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Conserved domains on  [gi|1907099395|ref|XP_036014350|]
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squalene synthase isoform X2 [Mus musculus]

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 ...
 18-276 2.42e-153

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: 433.02  E-value: 2.42e-153
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907099395  18 RFRMGGRRNFIPKMDQ---ISLEFRNLAEKYQTVIDDICHRMGCGMAEFVDKDVTSKQ---DWDKYCHYVAGLVGIGLSR 91
Cdd:TIGR01559  73 RFTESDNEKDRQVLDDfpvVSLEFLKLKPKYQEVIADITRRMGNGMADFIDKEVTNEQtvgDYDKYCHYVAGLVGIGLSR 152

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907099395  92 LFSASEFEDPIVGEDIECANSMGLFLQKTNIIRDYLEDQQEGRKFWPQEVWGRYIKKLEDFAKPENVDVAVQCLNELITN 171
Cdd:TIGR01559 153 LFVASGFEDPSLGESEALSNSMGLFLQKTNIIRDYLEDINEGRMFWPREIWSKYAKKLGDFKKPENSDKALQCLNELVTN 232

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907099395 172 TLQHIPDVLTYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGVVKIRKGQAVTLMMDATNMPAVKAIIYQYIEEI 251
Cdd:TIGR01559 233 ALHHATDCLTYLSRLRDQSIFNFCAIPQVMAIATLALCYNNPQVFQGNVKIRKGTTVKLILDSTNMPAVYDIFYRYARKI 312

                         250       260
                  ....*....|....*....|....*
gi 1907099395 252 YHRIPNSDPSSSKTKQVISKIRTQN 276
Cdd:TIGR01559 313 YHKIDPNDPNFSKTLIIISKIEQQC 337
 
Name Accession Description Interval E-value
squal_synth TIGR01559
farnesyl-diphosphate farnesyltransferase; This model describes farnesyl-diphosphate ...
 18-276 2.42e-153

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: 433.02  E-value: 2.42e-153
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907099395  18 RFRMGGRRNFIPKMDQ---ISLEFRNLAEKYQTVIDDICHRMGCGMAEFVDKDVTSKQ---DWDKYCHYVAGLVGIGLSR 91
Cdd:TIGR01559  73 RFTESDNEKDRQVLDDfpvVSLEFLKLKPKYQEVIADITRRMGNGMADFIDKEVTNEQtvgDYDKYCHYVAGLVGIGLSR 152

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907099395  92 LFSASEFEDPIVGEDIECANSMGLFLQKTNIIRDYLEDQQEGRKFWPQEVWGRYIKKLEDFAKPENVDVAVQCLNELITN 171
Cdd:TIGR01559 153 LFVASGFEDPSLGESEALSNSMGLFLQKTNIIRDYLEDINEGRMFWPREIWSKYAKKLGDFKKPENSDKALQCLNELVTN 232

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907099395 172 TLQHIPDVLTYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGVVKIRKGQAVTLMMDATNMPAVKAIIYQYIEEI 251
Cdd:TIGR01559 233 ALHHATDCLTYLSRLRDQSIFNFCAIPQVMAIATLALCYNNPQVFQGNVKIRKGTTVKLILDSTNMPAVYDIFYRYARKI 312

                         250       260
                  ....*....|....*....|....*
gi 1907099395 252 YHRIPNSDPSSSKTKQVISKIRTQN 276
Cdd:TIGR01559 313 YHKIDPNDPNFSKTLIIISKIEQQC 337
Trans_IPPS_HH cd00683
Trans-Isoprenyl Diphosphate Synthases, head-to-head; These trans-Isoprenyl Diphosphate ...
 32-227 1.21e-53

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: 176.66  E-value: 1.21e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907099395  32 DQISLEFRNLAEkYQTVIDDICHRMGCGMAEFVDK-DVTSKQDWDKYCHYVAGLVGIGLSRLFSASEFEdpivgEDIECA 110
Cdd:cd00683    75 HPVLRALADLAR-RYGIPREPFRDLLAGMAMDLDKrRYETLDELDEYCYYVAGVVGLMLLRVFGASSDE-----AALERA 148

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907099395 111 NSMGLFLQKTNIIRDYLEDQQEGRKFWPQEVWGRYIKKLEDFAKPENVDVAVQCLNELITNTLQHIPDVLTYLSRLRnqS 190
Cdd:cd00683   149 RALGLALQLTNILRDVGEDARRGRIYLPREELARFGVTLEDLLAPENSPAFRALLRRLIARARAHYREALAGLAALP--R 226

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1907099395 191 VFNFCAIPQVMAIATLAACYNNQQVFKGVVKIRKGQA 227
Cdd:cd00683   227 RSRFCVRAAAMLYRTILDEIEARGYDVLSVRVRVPKA 263
SQS_PSY pfam00494
Squalene/phytoene synthase;
18-226 2.69e-34

Squalene/phytoene synthase;


Pssm-ID: 425717 [Multi-domain]  Cd Length: 261  Bit Score: 125.86  E-value: 2.69e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907099395  18 RFRMGGRRNFIPKMDQISLEFRNLAEKYQTVIDDiCHRMGCGMAEFVDKD-VTSKQDWDKYCHYVAGLVGIGLSRLFSAS 96
Cdd:pfam00494  57 ALDGAYARRLKPARHPVLRALADLIRRYQLPKEP-FLELIDGMEMDLEFTrYETLAELEEYCYYVAGVVGLLLLRLLGAR 135

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907099395  97 EFEDpivgEDIECANSMGLFLQKTNIIRDYLEDQQEGRKFWPQEVWGRYIKKLEDFAKPENVDVAVQCLNELITNTLQHI 176
Cdd:pfam00494 136 SDEA----ALLEAASHLGLALQLTNILRDVGEDARRGRVYLPAEVLKRFGVSEEDLLRGRASPALRALLRELAERARAHL 211

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1907099395 177 PDVLTYLSRLRNQSVFnFCAIPQVMAIATLAACYNNQ-QVFKGVVKIRKGQ 226
Cdd:pfam00494 212 REARPLLALLPRRARP-AVLLAAVLYRAILRRLEAAGyDVLRRRVKLSRRR 261
ERG9 COG1562
Phytoene/squalene synthetase [Lipid transport and metabolism];
59-234 2.28e-17

Phytoene/squalene synthetase [Lipid transport and metabolism];


Pssm-ID: 441170 [Multi-domain]  Cd Length: 278  Bit Score: 80.62  E-value: 2.28e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907099395  59 GMAEFVDKDV-TSKQDWDKYCHYVAGLVGIGLSRLFSASEfedpivGEDIECANSMGLFLQKTNIIRDYLEDQQEGRKFW 137
Cdd:COG1562   105 GMEMDLTKTRyATFAELEDYCYRVAGVVGLLLLRVFGADD------PEALAAADALGVALQLTNILRDVGEDARRGRVYL 178

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907099395 138 PQEVWGRYIKKLEDFAKPENVDVAVQCLNELITNTLQHIPDVLTYLSRLRNQSVFnFCAIPQVMAIATLAACYNNQ-QVF 216
Cdd:COG1562   179 PLDDLARFGVTEEDLLAGRASPALRALLRFLAARARALLREALAGIPALPRRARR-AVLLAAALYRAILDKIERRGyDVL 257

                         170
                  ....*....|....*...
gi 1907099395 217 KGVVKIRKGQAVTLMMDA 234
Cdd:COG1562   258 RRRVRLSRLRKLWLLWRA 275
PLN02632 PLN02632
phytoene synthase
 72-140 6.65e-07

phytoene synthase


Pssm-ID: 215339  Cd Length: 334  Bit Score: 50.10  E-value: 6.65e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907099395  72 QDWDK---YCHYVAGLVGI------GLSRLFSASEfedpivgEDI-ECANSMGLFLQKTNIIRDYLEDQQEGRKFWPQE 140
Cdd:PLN02632  159 ENFDElylYCYYVAGTVGLmsvpvmGIAPESKAST-------ESVyNAALALGIANQLTNILRDVGEDARRGRVYLPQD 230
 
Name Accession Description Interval E-value
squal_synth TIGR01559
farnesyl-diphosphate farnesyltransferase; This model describes farnesyl-diphosphate ...
 18-276 2.42e-153

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: 433.02  E-value: 2.42e-153
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907099395  18 RFRMGGRRNFIPKMDQ---ISLEFRNLAEKYQTVIDDICHRMGCGMAEFVDKDVTSKQ---DWDKYCHYVAGLVGIGLSR 91
Cdd:TIGR01559  73 RFTESDNEKDRQVLDDfpvVSLEFLKLKPKYQEVIADITRRMGNGMADFIDKEVTNEQtvgDYDKYCHYVAGLVGIGLSR 152

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907099395  92 LFSASEFEDPIVGEDIECANSMGLFLQKTNIIRDYLEDQQEGRKFWPQEVWGRYIKKLEDFAKPENVDVAVQCLNELITN 171
Cdd:TIGR01559 153 LFVASGFEDPSLGESEALSNSMGLFLQKTNIIRDYLEDINEGRMFWPREIWSKYAKKLGDFKKPENSDKALQCLNELVTN 232

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907099395 172 TLQHIPDVLTYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGVVKIRKGQAVTLMMDATNMPAVKAIIYQYIEEI 251
Cdd:TIGR01559 233 ALHHATDCLTYLSRLRDQSIFNFCAIPQVMAIATLALCYNNPQVFQGNVKIRKGTTVKLILDSTNMPAVYDIFYRYARKI 312

                         250       260
                  ....*....|....*....|....*
gi 1907099395 252 YHRIPNSDPSSSKTKQVISKIRTQN 276
Cdd:TIGR01559 313 YHKIDPNDPNFSKTLIIISKIEQQC 337
Trans_IPPS_HH cd00683
Trans-Isoprenyl Diphosphate Synthases, head-to-head; These trans-Isoprenyl Diphosphate ...
 32-227 1.21e-53

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: 176.66  E-value: 1.21e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907099395  32 DQISLEFRNLAEkYQTVIDDICHRMGCGMAEFVDK-DVTSKQDWDKYCHYVAGLVGIGLSRLFSASEFEdpivgEDIECA 110
Cdd:cd00683    75 HPVLRALADLAR-RYGIPREPFRDLLAGMAMDLDKrRYETLDELDEYCYYVAGVVGLMLLRVFGASSDE-----AALERA 148

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907099395 111 NSMGLFLQKTNIIRDYLEDQQEGRKFWPQEVWGRYIKKLEDFAKPENVDVAVQCLNELITNTLQHIPDVLTYLSRLRnqS 190
Cdd:cd00683   149 RALGLALQLTNILRDVGEDARRGRIYLPREELARFGVTLEDLLAPENSPAFRALLRRLIARARAHYREALAGLAALP--R 226

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1907099395 191 VFNFCAIPQVMAIATLAACYNNQQVFKGVVKIRKGQA 227
Cdd:cd00683   227 RSRFCVRAAAMLYRTILDEIEARGYDVLSVRVRVPKA 263
SQS_PSY pfam00494
Squalene/phytoene synthase;
18-226 2.69e-34

Squalene/phytoene synthase;


Pssm-ID: 425717 [Multi-domain]  Cd Length: 261  Bit Score: 125.86  E-value: 2.69e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907099395  18 RFRMGGRRNFIPKMDQISLEFRNLAEKYQTVIDDiCHRMGCGMAEFVDKD-VTSKQDWDKYCHYVAGLVGIGLSRLFSAS 96
Cdd:pfam00494  57 ALDGAYARRLKPARHPVLRALADLIRRYQLPKEP-FLELIDGMEMDLEFTrYETLAELEEYCYYVAGVVGLLLLRLLGAR 135

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907099395  97 EFEDpivgEDIECANSMGLFLQKTNIIRDYLEDQQEGRKFWPQEVWGRYIKKLEDFAKPENVDVAVQCLNELITNTLQHI 176
Cdd:pfam00494 136 SDEA----ALLEAASHLGLALQLTNILRDVGEDARRGRVYLPAEVLKRFGVSEEDLLRGRASPALRALLRELAERARAHL 211

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1907099395 177 PDVLTYLSRLRNQSVFnFCAIPQVMAIATLAACYNNQ-QVFKGVVKIRKGQ 226
Cdd:pfam00494 212 REARPLLALLPRRARP-AVLLAAVLYRAILRRLEAAGyDVLRRRVKLSRRR 261
ERG9 COG1562
Phytoene/squalene synthetase [Lipid transport and metabolism];
59-234 2.28e-17

Phytoene/squalene synthetase [Lipid transport and metabolism];


Pssm-ID: 441170 [Multi-domain]  Cd Length: 278  Bit Score: 80.62  E-value: 2.28e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907099395  59 GMAEFVDKDV-TSKQDWDKYCHYVAGLVGIGLSRLFSASEfedpivGEDIECANSMGLFLQKTNIIRDYLEDQQEGRKFW 137
Cdd:COG1562   105 GMEMDLTKTRyATFAELEDYCYRVAGVVGLLLLRVFGADD------PEALAAADALGVALQLTNILRDVGEDARRGRVYL 178

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907099395 138 PQEVWGRYIKKLEDFAKPENVDVAVQCLNELITNTLQHIPDVLTYLSRLRNQSVFnFCAIPQVMAIATLAACYNNQ-QVF 216
Cdd:COG1562   179 PLDDLARFGVTEEDLLAGRASPALRALLRFLAARARALLREALAGIPALPRRARR-AVLLAAALYRAILDKIERRGyDVL 257

                         170
                  ....*....|....*...
gi 1907099395 217 KGVVKIRKGQAVTLMMDA 234
Cdd:COG1562   258 RRRVRLSRLRKLWLLWRA 275
Trans_IPPS cd00867
Trans-Isoprenyl Diphosphate Synthases; Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of ...
 34-151 3.94e-16

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: 76.23  E-value: 3.94e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907099395  34 ISLEFRNLAE----KYQTVIDDICHRMGCGMAEFVDKDVTSKQDWD---KYCHY-VAGLVGIGLSRLFSASEFEDPIVGE 105
Cdd:cd00867    71 LARAFQLLARlgypRALELFAEALRELLEGQALDLEFERDTYETLDeylEYCRYkTAGLVGLLCLLGAGLSGADDEQAEA 150

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907099395 106 DIECANSMGLFLQKTNIIRDY----------LEDQQEGRKFWPQEVWGRYIKKLED 151
Cdd:cd00867   151 LKDYGRALGLAFQLTDDLLDVfgdaeelgkvGSDLREGRITLPVILARERAAEYAE 206
Isoprenoid_Biosyn_C1 cd00385
Isoprenoid Biosynthesis enzymes, Class 1; Superfamily of trans-isoprenyl diphosphate synthases ...
 34-204 3.12e-14

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: 70.99  E-value: 3.12e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907099395  34 ISLEFRNLAE----KYQTVIDDICHRMGCGM---AEFVDKDVTSKQDWDKYCHYV-AGLVGIGLSRLFSASEFEDPIVGE 105
Cdd:cd00385    65 LADAFEELARegspEALEILAEALLDLLEGQlldLKWRREYVPTLEEYLEYCRYKtAGLVGALCLLGAGLSGGEAELLEA 144

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907099395 106 DIECANSMGLFLQKTNIIRDYLEDQQ--EGRKFWPQEVWGRYIKKLEDFAKPENVDVAVQCLNELITNTLQHIPDVLTYL 183
Cdd:cd00385   145 LRKLGRALGLAFQLTNDLLDYEGDAErgEGKCTLPVLYALEYGVPAEDLLLVEKSGSLEEALEELAKLAEEALKELNELI 224

                         170       180
                  ....*....|....*....|.
gi 1907099395 184 SRLRnqSVFNFCAIPQVMAIA 204
Cdd:cd00385   225 LSLP--DVPRALLALALNLYR 243
HpnD TIGR03465
squalene synthase HpnD; The genes of this family are often found in the same genetic locus ...
 42-145 9.59e-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: 55.36  E-value: 9.59e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907099395  42 AEKYQTVIDdichrmGCGMaefvDKDVTSKQDWDK---YCHYVAGLVGIGLSRLFSASEfedpivGEDIECANSMGLFLQ 118
Cdd:TIGR03465  84 QEDFLEVID------GMEM----DLEQTRYPDFAEldlYCDRVAGAVGRLSARIFGATD------ARTLEYAHHLGRALQ 147

                          90       100
                  ....*....|....*....|....*..
gi 1907099395 119 KTNIIRDYLEDQQEGRKFWPQEVWGRY 145
Cdd:TIGR03465 148 LTNILRDVGEDARRGRIYLPAEELQRF 174
PLN02632 PLN02632
phytoene synthase
 72-140 6.65e-07

phytoene synthase


Pssm-ID: 215339  Cd Length: 334  Bit Score: 50.10  E-value: 6.65e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907099395  72 QDWDK---YCHYVAGLVGI------GLSRLFSASEfedpivgEDI-ECANSMGLFLQKTNIIRDYLEDQQEGRKFWPQE 140
Cdd:PLN02632  159 ENFDElylYCYYVAGTVGLmsvpvmGIAPESKAST-------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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