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Conserved domains on  [gi|567757587|ref|NP_001274678|]
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squalene synthase isoform 2 [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 ...
 1-306 0e+00

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 TIGR01559:

Pssm-ID: 469660  Cd Length: 337  Bit Score: 578.24  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587    1 MRNAVCIFYLVLRALDTLEDDMTISVEKKVPLLHNFHSFLYQPDWRFMES-KEKDRQVLEDFPTISLEFRNLAEKYQTVI 79
Cdd:TIGR01559  28 LRNAVCIFYLVLRALDTVEDDMTISVDKKIPLLRDFHEKIYDPDWRFTESdNEKDRQVLDDFPVVSLEFLKLKPKYQEVI 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587   80 ADICRRMGIGMAEFLDKHVTSEQ---EWDKYCHYVAGLVGIGLSRLFSASEFEDPLVGEDTERANSMGLFLQKTNIIRDY 156
Cdd:TIGR01559 108 ADITRRMGNGMADFIDKEVTNEQtvgDYDKYCHYVAGLVGIGLSRLFVASGFEDPSLGESEALSNSMGLFLQKTNIIRDY 187

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587  157 LEDQQGGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLSRLRNQSVFNFCAIPQVMAIATL 236
Cdd:TIGR01559 188 LEDINEGRMFWPREIWSKYAKKLGDFKKPENSDKALQCLNELVTNALHHATDCLTYLSRLRDQSIFNFCAIPQVMAIATL 267

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587  237 AACYNNQQVFKGAVKIRKGQAVTLMMDATNMPAVKAIIYQYMEEIYHRIPDSDPSSSKTRQIISTIRTQN 306
Cdd:TIGR01559 268 ALCYNNPQVFQGNVKIRKGTTVKLILDSTNMPAVYDIFYRYARKIYHKIDPNDPNFSKTLIIISKIEQQC 337
 
Name Accession Description Interval E-value
squal_synth TIGR01559
farnesyl-diphosphate farnesyltransferase; This model describes farnesyl-diphosphate ...
 1-306 0e+00

farnesyl-diphosphate farnesyltransferase; This model describes farnesyl-diphosphate farnesyltransferase, also known as squalene synthase, as found in eukaryotes. This family is related to phytoene synthases. Tentatively identified archaeal homologs (excluded from this model) lack the C-terminal predicted transmembrane region universally conserved among members of this family.


Pssm-ID: 188157  Cd Length: 337  Bit Score: 578.24  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587    1 MRNAVCIFYLVLRALDTLEDDMTISVEKKVPLLHNFHSFLYQPDWRFMES-KEKDRQVLEDFPTISLEFRNLAEKYQTVI 79
Cdd:TIGR01559  28 LRNAVCIFYLVLRALDTVEDDMTISVDKKIPLLRDFHEKIYDPDWRFTESdNEKDRQVLDDFPVVSLEFLKLKPKYQEVI 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587   80 ADICRRMGIGMAEFLDKHVTSEQ---EWDKYCHYVAGLVGIGLSRLFSASEFEDPLVGEDTERANSMGLFLQKTNIIRDY 156
Cdd:TIGR01559 108 ADITRRMGNGMADFIDKEVTNEQtvgDYDKYCHYVAGLVGIGLSRLFVASGFEDPSLGESEALSNSMGLFLQKTNIIRDY 187

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587  157 LEDQQGGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLSRLRNQSVFNFCAIPQVMAIATL 236
Cdd:TIGR01559 188 LEDINEGRMFWPREIWSKYAKKLGDFKKPENSDKALQCLNELVTNALHHATDCLTYLSRLRDQSIFNFCAIPQVMAIATL 267

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587  237 AACYNNQQVFKGAVKIRKGQAVTLMMDATNMPAVKAIIYQYMEEIYHRIPDSDPSSSKTRQIISTIRTQN 306
Cdd:TIGR01559 268 ALCYNNPQVFQGNVKIRKGTTVKLILDSTNMPAVYDIFYRYARKIYHKIDPNDPNFSKTLIIISKIEQQC 337
Trans_IPPS_HH cd00683
Trans-Isoprenyl Diphosphate Synthases, head-to-head; These trans-Isoprenyl Diphosphate ...
 1-257 4.72e-76

Trans-Isoprenyl Diphosphate Synthases, head-to-head; These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze a head-to-head (HH) (1'-1) condensation reaction. This CD includes squalene and phytoene synthases which catalyze the 1'-1 condensation of two 15-carbon (farnesyl) and 20-carbon (geranylgeranyl) isoprenyl diphosphates, respectively. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DXXXD) located on opposite walls. These residues mediate binding of prenyl phosphates. A two-step reaction has been proposed for squalene synthase (farnesyl-diphosphate farnesyltransferase) in which, two molecules of FPP react to form a stable cyclopropylcarbinyl diphosphate intermediate, and then the intermediate undergoes heterolysis, isomerization, and reduction with NADPH to form squalene, a precursor of cholestrol. The carotenoid biosynthesis enzyme, phytoene synthase (CrtB), catalyzes the condensation reaction of two molecules of geranylgeranyl diphosphate to produce phytoene, a precursor of beta-carotene. These enzymes produce the triterpene and tetraterpene precursors for many diverse sterol and carotenoid end products and are widely distributed among eukareya, bacteria, and archaea.


Pssm-ID: 173831 [Multi-domain]  Cd Length: 265  Bit Score: 235.21  E-value: 4.72e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587   1 MRNAVCIFYLVLRALDTLEDDMTISVEKKVPLLHNFHSFLYQPDWrfmeskekdrqVLEDFPTISLEFRNLAEkYQTVIA 80
Cdd:cd00683   25 LRRAVCALYAFCRAADDIVDDPAAPPDEKLALLDAFRAELDAAYW-----------GGAPTHPVLRALADLAR-RYGIPR 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587  81 DICRRMGIGMAEFLDKH-VTSEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLvgedtERANSMGLFLQKTNIIRDYLED 159
Cdd:cd00683   93 EPFRDLLAGMAMDLDKRrYETLDELDEYCYYVAGVVGLMLLRVFGASSDEAAL-----ERARALGLALQLTNILRDVGED 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587 160 QQGGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLSRLRnqSVFNFCAIPQVMAIATLAAC 239
Cdd:cd00683  168 ARRGRIYLPREELARFGVTLEDLLAPENSPAFRALLRRLIARARAHYREALAGLAALP--RRSRFCVRAAAMLYRTILDE 245

                        250
                 ....*....|....*...
gi 567757587 240 YNNQQVFKGAVKIRKGQA 257
Cdd:cd00683  246 IEARGYDVLSVRVRVPKA 263
SQS_PSY pfam00494
Squalene/phytoene synthase;
1-256 5.39e-44

Squalene/phytoene synthase;


Pssm-ID: 425717 [Multi-domain]  Cd Length: 261  Bit Score: 152.44  E-value: 5.39e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587    1 MRNAVCIFYLVLRALDTLEDDMTISVEKKVPLLHNFHSFLYQPDWRfmeskekdrQVLEDFPTISLEFRNLAEKYQtVIA 80
Cdd:pfam00494  19 LRRAVFALYAFCREADDIVDEVSDPPAAKRARLDWWRDALDGAYAR---------RLKPARHPVLRALADLIRRYQ-LPK 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587   81 DICRRMGIGMAEFLDKH-VTSEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLVgedtERANSMGLFLQKTNIIRDYLED 159
Cdd:pfam00494  89 EPFLELIDGMEMDLEFTrYETLAELEEYCYYVAGVVGLLLLRLLGARSDEAALL----EAASHLGLALQLTNILRDVGED 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587  160 QQGGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLSRLRNQSVFnFCAIPQVMAIATLAAC 239
Cdd:pfam00494 165 ARRGRVYLPAEVLKRFGVSEEDLLRGRASPALRALLRELAERARAHLREARPLLALLPRRARP-AVLLAAVLYRAILRRL 243

                         250
                  ....*....|....*...
gi 567757587  240 YNNQ-QVFKGAVKIRKGQ 256
Cdd:pfam00494 244 EAAGyDVLRRRVKLSRRR 261
ERG9 COG1562
Phytoene/squalene synthetase [Lipid transport and metabolism];
1-264 7.68e-20

Phytoene/squalene synthetase [Lipid transport and metabolism];


Pssm-ID: 441170 [Multi-domain]  Cd Length: 278  Bit Score: 87.94  E-value: 7.68e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587   1 MRNAVCIFYLVLRALDTLEDDMTISVEKKVpLLHNFHSFLyqpdwrfmeskekdRQVLEDFPTISLEFRNLAekyqtvia 80
Cdd:COG1562   30 LRRAVYALYAFCREADDIVDEVSDPAEREA-RLDWWRAEL--------------DAAYAGGPADHPVLAALA-------- 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587  81 DICRRMGI----------GMAEFLDKHV-TSEQEWDKYCHYVAGLVGIGLSRLFSASEfEDPLvgedtERANSMGLFLQK 149
Cdd:COG1562   87 DTVRRYGLprelfldlidGMEMDLTKTRyATFAELEDYCYRVAGVVGLLLLRVFGADD-PEAL-----AAADALGVALQL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587 150 TNIIRDYLEDQQGGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLSRLRNQSVFnFCAIPQ 229
Cdd:COG1562  161 TNILRDVGEDARRGRVYLPLDDLARFGVTEEDLLAGRASPALRALLRFLAARARALLREALAGIPALPRRARR-AVLLAA 239

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 567757587 230 VMAIATLAACYNNQ-QVFKGAVKIRKGQAVTLMMDA 264
Cdd:COG1562  240 ALYRAILDKIERRGyDVLRRRVRLSRLRKLWLLWRA 275
PLN02632 PLN02632
phytoene synthase
 107-170 2.76e-06

phytoene synthase


Pssm-ID: 215339  Cd Length: 334  Bit Score: 48.56  E-value: 2.76e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 567757587 107 YCHYVAGLVGI------GLSRLFSASEfedplvgEDT-ERANSMGLFLQKTNIIRDYLEDQQGGREFWPQE 170
Cdd:PLN02632 167 YCYYVAGTVGLmsvpvmGIAPESKAST-------ESVyNAALALGIANQLTNILRDVGEDARRGRVYLPQD 230
 
Name Accession Description Interval E-value
squal_synth TIGR01559
farnesyl-diphosphate farnesyltransferase; This model describes farnesyl-diphosphate ...
 1-306 0e+00

farnesyl-diphosphate farnesyltransferase; This model describes farnesyl-diphosphate farnesyltransferase, also known as squalene synthase, as found in eukaryotes. This family is related to phytoene synthases. Tentatively identified archaeal homologs (excluded from this model) lack the C-terminal predicted transmembrane region universally conserved among members of this family.


Pssm-ID: 188157  Cd Length: 337  Bit Score: 578.24  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587    1 MRNAVCIFYLVLRALDTLEDDMTISVEKKVPLLHNFHSFLYQPDWRFMES-KEKDRQVLEDFPTISLEFRNLAEKYQTVI 79
Cdd:TIGR01559  28 LRNAVCIFYLVLRALDTVEDDMTISVDKKIPLLRDFHEKIYDPDWRFTESdNEKDRQVLDDFPVVSLEFLKLKPKYQEVI 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587   80 ADICRRMGIGMAEFLDKHVTSEQ---EWDKYCHYVAGLVGIGLSRLFSASEFEDPLVGEDTERANSMGLFLQKTNIIRDY 156
Cdd:TIGR01559 108 ADITRRMGNGMADFIDKEVTNEQtvgDYDKYCHYVAGLVGIGLSRLFVASGFEDPSLGESEALSNSMGLFLQKTNIIRDY 187

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587  157 LEDQQGGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLSRLRNQSVFNFCAIPQVMAIATL 236
Cdd:TIGR01559 188 LEDINEGRMFWPREIWSKYAKKLGDFKKPENSDKALQCLNELVTNALHHATDCLTYLSRLRDQSIFNFCAIPQVMAIATL 267

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587  237 AACYNNQQVFKGAVKIRKGQAVTLMMDATNMPAVKAIIYQYMEEIYHRIPDSDPSSSKTRQIISTIRTQN 306
Cdd:TIGR01559 268 ALCYNNPQVFQGNVKIRKGTTVKLILDSTNMPAVYDIFYRYARKIYHKIDPNDPNFSKTLIIISKIEQQC 337
Trans_IPPS_HH cd00683
Trans-Isoprenyl Diphosphate Synthases, head-to-head; These trans-Isoprenyl Diphosphate ...
 1-257 4.72e-76

Trans-Isoprenyl Diphosphate Synthases, head-to-head; These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze a head-to-head (HH) (1'-1) condensation reaction. This CD includes squalene and phytoene synthases which catalyze the 1'-1 condensation of two 15-carbon (farnesyl) and 20-carbon (geranylgeranyl) isoprenyl diphosphates, respectively. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DXXXD) located on opposite walls. These residues mediate binding of prenyl phosphates. A two-step reaction has been proposed for squalene synthase (farnesyl-diphosphate farnesyltransferase) in which, two molecules of FPP react to form a stable cyclopropylcarbinyl diphosphate intermediate, and then the intermediate undergoes heterolysis, isomerization, and reduction with NADPH to form squalene, a precursor of cholestrol. The carotenoid biosynthesis enzyme, phytoene synthase (CrtB), catalyzes the condensation reaction of two molecules of geranylgeranyl diphosphate to produce phytoene, a precursor of beta-carotene. These enzymes produce the triterpene and tetraterpene precursors for many diverse sterol and carotenoid end products and are widely distributed among eukareya, bacteria, and archaea.


Pssm-ID: 173831 [Multi-domain]  Cd Length: 265  Bit Score: 235.21  E-value: 4.72e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587   1 MRNAVCIFYLVLRALDTLEDDMTISVEKKVPLLHNFHSFLYQPDWrfmeskekdrqVLEDFPTISLEFRNLAEkYQTVIA 80
Cdd:cd00683   25 LRRAVCALYAFCRAADDIVDDPAAPPDEKLALLDAFRAELDAAYW-----------GGAPTHPVLRALADLAR-RYGIPR 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587  81 DICRRMGIGMAEFLDKH-VTSEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLvgedtERANSMGLFLQKTNIIRDYLED 159
Cdd:cd00683   93 EPFRDLLAGMAMDLDKRrYETLDELDEYCYYVAGVVGLMLLRVFGASSDEAAL-----ERARALGLALQLTNILRDVGED 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587 160 QQGGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLSRLRnqSVFNFCAIPQVMAIATLAAC 239
Cdd:cd00683  168 ARRGRIYLPREELARFGVTLEDLLAPENSPAFRALLRRLIARARAHYREALAGLAALP--RRSRFCVRAAAMLYRTILDE 245

                        250
                 ....*....|....*...
gi 567757587 240 YNNQQVFKGAVKIRKGQA 257
Cdd:cd00683  246 IEARGYDVLSVRVRVPKA 263
SQS_PSY pfam00494
Squalene/phytoene synthase;
1-256 5.39e-44

Squalene/phytoene synthase;


Pssm-ID: 425717 [Multi-domain]  Cd Length: 261  Bit Score: 152.44  E-value: 5.39e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587    1 MRNAVCIFYLVLRALDTLEDDMTISVEKKVPLLHNFHSFLYQPDWRfmeskekdrQVLEDFPTISLEFRNLAEKYQtVIA 80
Cdd:pfam00494  19 LRRAVFALYAFCREADDIVDEVSDPPAAKRARLDWWRDALDGAYAR---------RLKPARHPVLRALADLIRRYQ-LPK 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587   81 DICRRMGIGMAEFLDKH-VTSEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLVgedtERANSMGLFLQKTNIIRDYLED 159
Cdd:pfam00494  89 EPFLELIDGMEMDLEFTrYETLAELEEYCYYVAGVVGLLLLRLLGARSDEAALL----EAASHLGLALQLTNILRDVGED 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587  160 QQGGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLSRLRNQSVFnFCAIPQVMAIATLAAC 239
Cdd:pfam00494 165 ARRGRVYLPAEVLKRFGVSEEDLLRGRASPALRALLRELAERARAHLREARPLLALLPRRARP-AVLLAAVLYRAILRRL 243

                         250
                  ....*....|....*...
gi 567757587  240 YNNQ-QVFKGAVKIRKGQ 256
Cdd:pfam00494 244 EAAGyDVLRRRVKLSRRR 261
Trans_IPPS cd00867
Trans-Isoprenyl Diphosphate Synthases; Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of ...
 1-199 7.66e-25

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: 100.88  E-value: 7.66e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587   1 MRNAVCIFYLVLRALDTLEDDMTISVEKKVPLLHNFhsflyqpdwrfmeskEKDRQVLEDFPTISLEFRNLAE----KYQ 76
Cdd:cd00867   23 LAAAVELLHAASLVHDDIVDDSDLRRGKPTAHLRRF---------------GNALAILAGDYLLARAFQLLARlgypRAL 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587  77 TVIADICRRMGIGMAEFLDKH---VTSEQEWDKYCHY-VAGLVGIGLSRLFSASEFEDPLVGEDTERANSMGLFLQKTNI 152
Cdd:cd00867   88 ELFAEALRELLEGQALDLEFErdtYETLDEYLEYCRYkTAGLVGLLCLLGAGLSGADDEQAEALKDYGRALGLAFQLTDD 167

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 567757587 153 IRDYLEDQQG----------GREFWPQEVWSRYVKKLgdfakpenIDLAVQCLNELI 199
Cdd:cd00867  168 LLDVFGDAEElgkvgsdlreGRITLPVILARERAAEY--------AEEAYAALEALP 216
Isoprenoid_Biosyn_C1 cd00385
Isoprenoid Biosynthesis enzymes, Class 1; Superfamily of trans-isoprenyl diphosphate synthases ...
 2-234 1.54e-22

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: 94.87  E-value: 1.54e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587   2 RNAVCIFYLVLRALDTLEDDMTISVEKkvPLLHnfhsflyqpdwRFMESKEKDRQVLEDFPTISLEFRNLAE----KYQT 77
Cdd:cd00385   16 RAAVEKLHAASLVHDDIVDDSGTRRGL--PTAH-----------LAVAIDGLPEAILAGDLLLADAFEELARegspEALE 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587  78 VIADICRRMGIGM---AEFLDKHVTSEQEWDKYCHYV-AGLVGIGLSRLFSASEFEDPLVGEDTERANSMGLFLQKTNII 153
Cdd:cd00385   83 ILAEALLDLLEGQlldLKWRREYVPTLEEYLEYCRYKtAGLVGALCLLGAGLSGGEAELLEALRKLGRALGLAFQLTNDL 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587 154 RDYLEDQQ--GGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLSRLRnqSVFNFCAIPQVM 231
Cdd:cd00385  163 LDYEGDAErgEGKCTLPVLYALEYGVPAEDLLLVEKSGSLEEALEELAKLAEEALKELNELILSLP--DVPRALLALALN 240


                 ...
gi 567757587 232 AIA 234
Cdd:cd00385  241 LYR 243
ERG9 COG1562
Phytoene/squalene synthetase [Lipid transport and metabolism];
1-264 7.68e-20

Phytoene/squalene synthetase [Lipid transport and metabolism];


Pssm-ID: 441170 [Multi-domain]  Cd Length: 278  Bit Score: 87.94  E-value: 7.68e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587   1 MRNAVCIFYLVLRALDTLEDDMTISVEKKVpLLHNFHSFLyqpdwrfmeskekdRQVLEDFPTISLEFRNLAekyqtvia 80
Cdd:COG1562   30 LRRAVYALYAFCREADDIVDEVSDPAEREA-RLDWWRAEL--------------DAAYAGGPADHPVLAALA-------- 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587  81 DICRRMGI----------GMAEFLDKHV-TSEQEWDKYCHYVAGLVGIGLSRLFSASEfEDPLvgedtERANSMGLFLQK 149
Cdd:COG1562   87 DTVRRYGLprelfldlidGMEMDLTKTRyATFAELEDYCYRVAGVVGLLLLRVFGADD-PEAL-----AAADALGVALQL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 567757587 150 TNIIRDYLEDQQGGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLSRLRNQSVFnFCAIPQ 229
Cdd:COG1562  161 TNILRDVGEDARRGRVYLPLDDLARFGVTEEDLLAGRASPALRALLRFLAARARALLREALAGIPALPRRARR-AVLLAA 239

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 567757587 230 VMAIATLAACYNNQ-QVFKGAVKIRKGQAVTLMMDA 264
Cdd:COG1562  240 ALYRAILDKIERRGyDVLRRRVRLSRLRKLWLLWRA 275
HpnD TIGR03465
squalene synthase HpnD; The genes of this family are often found in the same genetic locus ...
 100-175 1.67e-09

squalene synthase HpnD; The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. In the organisms Zymomonas mobilis and Bradyrhizobium japonicum these genes have been characterized as squalene synthases (farnesyl-pyrophosphate ligases). Often, these genes appear in tandem with the HpnC gene which appears to have resulted from an ancient gene duplication event. Presumably these proteins form a heteromeric complex, but this has not yet been experimentally demonstrated.


Pssm-ID: 163278  Cd Length: 266  Bit Score: 57.68  E-value: 1.67e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 567757587  100 SEQEWDKYCHYVAGLVGIGLSRLFSASEfedplvgEDTER-ANSMGLFLQKTNIIRDYLEDQQGGREFWPQEVWSRY 175
Cdd:TIGR03465 105 DFAELDLYCDRVAGAVGRLSARIFGATD-------ARTLEyAHHLGRALQLTNILRDVGEDARRGRIYLPAEELQRF 174
PLN02632 PLN02632
phytoene synthase
 107-170 2.76e-06

phytoene synthase


Pssm-ID: 215339  Cd Length: 334  Bit Score: 48.56  E-value: 2.76e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 567757587 107 YCHYVAGLVGI------GLSRLFSASEfedplvgEDT-ERANSMGLFLQKTNIIRDYLEDQQGGREFWPQE 170
Cdd:PLN02632 167 YCYYVAGTVGLmsvpvmGIAPESKAST-------ESVyNAALALGIANQLTNILRDVGEDARRGRVYLPQD 230
 
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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