMKDSPEYVFQLMDGLKqts 160 Bacteroides the...
YP_002309266  86 NWVKSTGCKVMNLLCKGSLKHCTKQLRKTPEQHLVDIKEVLRNAKKMDIIINIYLEDWSNGMTDNPDYVFFLMDNLKdtn 165 Candidatus Azob...
ZP_02033774   84 NWIEAAGCRVVNLLCKGSYKHVTEQLRKTPEQHFADIRSVINQAIERGIAVNIYLEDWSNGIKNSPEYVFQAVDSLRdlp 163 Parabacteroides...
ZP_04773415  106 DWICGAGGQVLNLLAKGSEKHCRGQLGKTLDEHAADVRATIAAAQSRGLRVNLYLEDWSNGYRDNPDYVYGLVERLAdvg 185 Allochromatium ...
ZP_01898551   91 DWITSSGAKVINLLTKGSEKHCTEQLRKTPSQHIADVRETIYYAIEQGLSVNIYLEDWSNGYSDNPEYVYNMVSELSdlp 170 Moritella sp. PE36
ZP_01999460   91 DWAKSVGVKRVNLLTKGSYKHCTEQLRKTPEQHAVDIEETVRYATDNGIEVNIYLEDFSNGIKTSPDYVYTIIDFLLtlp 170 Beggiatoa sp. PS
Feature 1              # #                           # #                                         
3BLE_A       183 IERIFLPDTLGVLSPEETFQGVDSLIQKYPDIHFEFHGHNDYDLSVANSLQAIRAGvKGLHASINGLGERAGNTPLEALV 262 Leptospira inte...
YP_001838677 171 IKRFYLADTLGVMSPEEVKKAVTDLVSLFPNLWFEFHGHNDYDLAVANCLEAVKAGaRGLHVAVNGLGERAGNSPLEAVV 250 Leptospira bifl...
ZP_01721225  161 IKRIMLPDTLGLLSPEETKAFLLDISEKYPSVHFDFHAHNDYDLSVANVMEAILNGaSGIHTTINGLGERAGNAPLESVI 240 Algoriphagus sp...
YP_003088042 169 VKRILLPDTLGILTPFESYTFIKEIVDRYPDQHFEFHGHNDYDLGVANVMEALRAGvQGLHLTVNGMGERTGNAPLASTI 248 Dyadobacter fer...
NP_810771    161 IRRYMLPDTLGILNPLQVIEYMRKMKKRYPNTHFDFHAHNDYDLAVSNVLAAVLSGvRGLHTTINGLGERAGNAPLSSVQ 240 Bacteroides the...
YP_002309266 166 IQHFMLPDTLGILNPFNTNIFCKRIRERYPNIQLDFHAHNDYDLAVGNVFAAVNAGiTGIHTTINGLGERAGNAPLASVI 245 Candidatus Azob...
ZP_02033774  164 IRRFMLPDTLGILNPGNTYEYCKEMVTRYPDLKFDFHAHNDYDLAVANVYSAVRAGiKGLHTTLNGLGERAGNAPLSSVL 243 Parabacteroides...
ZP_04773415  186 IGHFMLPDTLGVMTPDQVFTAISDMVGRFPSLQFDFHPHNDYGLATANVLAAVQAGaAAVHCTVNCLGERAGNASLAEVA 265 Allochromatium ...
ZP_01898551  171 IQHYMLPDTLGIMSPDEVHTSLSDMIRRFPQLKFDFHPHNDYGLATANALTAAKVGiSAIHCTVNCLGERAGNASLAEVA 250 Moritella sp. PE36
ZP_01999460  171 IKRIMLPDTLGIFQPFETYAYISTVVKKYPTVHFDFHSHNDYGLGTANAMAAIKAGiKGIHATVNGMGERAGNASLDEVI 250 Beggiatoa sp. PS
Feature 1                                                 
3BLE_A       263 TTIHdks-nsKTNINEIAITEASRLVEVFSGKRISANRPIV 302 Leptospira interrogans
YP_001838677 251 TSLHdkt-kfRTSIVEKEITNASRLVEVFSGKRISDNRPIV 290 Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)'
ZP_01721225  241 AVIKdft-kfEINVQEQKIYRVSKLVEQFSGQHIPANKPVV 280 Algoriphagus sp. PR1
YP_003088042 249 AVINdlmpecTTAVNEKSLYSISKLVETFSGIRIPANKPIV 289 Dyadobacter fermentans DSM 18053
NP_810771    241 AILKdhf-naMTNIDESRLNDVSRVVESYSGIVIPANKPIV 280 Bacteroides thetaiotaomicron VPI-5482
YP_002309266 246 ATLHdql-kiKTNIVEEHLNWASRTIESYSGVRIPNNKPVI 285 Candidatus Azobacteroides pseudotrichonymphae genomova...
ZP_02033774  244 AVLKdql-gvDTTLREERINYASRLVETFSGVHIPPNKPII 283 Parabacteroides merdae ATCC 43184
ZP_04773415  266 VNLRdql-dcALGIDETHLARVSELVESFSGKRISDNAPIV 305 Allochromatium vinosum DSM 180
ZP_01898551  251 VVLKdkl-giESSINEQRIHQISQMIENFSGKITSANAPII 290 Moritella sp. PE36
ZP_01999460  251 VSSKdfl-pvKFNIDEKKLHAISQTIETFSGVRMANNKPIY 290 Beggiatoa sp. PS

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