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Conserved domains on  [gi|1907157782|ref|XP_036020435|]
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NADH dehydrogenase (ubiquinone) complex I, assembly factor 6 isoform X11 [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 ...
 30-202 4.53e-34

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 pfam00494:

Pssm-ID: 469660 [Multi-domain]  Cd Length: 261  Bit Score: 122.01  E-value: 4.53e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157782  30 RLVKDSVSEKTIGLMRMQFWKKAVEDMYCDN--PPHQPVAIELWK-------------------EKNLDDKAYRSMQELE 88
Cdd:pfam00494  35 DIVDEVSDPPAAKRARLDWWRDALDGAYARRlkPARHPVLRALADlirryqlpkepflelidgmEMDLEFTRYETLAELE 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157782  89 NYAENTQGSLLYLTLEVLGV--KDLHADHAASHIGKAQGIVTCLRATPYHSSRRQVFLPMDVCVQHGVSQEDFLRRNQDK 166
Cdd:pfam00494 115 EYCYYVAGVVGLLLLRLLGArsDEAALLEAASHLGLALQLTNILRDVGEDARRGRVYLPAEVLKRFGVSEEDLLRGRASP 194

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1907157782 167 NVRDVVYDIASQAHLHLKHARSFHRSVPAEAFPAFL 202
Cdd:pfam00494 195 ALRALLRELAERARAHLREARPLLALLPRRARPAVL 230
 
Name Accession Description Interval E-value
SQS_PSY pfam00494
Squalene/phytoene synthase;
30-202 4.53e-34

Squalene/phytoene synthase;


Pssm-ID: 425717 [Multi-domain]  Cd Length: 261  Bit Score: 122.01  E-value: 4.53e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157782  30 RLVKDSVSEKTIGLMRMQFWKKAVEDMYCDN--PPHQPVAIELWK-------------------EKNLDDKAYRSMQELE 88
Cdd:pfam00494  35 DIVDEVSDPPAAKRARLDWWRDALDGAYARRlkPARHPVLRALADlirryqlpkepflelidgmEMDLEFTRYETLAELE 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157782  89 NYAENTQGSLLYLTLEVLGV--KDLHADHAASHIGKAQGIVTCLRATPYHSSRRQVFLPMDVCVQHGVSQEDFLRRNQDK 166
Cdd:pfam00494 115 EYCYYVAGVVGLLLLRLLGArsDEAALLEAASHLGLALQLTNILRDVGEDARRGRVYLPAEVLKRFGVSEEDLLRGRASP 194

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1907157782 167 NVRDVVYDIASQAHLHLKHARSFHRSVPAEAFPAFL 202
Cdd:pfam00494 195 ALRALLRELAERARAHLREARPLLALLPRRARPAVL 230
ERG9 COG1562
Phytoene/squalene synthetase [Lipid transport and metabolism];
34-202 9.47e-20

Phytoene/squalene synthetase [Lipid transport and metabolism];


Pssm-ID: 441170 [Multi-domain]  Cd Length: 278  Bit Score: 84.47  E-value: 9.47e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157782  34 DSVSEKTIGLMRMQFWKKAVEDMYCDNPPHQPVAIELWK-------------------EKNLDDKAYRSMQELENYAENT 94
Cdd:COG1562    49 DEVSDPAEREARLDWWRAELDAAYAGGPADHPVLAALADtvrryglprelfldlidgmEMDLTKTRYATFAELEDYCYRV 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157782  95 QGSLLYLTLEVLGVKDLHADHAASHIGKAQGIVTCLRATPYHSSRRQVFLPMDVCVQHGVSQEDFLRRNQDKNVRDVVYD 174
Cdd:COG1562   129 AGVVGLLLLRVFGADDPEALAAADALGVALQLTNILRDVGEDARRGRVYLPLDDLARFGVTEEDLLAGRASPALRALLRF 208

                         170       180
                  ....*....|....*....|....*....
gi 1907157782 175 IASQAHLHLKHARSFHRSVPAEA-FPAFL 202
Cdd:COG1562   209 LAARARALLREALAGIPALPRRArRAVLL 237
Trans_IPPS_HH cd00683
Trans-Isoprenyl Diphosphate Synthases, head-to-head; These trans-Isoprenyl Diphosphate ...
 28-206 6.77e-05

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: 42.61  E-value: 6.77e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157782  28 WLR----LVKDSVSEKTIGLMRMQFWKKAVEDMYCDNPPHQPVAIELWK-------------------EKNLDDKAYRSM 84
Cdd:cd00683    35 FCRaaddIVDDPAAPPDEKLALLDAFRAELDAAYWGGAPTHPVLRALADlarrygiprepfrdllagmAMDLDKRRYETL 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157782  85 QELENYAENTQGSLLYLTLEVLGVKDLH-ADHAASHIGKAQGIVTCLR--ATPYHSSRrqVFLPMDVCVQHGVSQEDFLR 161
Cdd:cd00683   115 DELDEYCYYVAGVVGLMLLRVFGASSDEaALERARALGLALQLTNILRdvGEDARRGR--IYLPREELARFGVTLEDLLA 192

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1907157782 162 RNQDKNVRDVVYDIASQAHLHLKHARSFHRSVPAEA-FPAFLQTVL 206
Cdd:cd00683   193 PENSPAFRALLRRLIARARAHYREALAGLAALPRRSrFCVRAAAML 238
PLN02632 PLN02632
phytoene synthase
 49-187 3.29e-04

phytoene synthase


Pssm-ID: 215339  Cd Length: 334  Bit Score: 40.47  E-value: 3.29e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157782  49 WKKAVEDMYCDNP------------PHQPVAIELWKE------KNLDDKAYRSMQELENYAENTQGSLLYLTLEVLGV-- 108
Cdd:PLN02632  108 WEARLEDLFDGRPydmldaaladtvSKFPLDIQPFRDmiegmrMDLVKSRYENFDELYLYCYYVAGTVGLMSVPVMGIap 187

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157782 109 ----KDLHADHAASHIGKAQGIVTCLRATPYHSSRRQVFLPMDVCVQHGVSQEDFLRRNQDKNVRDVVYDIASQAHLHLK 184
Cdd:PLN02632  188 eskaSTESVYNAALALGIANQLTNILRDVGEDARRGRVYLPQDELAQFGLTDEDIFAGKVTDKWRAFMKFQIKRARMYFA 267


                  ...
gi 1907157782 185 HAR 187
Cdd:PLN02632  268 EAE 270
 
Name Accession Description Interval E-value
SQS_PSY pfam00494
Squalene/phytoene synthase;
30-202 4.53e-34

Squalene/phytoene synthase;


Pssm-ID: 425717 [Multi-domain]  Cd Length: 261  Bit Score: 122.01  E-value: 4.53e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157782  30 RLVKDSVSEKTIGLMRMQFWKKAVEDMYCDN--PPHQPVAIELWK-------------------EKNLDDKAYRSMQELE 88
Cdd:pfam00494  35 DIVDEVSDPPAAKRARLDWWRDALDGAYARRlkPARHPVLRALADlirryqlpkepflelidgmEMDLEFTRYETLAELE 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157782  89 NYAENTQGSLLYLTLEVLGV--KDLHADHAASHIGKAQGIVTCLRATPYHSSRRQVFLPMDVCVQHGVSQEDFLRRNQDK 166
Cdd:pfam00494 115 EYCYYVAGVVGLLLLRLLGArsDEAALLEAASHLGLALQLTNILRDVGEDARRGRVYLPAEVLKRFGVSEEDLLRGRASP 194

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1907157782 167 NVRDVVYDIASQAHLHLKHARSFHRSVPAEAFPAFL 202
Cdd:pfam00494 195 ALRALLRELAERARAHLREARPLLALLPRRARPAVL 230
ERG9 COG1562
Phytoene/squalene synthetase [Lipid transport and metabolism];
34-202 9.47e-20

Phytoene/squalene synthetase [Lipid transport and metabolism];


Pssm-ID: 441170 [Multi-domain]  Cd Length: 278  Bit Score: 84.47  E-value: 9.47e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157782  34 DSVSEKTIGLMRMQFWKKAVEDMYCDNPPHQPVAIELWK-------------------EKNLDDKAYRSMQELENYAENT 94
Cdd:COG1562    49 DEVSDPAEREARLDWWRAELDAAYAGGPADHPVLAALADtvrryglprelfldlidgmEMDLTKTRYATFAELEDYCYRV 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157782  95 QGSLLYLTLEVLGVKDLHADHAASHIGKAQGIVTCLRATPYHSSRRQVFLPMDVCVQHGVSQEDFLRRNQDKNVRDVVYD 174
Cdd:COG1562   129 AGVVGLLLLRVFGADDPEALAAADALGVALQLTNILRDVGEDARRGRVYLPLDDLARFGVTEEDLLAGRASPALRALLRF 208

                         170       180
                  ....*....|....*....|....*....
gi 1907157782 175 IASQAHLHLKHARSFHRSVPAEA-FPAFL 202
Cdd:COG1562   209 LAARARALLREALAGIPALPRRArRAVLL 237
Trans_IPPS_HH cd00683
Trans-Isoprenyl Diphosphate Synthases, head-to-head; These trans-Isoprenyl Diphosphate ...
 28-206 6.77e-05

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: 42.61  E-value: 6.77e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157782  28 WLR----LVKDSVSEKTIGLMRMQFWKKAVEDMYCDNPPHQPVAIELWK-------------------EKNLDDKAYRSM 84
Cdd:cd00683    35 FCRaaddIVDDPAAPPDEKLALLDAFRAELDAAYWGGAPTHPVLRALADlarrygiprepfrdllagmAMDLDKRRYETL 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157782  85 QELENYAENTQGSLLYLTLEVLGVKDLH-ADHAASHIGKAQGIVTCLR--ATPYHSSRrqVFLPMDVCVQHGVSQEDFLR 161
Cdd:cd00683   115 DELDEYCYYVAGVVGLMLLRVFGASSDEaALERARALGLALQLTNILRdvGEDARRGR--IYLPREELARFGVTLEDLLA 192

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1907157782 162 RNQDKNVRDVVYDIASQAHLHLKHARSFHRSVPAEA-FPAFLQTVL 206
Cdd:cd00683   193 PENSPAFRALLRRLIARARAHYREALAGLAALPRRSrFCVRAAAML 238
PLN02632 PLN02632
phytoene synthase
 49-187 3.29e-04

phytoene synthase


Pssm-ID: 215339  Cd Length: 334  Bit Score: 40.47  E-value: 3.29e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157782  49 WKKAVEDMYCDNP------------PHQPVAIELWKE------KNLDDKAYRSMQELENYAENTQGSLLYLTLEVLGV-- 108
Cdd:PLN02632  108 WEARLEDLFDGRPydmldaaladtvSKFPLDIQPFRDmiegmrMDLVKSRYENFDELYLYCYYVAGTVGLMSVPVMGIap 187

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907157782 109 ----KDLHADHAASHIGKAQGIVTCLRATPYHSSRRQVFLPMDVCVQHGVSQEDFLRRNQDKNVRDVVYDIASQAHLHLK 184
Cdd:PLN02632  188 eskaSTESVYNAALALGIANQLTNILRDVGEDARRGRVYLPQDELAQFGLTDEDIFAGKVTDKWRAFMKFQIKRARMYFA 267


                  ...
gi 1907157782 185 HAR 187
Cdd:PLN02632  268 EAE 270
 
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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