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Conserved domains on  [gi|2462609588|ref|XP_054211945|]
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all trans-polyprenyl-diphosphate synthase PDSS2 isoform X7 [Homo sapiens]

Protein Classification

isoprenoid biosynthesis enzyme family protein( domain architecture ID 89)

isoprenoid biosynthesis enzyme family protein

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Isoprenoid_Biosyn_C1 super family cl00210
Isoprenoid Biosynthesis enzymes, Class 1; Superfamily of trans-isoprenyl diphosphate synthases ...
68-354 3.11e-37

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.


The actual alignment was detected with superfamily member CHL00151:

Pssm-ID: 469660  Cd Length: 323  Bit Score: 136.46  E-value: 3.11e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588  68 SLRCLLSDELSNIAMQVRKLVGTQHPLLTTA--------------------------------SQRSLAEITELIHIALL 115
Cdd:CHL00151    6 NLLTPIEEELLILEDNLKKLIGSGHPILYAAakhlfsaggkrirpaivllvakatggnmeiktSQQRLAEITEIIHTASL 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 116 VHRGIVNLNELQSSDgPLKDMQFGNKIAILSGDFLLANACNGLALLQNTKVVELLASALMDLVQGVYHENSTSKESYITd 195
Cdd:CHL00151   86 VHDDVIDECSIRRGI-PTVHKIFGTKIAVLAGDFLFAQSSWYLANLNNLEVVKLISKVITDFAEGEIRQGLVQFDTTLS- 163
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 196 digISTWKEQTFLSHGALLAKSCQAAMELAKHDAEVQNMAFQYGKHMAMSHKINSDVQPFI-------KEKTSDSMTFNL 268
Cdd:CHL00151  164 ---ILNYIEKSFYKTASLIAASCKAAALLSDADEKDHNDFYLYGKHLGLAFQIIDDVLDITssteslgKPIGSDLKNGNL 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 269 nSAPVV--LHQEFLGRDLWIKQIGEAQekgrlDYAKLRERIKAGKGVTSAIDLCRYHGNKALEALESFPPSEARSALENI 346
Cdd:CHL00151  241 -TAPVLfaLTQNSKLAKLIEREFCETK-----DISQALQIIKETNGIEKAKDLALEHMQAAIQCLKFLPPSSAKDSLIEI 314

                  ....*....
gi 2462609588 347 V-FAVTRFS 354
Cdd:CHL00151  315 AnFIINRLN 323
 
Name Accession Description Interval E-value
preA CHL00151
prenyl transferase; Reviewed
68-354 3.11e-37

prenyl transferase; Reviewed


Pssm-ID: 164542  Cd Length: 323  Bit Score: 136.46  E-value: 3.11e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588  68 SLRCLLSDELSNIAMQVRKLVGTQHPLLTTA--------------------------------SQRSLAEITELIHIALL 115
Cdd:CHL00151    6 NLLTPIEEELLILEDNLKKLIGSGHPILYAAakhlfsaggkrirpaivllvakatggnmeiktSQQRLAEITEIIHTASL 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 116 VHRGIVNLNELQSSDgPLKDMQFGNKIAILSGDFLLANACNGLALLQNTKVVELLASALMDLVQGVYHENSTSKESYITd 195
Cdd:CHL00151   86 VHDDVIDECSIRRGI-PTVHKIFGTKIAVLAGDFLFAQSSWYLANLNNLEVVKLISKVITDFAEGEIRQGLVQFDTTLS- 163
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 196 digISTWKEQTFLSHGALLAKSCQAAMELAKHDAEVQNMAFQYGKHMAMSHKINSDVQPFI-------KEKTSDSMTFNL 268
Cdd:CHL00151  164 ---ILNYIEKSFYKTASLIAASCKAAALLSDADEKDHNDFYLYGKHLGLAFQIIDDVLDITssteslgKPIGSDLKNGNL 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 269 nSAPVV--LHQEFLGRDLWIKQIGEAQekgrlDYAKLRERIKAGKGVTSAIDLCRYHGNKALEALESFPPSEARSALENI 346
Cdd:CHL00151  241 -TAPVLfaLTQNSKLAKLIEREFCETK-----DISQALQIIKETNGIEKAKDLALEHMQAAIQCLKFLPPSSAKDSLIEI 314

                  ....*....
gi 2462609588 347 V-FAVTRFS 354
Cdd:CHL00151  315 AnFIINRLN 323
IspA COG0142
Geranylgeranyl pyrophosphate synthase [Coenzyme transport and metabolism]; Geranylgeranyl ...
103-352 2.09e-17

Geranylgeranyl pyrophosphate synthase [Coenzyme transport and metabolism]; Geranylgeranyl pyrophosphate synthase is part of the Pathway/BioSystem: Isoprenoid biosynthesis


Pssm-ID: 439912 [Multi-domain]  Cd Length: 329  Bit Score: 81.81  E-value: 2.09e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 103 LAEITELIHIALLVH----------RGIVNLNElqssdgplkdmQFGNKIAILSGDFLLANAcngLALL-------QNTK 165
Cdd:COG0142    70 AAAAVELIHTASLVHddvmddddlrRGKPTVHA-----------RFGEATAILAGDALLALA---FELLaelgdpeRRLR 135
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 166 VVELLASALMDLVQG----VYHEN--STSKESYITddigISTWKeqTflshGALLAKSCQAAMELAKHDAEVQN------ 233
Cdd:COG0142   136 ALRILARAARGMCEGqaldLEAEGrlDVTLEEYLR----VIRLK--T----AALFAAALRLGAILAGADEEQVEalrryg 205
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 234 ----MAFQ--------------YGKhmamshKINSDvqpfIKEKTsdsMTFnlnsaPVVLHQEfLGRDLWIKQIGEAQEK 295
Cdd:COG0142   206 rnlgLAFQirddildvtgdpevLGK------PAGSD----LREGK---PTL-----PLLLALE-RADPEERAELRELLGK 266
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462609588 296 GRLDYAKL---RERIKAGKGVTSAIDLCRYHGNKALEALESFPPSEARSALENIV-FAVTR 352
Cdd:COG0142   267 PDLDEEDLaevRALLRESGALEYARELARELAEEALAALAALPDSEAREALRALAdYVVER 327
Trans_IPPS_HT cd00685
Trans-Isoprenyl Diphosphate Synthases, head-to-tail; These trans-Isoprenyl Diphosphate ...
97-352 9.47e-16

Trans-Isoprenyl Diphosphate Synthases, head-to-tail; These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze head-to-tail (HT) (1'-4) condensation reactions. This CD includes all-trans (E)-isoprenyl diphosphate synthases which synthesize various chain length (C10, C15, C20, C25, C30, C35, C40, C45, and C50) linear isoprenyl diphosphates from precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). They catalyze the successive 1'-4 condensation of the 5-carbon IPP to allylic substrates geranyl-, farnesyl-, or geranylgeranyl-diphosphate. Isoprenoid chain elongation 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 (DDXX(XX)D) 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, protecting and stabilizing reactive carbocation intermediates. Farnesyl diphosphate synthases produce the precursors of steroids, cholesterol, sesquiterpenes, farnsylated proteins, heme, and vitamin K12; and geranylgeranyl diphosphate and longer chain synthases produce the precursors of carotenoids, retinoids, diterpenes, geranylgeranylated chlorophylls, ubiquinone, and archaeal ether linked lipids. Isoprenyl diphosphate synthases are widely distributed among archaea, bacteria, and eukareya.


Pssm-ID: 173833  Cd Length: 259  Bit Score: 76.05  E-value: 9.47e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588  97 TASQRSLAEITELIHIALLVH----------RGIVNLNElqssdgplkdmQFGNKIAILSGDFLLANAC---NGLALLQN 163
Cdd:cd00685    38 LEAALRLAAAIELLHTASLVHddvmdnsdlrRGKPTVHK-----------VFGNATAILAGDYLLARAFellARLGNPYY 106
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 164 TKVVELLASALMDLVQG----VYHENST--SKESYITddigISTWKeqTflshGALLAKSCQAAMELAKHDAEVQNMAFQ 237
Cdd:cd00685   107 PRALELFSEAILELVEGqlldLLSEYDTdvTEEEYLR----IIRLK--T----AALFAAAPLLGALLAGADEEEAEALKR 176
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 238 YGKHMAMSHKINSDVQPFikekTSDSMTFNlnsapvvlhqeflgrdlwiKQIGEAQEKGR----LDYAkLRERIKAgkgv 313
Cdd:cd00685   177 FGRNLGLAFQIQDDILDL----FGDPETLG-------------------KPVGSDLREGKctlpVLLA-LRELARE---- 228
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 2462609588 314 tsaidlcryHGNKALEALESFPPSEARSALENIV-FAVTR 352
Cdd:cd00685   229 ---------YEEKALEALKALPESPAREALRALAdFILER 259
polyprenyl_synt pfam00348
Polyprenyl synthetase;
96-244 6.90e-15

Polyprenyl synthetase;


Pssm-ID: 459773  Cd Length: 251  Bit Score: 73.31  E-value: 6.90e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588  96 TTASQRSLAEITELIHIALLVH----------RGI--VNLnelqssdgplkdmQFGNKIAILSGDFLLANACNGLA-LLQ 162
Cdd:pfam00348  36 DLEKAIVLAWAVELLHAASLVHddimdnsdlrRGQptWHR-------------IFGNAIAINDGDYLYALAFQLLAkLFP 102
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 163 NTKVVELLASALMDLVQG----VYHEN----STSKESYITddigISTWKeqTflshGALLAKSCQAAMELAKHDAEVQNM 234
Cdd:pfam00348 103 NPELLELFSEVTLQTAEGqgldLLWRNdddlSCTEEEYLE----IVKYK--T----AYLFALAVKLGAILSGADDEVIEA 172
                         170
                  ....*....|
gi 2462609588 235 AFQYGKHMAM 244
Cdd:pfam00348 173 LKDYGLNLGL 182
 
Name Accession Description Interval E-value
preA CHL00151
prenyl transferase; Reviewed
68-354 3.11e-37

prenyl transferase; Reviewed


Pssm-ID: 164542  Cd Length: 323  Bit Score: 136.46  E-value: 3.11e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588  68 SLRCLLSDELSNIAMQVRKLVGTQHPLLTTA--------------------------------SQRSLAEITELIHIALL 115
Cdd:CHL00151    6 NLLTPIEEELLILEDNLKKLIGSGHPILYAAakhlfsaggkrirpaivllvakatggnmeiktSQQRLAEITEIIHTASL 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 116 VHRGIVNLNELQSSDgPLKDMQFGNKIAILSGDFLLANACNGLALLQNTKVVELLASALMDLVQGVYHENSTSKESYITd 195
Cdd:CHL00151   86 VHDDVIDECSIRRGI-PTVHKIFGTKIAVLAGDFLFAQSSWYLANLNNLEVVKLISKVITDFAEGEIRQGLVQFDTTLS- 163
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 196 digISTWKEQTFLSHGALLAKSCQAAMELAKHDAEVQNMAFQYGKHMAMSHKINSDVQPFI-------KEKTSDSMTFNL 268
Cdd:CHL00151  164 ---ILNYIEKSFYKTASLIAASCKAAALLSDADEKDHNDFYLYGKHLGLAFQIIDDVLDITssteslgKPIGSDLKNGNL 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 269 nSAPVV--LHQEFLGRDLWIKQIGEAQekgrlDYAKLRERIKAGKGVTSAIDLCRYHGNKALEALESFPPSEARSALENI 346
Cdd:CHL00151  241 -TAPVLfaLTQNSKLAKLIEREFCETK-----DISQALQIIKETNGIEKAKDLALEHMQAAIQCLKFLPPSSAKDSLIEI 314

                  ....*....
gi 2462609588 347 V-FAVTRFS 354
Cdd:CHL00151  315 AnFIINRLN 323
PLN02890 PLN02890
geranyl diphosphate synthase
98-338 7.65e-32

geranyl diphosphate synthase


Pssm-ID: 178478  Cd Length: 422  Bit Score: 123.88  E-value: 7.65e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588  98 ASQRSLAEITELIHIALLVHRGIVNLNELQSSDGPLkDMQFGNKIAILSGDFLLANACNGLALLQNTKVVELLASALMDL 177
Cdd:PLN02890  161 TRQQNIAEITEMIHVASLLHDDVLDDADTRRGVGSL-NVVMGNKLSVLAGDFLLSRACVALAALKNTEVVSLLATAVEHL 239
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 178 VQGVYHENSTSKESYITDDIgistWKEQTFLSHGALLAKSCQAAMELAKHDAEVQNMAFQYGKHMAMSHKINSDVQPFIK 257
Cdd:PLN02890  240 VTGETMQITSSREQRRSMDY----YMQKTYYKTASLISNSCKAVAILAGQTAEVAVLAFEYGRNLGLAFQLIDDVLDFTG 315
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 258 EKTS------DSMTFNLNSAPVVL-HQEFlgrdlwiKQIGEAQEKGRLDYAKLR---ERIKAGKGVTSAIDLCRYHGNKA 327
Cdd:PLN02890  316 TSASlgkgslSDIRHGVITAPILFaMEEF-------PQLREVVDRGFDNPANVDialEYLGKSRGIQRTRELAREHANLA 388
                         250
                  ....*....|.
gi 2462609588 328 LEALESFPPSE 338
Cdd:PLN02890  389 AAAIESLPETD 399
PLN02857 PLN02857
octaprenyl-diphosphate synthase
63-347 1.54e-30

octaprenyl-diphosphate synthase


Pssm-ID: 215462  Cd Length: 416  Bit Score: 120.34  E-value: 1.54e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588  63 PTSFMSLRCLLSDELSNIAMQVRKLVGTQHPLLTTAS-----------------------------------QRSLAEIT 107
Cdd:PLN02857   91 PISLSELFEPVADDLQQLNDNLQSIVGAENPVLMSAAeqifgaggkrmrpalvflvsrataelaglkeltteHRRLAEIT 170
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 108 ELIHIALLVHRGIVNLNELQSSDGPLKDMqFGNKIAILSGDFLLANACNGLALLQNTKVVELLASALMDLVQGVYHENSt 187
Cdd:PLN02857  171 EMIHTASLIHDDVLDESDMRRGKETVHQL-YGTRVAVLAGDFMFAQSSWYLANLDNLEVIKLISQVIKDFASGEIKQAS- 248
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 188 skeSYITDDIGISTWKEQTFLSHGALLAKSCQAAMELAKHDAEVQNMAFQYGKHMAMSHKINSDVQPFI-------KEKT 260
Cdd:PLN02857  249 ---SLFDCDVTLDEYLLKSYYKTASLIAASTKSAAIFSGVDSSVKEQMYEYGKNLGLAFQVVDDILDFTqsteqlgKPAG 325
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 261 SDSMTFNLnSAPVVLHqefLGRDLWIKQIGEAQ--EKGRLDYAKlrERIKAGKGVTSAIDLCRYHGNKALEALESFPPSE 338
Cdd:PLN02857  326 SDLAKGNL-TAPVIFA---LEKEPELREIIESEfcEEGSLEEAI--ELVNEGGGIERAQELAKEKADLAIQNLECLPRGA 399

                  ....*....
gi 2462609588 339 ARSALENIV 347
Cdd:PLN02857  400 FRSSLEDMV 408
IspA COG0142
Geranylgeranyl pyrophosphate synthase [Coenzyme transport and metabolism]; Geranylgeranyl ...
103-352 2.09e-17

Geranylgeranyl pyrophosphate synthase [Coenzyme transport and metabolism]; Geranylgeranyl pyrophosphate synthase is part of the Pathway/BioSystem: Isoprenoid biosynthesis


Pssm-ID: 439912 [Multi-domain]  Cd Length: 329  Bit Score: 81.81  E-value: 2.09e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 103 LAEITELIHIALLVH----------RGIVNLNElqssdgplkdmQFGNKIAILSGDFLLANAcngLALL-------QNTK 165
Cdd:COG0142    70 AAAAVELIHTASLVHddvmddddlrRGKPTVHA-----------RFGEATAILAGDALLALA---FELLaelgdpeRRLR 135
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 166 VVELLASALMDLVQG----VYHEN--STSKESYITddigISTWKeqTflshGALLAKSCQAAMELAKHDAEVQN------ 233
Cdd:COG0142   136 ALRILARAARGMCEGqaldLEAEGrlDVTLEEYLR----VIRLK--T----AALFAAALRLGAILAGADEEQVEalrryg 205
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 234 ----MAFQ--------------YGKhmamshKINSDvqpfIKEKTsdsMTFnlnsaPVVLHQEfLGRDLWIKQIGEAQEK 295
Cdd:COG0142   206 rnlgLAFQirddildvtgdpevLGK------PAGSD----LREGK---PTL-----PLLLALE-RADPEERAELRELLGK 266
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462609588 296 GRLDYAKL---RERIKAGKGVTSAIDLCRYHGNKALEALESFPPSEARSALENIV-FAVTR 352
Cdd:COG0142   267 PDLDEEDLaevRALLRESGALEYARELARELAEEALAALAALPDSEAREALRALAdYVVER 327
Trans_IPPS_HT cd00685
Trans-Isoprenyl Diphosphate Synthases, head-to-tail; These trans-Isoprenyl Diphosphate ...
97-352 9.47e-16

Trans-Isoprenyl Diphosphate Synthases, head-to-tail; These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze head-to-tail (HT) (1'-4) condensation reactions. This CD includes all-trans (E)-isoprenyl diphosphate synthases which synthesize various chain length (C10, C15, C20, C25, C30, C35, C40, C45, and C50) linear isoprenyl diphosphates from precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). They catalyze the successive 1'-4 condensation of the 5-carbon IPP to allylic substrates geranyl-, farnesyl-, or geranylgeranyl-diphosphate. Isoprenoid chain elongation 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 (DDXX(XX)D) 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, protecting and stabilizing reactive carbocation intermediates. Farnesyl diphosphate synthases produce the precursors of steroids, cholesterol, sesquiterpenes, farnsylated proteins, heme, and vitamin K12; and geranylgeranyl diphosphate and longer chain synthases produce the precursors of carotenoids, retinoids, diterpenes, geranylgeranylated chlorophylls, ubiquinone, and archaeal ether linked lipids. Isoprenyl diphosphate synthases are widely distributed among archaea, bacteria, and eukareya.


Pssm-ID: 173833  Cd Length: 259  Bit Score: 76.05  E-value: 9.47e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588  97 TASQRSLAEITELIHIALLVH----------RGIVNLNElqssdgplkdmQFGNKIAILSGDFLLANAC---NGLALLQN 163
Cdd:cd00685    38 LEAALRLAAAIELLHTASLVHddvmdnsdlrRGKPTVHK-----------VFGNATAILAGDYLLARAFellARLGNPYY 106
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 164 TKVVELLASALMDLVQG----VYHENST--SKESYITddigISTWKeqTflshGALLAKSCQAAMELAKHDAEVQNMAFQ 237
Cdd:cd00685   107 PRALELFSEAILELVEGqlldLLSEYDTdvTEEEYLR----IIRLK--T----AALFAAAPLLGALLAGADEEEAEALKR 176
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 238 YGKHMAMSHKINSDVQPFikekTSDSMTFNlnsapvvlhqeflgrdlwiKQIGEAQEKGR----LDYAkLRERIKAgkgv 313
Cdd:cd00685   177 FGRNLGLAFQIQDDILDL----FGDPETLG-------------------KPVGSDLREGKctlpVLLA-LRELARE---- 228
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 2462609588 314 tsaidlcryHGNKALEALESFPPSEARSALENIV-FAVTR 352
Cdd:cd00685   229 ---------YEEKALEALKALPESPAREALRALAdFILER 259
polyprenyl_synt pfam00348
Polyprenyl synthetase;
96-244 6.90e-15

Polyprenyl synthetase;


Pssm-ID: 459773  Cd Length: 251  Bit Score: 73.31  E-value: 6.90e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588  96 TTASQRSLAEITELIHIALLVH----------RGI--VNLnelqssdgplkdmQFGNKIAILSGDFLLANACNGLA-LLQ 162
Cdd:pfam00348  36 DLEKAIVLAWAVELLHAASLVHddimdnsdlrRGQptWHR-------------IFGNAIAINDGDYLYALAFQLLAkLFP 102
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 163 NTKVVELLASALMDLVQG----VYHEN----STSKESYITddigISTWKeqTflshGALLAKSCQAAMELAKHDAEVQNM 234
Cdd:pfam00348 103 NPELLELFSEVTLQTAEGqgldLLWRNdddlSCTEEEYLE----IVKYK--T----AYLFALAVKLGAILSGADDEVIEA 172
                         170
                  ....*....|
gi 2462609588 235 AFQYGKHMAM 244
Cdd:pfam00348 173 LKDYGLNLGL 182
Trans_IPPS cd00867
Trans-Isoprenyl Diphosphate Synthases; Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of ...
103-244 2.59e-09

Trans-Isoprenyl Diphosphate Synthases; Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of class 1 isoprenoid biosynthesis enzymes 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, diterpenes, ubiquinone, and archaeal ether linked lipids; and are widely distributed among archaea, bacteria, and eukareya. The enzymes in this family share the same 'isoprenoid synthase fold' and include the head-to-tail (HT) IPPS which 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. The head-to-head (HH) IPPS catalyze the successive 1'-1 condensation of 2 farnesyl or 2 geranylgeranyl isoprenoid diphosphates. Isoprenoid chain elongation 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. Mechanistically and structurally distinct, cis-IPPS are not included in this CD.


Pssm-ID: 173836  Cd Length: 236  Bit Score: 56.97  E-value: 2.59e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 103 LAEITELIHIALLVHRGIVNlNELQSSDGP-LKDMQFGNKIAILSGDFLLANACNGLALLQNTKVVELLASALMDLVQGV 181
Cdd:cd00867    23 LAAAVELLHAASLVHDDIVD-DSDLRRGKPtAHLRRFGNALAILAGDYLLARAFQLLARLGYPRALELFAEALRELLEGQ 101
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462609588 182 YHENSTSKESYITDDigisTWKEQTFLSHGALLAKSCQAAMELAKHDAEVQNMAFQYGKHMAM 244
Cdd:cd00867   102 ALDLEFERDTYETLD----EYLEYCRYKTAGLVGLLCLLGAGLSGADDEQAEALKDYGRALGL 160
Isoprenoid_Biosyn_C1 cd00385
Isoprenoid Biosynthesis enzymes, Class 1; Superfamily of trans-isoprenyl diphosphate synthases ...
103-245 2.06e-08

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.


Pssm-ID: 173830 [Multi-domain]  Cd Length: 243  Bit Score: 54.42  E-value: 2.06e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 103 LAEITELIHIALLVH----------RGIVNLNELQSsdgplkdmQFGNKIAILSGDFLLANACNGLALLQNTKVVELLAS 172
Cdd:cd00385    15 LRAAVEKLHAASLVHddivddsgtrRGLPTAHLAVA--------IDGLPEAILAGDLLLADAFEELAREGSPEALEILAE 86
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462609588 173 ALMDLVQGVYHENSTSKESYITDDigisTWKEQTFLSHGALLAKSCQAAMELAKHDAEVQNMAFQYGKHMAMS 245
Cdd:cd00385    87 ALLDLLEGQLLDLKWRREYVPTLE----EYLEYCRYKTAGLVGALCLLGAGLSGGEAELLEALRKLGRALGLA 155
PRK10888 PRK10888
octaprenyl diphosphate synthase; Provisional
102-354 6.86e-07

octaprenyl diphosphate synthase; Provisional


Pssm-ID: 182813  Cd Length: 323  Bit Score: 50.23  E-value: 6.86e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 102 SLAEITELIHIALLVHRGIVNLNELQSSDGPLKDMqFGNKIAILSGDFLLANACNGLALLQNTKVVELLASALMDLVQGV 181
Cdd:PRK10888   68 TIAALIEFIHTATLLHDDVVDESDMRRGKATANAA-FGNAASVLVGDFIYTRAFQMMTSLGSLKVLEVMSEAVNVIAEGE 146
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 182 YHENSTSKESYITDDIGISTWKEQTflshGALLAKSCQAAMELAKHDAEvQNMAFQ-YGKHMAMSHKINSDVQPFikekT 260
Cdd:PRK10888  147 VLQLMNVNDPDITEENYMRVIYSKT----ARLFEAAAQCSGILAGCTPE-QEKGLQdYGRYLGTAFQLIDDLLDY----S 217
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462609588 261 SDSMTFNLNSA-------PV--VLHQEFLGRDLWIKQIGEAQEKGrlDYAKLRERIKAGKGVTSAIDLCRY----HGNKA 327
Cdd:PRK10888  218 ADGETLGKNVGddlnegkPTlpLLHAMHHGTPEQAAMIRTAIEQG--NGRHLLEPVLEAMNACGSLEWTRQraeeEADKA 295
                         250       260
                  ....*....|....*....|....*...
gi 2462609588 328 LEALESFPPSEARSALENIV-FAVTRFS 354
Cdd:PRK10888  296 IAALQVLPDTPWREALIGLAhIAVQRDR 323
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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