5EAT,1DGP,1DI1,1EZF,1FPS,1JFA,1JFG,1KIZ,1N1B,1N1Z,1N24,1PS1,1UBX,1UBY


Conserved Protein Domain Family
Isoprenoid_Biosyn_C1

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cd00385: Isoprenoid_Biosyn_C1 
Click on image for an interactive view with Cn3D
Isoprenoid Biosynthesis enzymes, Class 1
Superfamily of trans-isoprenyl diphosphate synthases (IPPS) and class I terpene cyclases which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, and diterpenes; and are widely distributed among archaea, bacteria, and eukaryota.The enzymes in this superfamily share the same 'isoprenoid synthase fold' and include several subgroups. The head-to-tail (HT) IPPS catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates. Cyclic monoterpenes, diterpenes, and sesquiterpenes, are formed from their respective linear isoprenoid diphosphates by class I terpene cyclases. The head-to-head (HH) IPPS catalyze the successive 1'-1 condensation of 2 farnesyl or 2 geranylgeranyl isoprenoid diphosphates. Cyclization of these 30- and 40-carbon linear forms are catalyzed by class II cyclases. Both the isoprenoid chain elongation reactions and the class I terpene cyclization reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational changes that close the active site to solvent, stabilizing reactive carbocation intermediates. Generally, the enzymes in this family exhibit an all-trans reaction pathway, an exception, is the cis-trans terpene cyclase, trichodiene synthase. Mechanistically and structurally distinct, class II terpene cyclases and cis-IPPS are not included in this CD.
Statistics
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PSSM-Id: 173830
View PSSM: cd00385
Aligned: 324 rows
Threshold Bit Score: 32.4668
Threshold Setting Gi: 7770093
Created: 6-Mar-2002
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 12 residues -Click on image for an interactive view with Cn3D
Feature 1:substrate binding pocket [chemical binding site]
Evidence:
  • Structure:5EAT; Terpene cyclase, 5-epi-aristolochene synthase, with Mg2+ and substrate analog farnesyl hydroxyphosphonate.
    View structure with Cn3D
  • Citation:PMID 9295271
  • Structure:1UBX; Linear IPPS, farnesyl diphosphate synthase, FPP-Mg2+ complex.
    View structure with Cn3D
  • Citation:PMID 8986756

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1        #                    #  ##  #   #                                              
5EAT        272 FWALGVYFEpqysqaRVMLVKTISMISIVDDTFDaygtvkeleaytdaiqrw------------dineidrlpdymkisy 339 common tobacco
P55351       17 NFPVASWIIhp--rhRALILAFYRFVRMADDIADhatlapdekllyld--------------------lleaellgkget 74  Rhizobium sp. NG...
CAA04732     36 NFPVASFLInp--eyRPIIMAFYQFARQADDVADnviaskkdrlaile--------------------dmrssltgesqs 93  Zymomonas mobilis
NP_274529    13 NFPVGSLILpr--rlRKPVHAVYAFARTADDMADegsmpsearlaglegl----------------qreldvlasggrsa 74  Neisseria mening...
NP_519773    30 DLYYSVLFLap--erRRATVALEAVRRELEDAVRdasdpavvqsklqww------------------rqelarlfdgrpe 89  Ralstonia solana...
NP_630831    24 NFPVAPFFLpr--awRTDLMAVYGFARLVDDIGDgdlapggadarllgvpedraddrllmldafeadlrrvfdgsdgapr 101 Streptomyces coe...
ZP_00044831  30 NFPVGSLLApa--rlRPHIHAVYAYARMADDFADssegspkeklqklddw-----------------qrrleaaqrgead 90  Magnetococcus sp...
ZP_00119855  23 SFSLGIHFLhk--klHDPVYAIYGFVRFADEIVDsfhgydkkrlmaqfr------------------rdtafalqdkisl 82  Cytophaga hutchi...
ZP_00013061  29 NFPVGSVLLpa--rlRPHVARFYAFARAIDDIADspdldaaakidrlqgf-----------------eeaitgrdttdpa 89  Rhodospirillum r...
ZP_00024286  17 SFYYSSLLLps--drRNALTALQAWRQELDAIVNenhdagvahqrldww------------------raelrrlydggaa 76  Ralstonia metall...
Feature 1                                                                          #            
5EAT        340 kaILDLYKDYekelssagrshivcHAIERMKEVVRNYNVEstwfiegytppvSEYLSNALAtttyYYLATTSYlgmksat 419 common tobacco
P55351       75 raEAVHLRTAldr---------rgMPPRHALDLLTAFRMDvtkqr---yenwDEVIDYCRYs--aMPVGRFVLdvhge-- 138 Rhizobium sp. NG...
CAA04732     94 epNAVVLRQTlinh-------gldHTIVHGLDLLEAFRRDvsvnr---yenwDALMDYCRYs--aSPVGRFVLdvhke-- 159 Zymomonas mobilis
NP_274529    75 hpLIARLDAEavv--------pfgLDLQPFYDLLSAFSQDvvktr---ygnfGELADYCRRs--aNPVGRIMLalygkt- 140 Neisseria mening...
NP_519773    90 hpATKALQPHlaa---------ydIGAVHLGELFAGVEADamqnr---yldwPNLRRHGDQv--aGVAGRLAAriagha- 154 Ralstonia solana...
NP_630831   102 hpLLRRLVPTvrr---------raLTPEPFLGLIAANRQDqlvar---yetyDDLLAYCELs--aNPVGRLVLavtgts- 166 Streptomyces coe...
ZP_00044831  91 hpVFRALAYTmqq---------mqLPIDPLRDLLMAFRMDitckh---ydttQELLEYCRYs--aNPVGRIVLrlagyr- 155 Magnetococcus sp...
ZP_00119855  83 npILNSFQHVvht---------ynIEWELIDTFLKSMEMDldqs----ahneQSYKEYIIGs--aEVVGLMCLrvfvkgd 147 Cytophaga hutchi...
ZP_00013061  90 yaKGHALRVSlea---------tgVPAIHGVELIAAFKQDavkgr---yatwAEMMDYCRLs--aAPVGRYLIdlhgg-- 153 Rhodospirillum r...
ZP_00024286  77 hpVSQALQPHld-----------aLPQAEMAEMLAATEMDlaqsr---yldeIGLLRYCRAs--gGTFGKLTArvlght- 139 Ralstonia metall...
Feature 1                           ##  #   #   #                                               
5EAT        420 eqdfewlsknpKILEASVIICRVIDDTATYEVEksrgqiaTGIECCMrdygi------------stkeaMAKFQNMAETA 487 common tobacco
P55351      139 ------saatwPASDVLCAGLQVCNHLQDCGKDflnlnrvYIPRDALsasgasieelgaaksslqmlqcLRSLAAKAEVL 212 Rhizobium sp. NG...
CAA04732    160 ------srnlwPMNDALCTALQVINHLQDCGKDyrmmnriYIPSDIMeavgatagdlgcfhaslplrqaIETAALKTKSL 233 Zymomonas mobilis
NP_274529   141 ------davcvAQSDGICTALQLVNFWQDVAVDwqk-grvYIPQDDLlkfgvseeqiaagradaafqrlMAYECRRAFRM 213 Neisseria mening...
NP_519773   155 ------qgrtlEFARLLALAEQLVHFIRNLGDDvrn-nrvYIPVDELqrfnvpaadlfnrrysdgfkalMGFQAERARAT 227 Ralstonia solana...
NP_630831   167 ------tperiRRSDEICTALQIVEHLQDVAEDlgr-driYLPAEDMkrfhvqeadlaapsanasvralIAYEAARARDL 239 Streptomyces coe...
ZP_00044831 156 ------detlmGYADAICTALQLTNHWQDLGEDpwngrplYLPREEMarfgvkeadilqrrfsaaaaelMMHLIAQTRAL 229 Magnetococcus sp...
ZP_00119855 148 v---dmyekqkPHAMSLGAAFQKVNFLRDAKEDfdslgrtYFPDVSMekfdr------------hikqnIESDIEKDFQH 212 Cytophaga hutchi...
ZP_00013061 154 ------sragyASSDALCVALQVINHLQDCQDDfrvldrvYLPADWLaaegasvsdldraactpglrrvLDRCLEGTRRL 227 Rhodospirillum r...
ZP_00024286 140 ------dprtlDAAEQLGLSLQRVRIVKDIGGDarh-griYIPVDTLqrlevpaadilqsrhsdrfvalMREQATQARAL 212 Ralstonia metall...
Feature 1                                   
5EAT        488 WKDINEGllrpt-pvstEFLTPILNLAR 514 common tobacco
P55351      213 LNGGGALvsqvkdfrlrFEVSVILSFAD 240 Rhizobium sp. NGR234
CAA04732    234 LKRSSSFsvaihdkrlgVEVAVIQRLAE 261 Zymomonas mobilis
NP_274529   214 LKAGSPLareln-grigLELRMIVLGAQ 240 Neisseria meningitidis MC58
NP_519773   228 HREALAAlpaed-rraqRPALIRGVLAM 254 Ralstonia solanacearum
NP_630831   240 LNEGAPLvgsvh-grlrLLLAGFVAGGR 266 Streptomyces coelicolor A3(2)
ZP_00044831 230 YLQGEPLltkvs-wplnLELGATWAGGM 256 Magnetococcus sp. MC-1
ZP_00119855 213 ALIGIKQlpa----esrLGVYLAYIYYK 236 Cytophaga hutchinsonii
ZP_00013061 228 LDAARPLpgdiidrrlgLEAAVIVSIAQ 255 Rhodospirillum rubrum
ZP_00024286 213 YGEALAAlprad-rrsqRAQLAFAAIQH 239 Ralstonia metallidurans

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