Conserved Protein Domain Family
DRE_TIM_NifV

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cd07939: DRE_TIM_NifV 
Streptomyces rubellomurinus FrbC and related proteins, catalytic TIM barrel domain
FrbC (NifV) of Streptomyces rubellomurinus catalyzes the condensation of acetyl-CoA and alpha-ketoglutarate to form homocitrate and CoA, a reaction similar to one catalyzed by homocitrate synthase. The gene encoding FrbC is one of several genes required for the biosynthesis of FR900098, a potent antimalarial antibiotic. This protein is also required for assembly of the nitrogenase MoFe complex but its exact role is unknown. This family also includes the NifV proteins of Heliobacterium chlorum and Gluconacetobacter diazotrophicus, which appear to be orthologous to FrbC. 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: 163677
View PSSM: cd07939
Aligned: 47 rows
Threshold Bit Score: 347.956
Threshold Setting Gi: 225164849
Created: 14-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              ##  #                          #                            # #           
ABB90392       7 LEDTTLRDGEQTPGVAFSKETKTAILNALIEAGVTSIEIGIPaMGGEELDFIKSVVDrqdeaRLVVWHRGVREDVERSLD 86  Streptomyces ru...
NP_907562      4 INDTTLRDGEQAPTVAFTQEEKCEIAKLLYEAGADELEIGIPaMGEAEREDIRAILSlglplRLMSWNRATQSDLEASLA 83  Wolinella succi...
NP_622149     11 IVDTTLRDGEQTAGVVFANNEKIRIAQMLDEIGIDQLEVGIPtMGGDEKETVAKIAKlglkaSIMAWNRAVVKDVQESLE 90  Thermoanaerobac...
YP_001568719   3 IVDTTLRDGEQTAGVVFANEEKVQIAKMLAELGVYQIEAGIPtMGGDEKEAIKKISKldlgvSIMGWNRAVIKDVEESID 82  Petrotoga mobil...
YP_002251336   8 IVDTTLRDGEQTAGVVFSKAEKLQIARMLDEIGVHQIEAGIPvMGGDEEEAIKAIVKaglkaSIMGWNRAVISDIEASLR 87  Dictyoglomus th...
NP_951991     11 IDDTTLRDGEQTAGVVFSKKEKIAIARMLDSIGVRELECGIPaMGEDERAAVRALVDlglsaRLITWNRALVADIQASID 90  Geobacter sulfu...
ZP_03905888    3 IDDTTLRDGEQTPGVAFSRKEKLTIVKHLDAIGVQEIEAGIPvMGLAESRMFESIMElgldaRIIAWNRALIGDVQASIA 82  Denitrovibrio a...
NP_487008      6 INDTTLRDGEQAAGVAFSVEEKIAIAKFLDAIGVHEIEVGIPaMGKAEQEAIANIVKldlsaNLLGWNRAVIADIQASIA 85  Nostoc sp. PCC ...
YP_001716589   6 LVDTTLRDGEQTPGLVFSTEEKVAVASALDRLGVELIEAGIPaMGVDEQKAVRAVLGaglraRVLAWNRAHPSDIEASLA 85  Candidatus Desu...
YP_475234      7 INDTTLRDGEQAAGVAFQIPEKISIAALLDAIGVPEIEVGIPaMGAVETEAIRAMLSlglraHLLGWNRAVPSDILASIR 86  Synechococcus s...
Feature 1                                                          #                           # 
ABB90392      87 LGFTSVHVGLPTSaghlkasvrkdRTWLLATARDMVKMAKDRgaFVSISAEDIARTEISFLQEYAGVVAEAGADRLRLSD 166 Streptomyces ru...
NP_907562     84 CGMKAVDLSIPVStkmvaakfrgkYAKVLSNLEETLTIAKKEglFVCVGMEDTSRANARFLKEVIALAMERGADRVRFCD 163 Wolinella succi...
NP_622149     91 CGVDAVAISISTSdihiehklkktRQWVLDSMTEAVRFAKKEgvYVSVNAEDASRTDMNFLIEFARCAKQAGADRLRFCD 170 Thermoanaerobac...
YP_001568719  83 CGVDAVAISISTSdihikhklkkdRDWVLKSMVDATKFAKKHnlYVSVNAEDASRTDMDFLIKFAKEAKEAGADRLRYCD 162 Petrotoga mobil...
YP_002251336  88 CGVDAVAISISTSdihikyklkktREWVLENMVKATEFAKKHgvYVSVNAEDASRTDMEFLLQFAKAAKEAGADRLRYCD 167 Dictyoglomus th...
NP_951991     91 CGITAVDISLSVSdqmiahklrkdRRWVKEQLRHSLGFAKEKglYVSVGGEDSSRADLLFLVELMEVARDMGADRFRFCD 170 Geobacter sulfu...
ZP_03905888   83 AGANSIEISLPMSdvqintklnktRGWILDQVKSVLDFCANHdlYISVGGEDASRADFDFLAEYIRTIEAHGADRFRFCD 162 Denitrovibrio a...
NP_487008     86 CGLQRVHISIPVSaiqiavkfhgqWQVVLQKLHDSISFAVDQglFVSIGGEDSSRAEESFLLDVVLAAQEWGASRFRFCD 165 Nostoc sp. PCC ...
YP_001716589  86 CGATCLQISFPVSdihlqhklgrtRSWLLARLEEVMALAVAPgrEVAVGAEDASRADPAFLRLFAKKAEEAGACRLRYCD 165 Candidatus Desu...
YP_475234     87 CGLKRIHISVPVSdrqiaakfqgdRPRLLRQLRQCVEMALEQglWVSVGAEDASRTSLEQVIELAQMAQSWGCRRFRYCD 166 Synechococcus s...
Feature 1                                    # #                                                 
ABB90392     167 TVGLLGPEAYGERVAAVLSAad-idVQCHAHNDFGLATANTLAGLKAGARYFHVTVNAIGERAGMADLAQVVVALKklyd 245 Streptomyces ru...
NP_907562    164 TVGILTPLQTYRAIRSLRRHct-lpVEMHCHNDYGMAVANSIAGIEAGAQSVNTTVIGIGERAGNAGFEQVLLSLIgqfg 242 Wolinella succi...
NP_622149    171 TVGFLDPFKTYEMVKAIKDAvd-ieIEMHTHNDFGMATANALAGVKAGAKFVGVTVNGLGERAGNAALEEVVMALKyvyk 249 Thermoanaerobac...
YP_001568719 163 TVGMMEPFSIYEHIRRIIDEvg-inVEMHTHNDFGLATANTLAGIRAGAKYAGVTVNGLGERAGNAALEEVVMALKyiyk 241 Petrotoga mobil...
YP_002251336 168 TVGIMEPFTMYEVIKTIIEKvg-ipVEMHTHNDFGMATANALAGVRAGATYVGVTVNGLGERAGNAALEEVVMALKyiyn 246 Dictyoglomus th...
NP_951991    171 TLGILDPFTMYEKVRTLRTAvpeldIEVHTHNDLGMATANAIAGIKAGARFVNTTVNGLGERAGNAALEEVVMALKlacg 250 Geobacter sulfu...
ZP_03905888  163 TVGILDPFKTYELTAKIREIts-mdIEIHTHNDFGMATANALAAVRAGATHVNTTVIGLGERAGNAPLEEIIMASRhvyg 241 Denitrovibrio a...
NP_487008    166 TVGILDPFTTHAKVKQLVASlt-ipVEMHTHNDFGLATANALAGTKAGALSVNTTVNGLGERAGNAALEEVVMALKhlyh 244 Nostoc sp. PCC ...
YP_001716589 166 TVGVLDPFRSRDAVSDLTHKln-ipLEFHAHNDFGMATANTLAAVKGGAAYLDVTVNGLGERAGNASLSAVARGLRqfyg 244 Candidatus Desu...
YP_475234    167 TVGVLDPFSTYKQIRRLVRAid-ipVEMHTHDDLGMATANALAGIRAGAQSVNTTVNGLGERAGNAPLEEVVMALRctlg 245 Synechococcus s...
Feature 1                            
ABB90392     246 rDLGIDLTKLKKVSRLVAEA 265 Streptomyces rubellomurinus
NP_907562    243 qNRTLDSTILKALVQKVAKA 262 Wolinella succinogenes DSM 1740
NP_622149    250 mDLGIDTSRFREISEYVALA 269 Thermoanaerobacter tengcongensis MB4
YP_001568719 242 nDLGIKTHLLKEVCEYVAKA 261 Petrotoga mobilis SJ95
YP_002251336 247 iDLGIKTYKLRELSEYVAKA 266 Dictyoglomus thermophilum H-6-12
NP_951991    251 cDPGIDTQRFHEISRFVGRA 270 Geobacter sulfurreducens PCA
ZP_03905888  242 mDDAFDTKTMRSLSEYVAQA 261 Denitrovibrio acetiphilus DSM 12809
NP_487008    245 hDLGIDTRRLLEISQLVASA 264 Nostoc sp. PCC 7120
YP_001716589 245 mEVVREETELAMLEGWVNSV 264 Candidatus Desulforudis audaxviator MP104C
YP_475234    246 iDVGVDTRRLRELSQQVARA 265 Synechococcus sp. JA-3-3Ab

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