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Conserved domains on  [gi|767943184|ref|XP_011534265|]
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all trans-polyprenyl-diphosphate synthase PDSS2 isoform X14 [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 ...
 68-208 3.81e-16

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: 75.98  E-value: 3.81e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767943184  68 SLRCLLSDELSNIAMQVRKLVGTQHPLLT-TARGLVhdSWNSLQLRGLVVLLISKAAGpssvntscQNYDMVSGiyscQR 146
Cdd:CHL00151   6 NLLTPIEEELLILEDNLKKLIGSGHPILYaAAKHLF--SAGGKRIRPAIVLLVAKATG--------GNMEIKTS----QQ 71

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767943184 147 SLAEITELIHIALLVHRGIVNLNELQSSDgPLKDMQFGNKIAILSGDFLLANACNGLALLQN 208
Cdd:CHL00151  72 RLAEITEIIHTASLVHDDVIDECSIRRGI-PTVHKIFGTKIAVLAGDFLFAQSSWYLANLNN 132
 
Name Accession Description Interval E-value
preA CHL00151
prenyl transferase; Reviewed
 68-208 3.81e-16

prenyl transferase; Reviewed


Pssm-ID: 164542  Cd Length: 323  Bit Score: 75.98  E-value: 3.81e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767943184  68 SLRCLLSDELSNIAMQVRKLVGTQHPLLT-TARGLVhdSWNSLQLRGLVVLLISKAAGpssvntscQNYDMVSGiyscQR 146
Cdd:CHL00151   6 NLLTPIEEELLILEDNLKKLIGSGHPILYaAAKHLF--SAGGKRIRPAIVLLVAKATG--------GNMEIKTS----QQ 71

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767943184 147 SLAEITELIHIALLVHRGIVNLNELQSSDgPLKDMQFGNKIAILSGDFLLANACNGLALLQN 208
Cdd:CHL00151  72 RLAEITEIIHTASLVHDDVIDECSIRRGI-PTVHKIFGTKIAVLAGDFLFAQSSWYLANLNN 132
polyprenyl_synt pfam00348
Polyprenyl synthetase;
110-199 3.07e-08

Polyprenyl synthetase;


Pssm-ID: 459773  Cd Length: 251  Bit Score: 52.89  E-value: 3.07e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767943184  110 QLRGLVVLLISKAagpssvntsCQNYDmvsgIYSCQRSLAEITELIHIALLVH----------RGI--VNLnelqssdgp 177
Cdd:pfam00348  18 RIRPLLVLLSAEA---------LGGPE----DLEKAIVLAWAVELLHAASLVHddimdnsdlrRGQptWHR--------- 75

                          90       100
                  ....*....|....*....|..
gi 767943184  178 lkdmQFGNKIAILSGDFLLANA 199
Cdd:pfam00348  76 ----IFGNAIAINDGDYLYALA 93
Trans_IPPS_HT cd00685
Trans-Isoprenyl Diphosphate Synthases, head-to-tail; These trans-Isoprenyl Diphosphate ...
 110-197 9.06e-08

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: 51.40  E-value: 9.06e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767943184 110 QLRGLVVLLISKAAGPSSVNTscqnydmvsgiyscQRSLAEITELIHIALLVH----------RGIVNLNElqssdgplk 179
Cdd:cd00685   20 RLRPLLVLLAARALGGPELEA--------------ALRLAAAIELLHTASLVHddvmdnsdlrRGKPTVHK--------- 76

                         90
                 ....*....|....*...
gi 767943184 180 dmQFGNKIAILSGDFLLA 197
Cdd:cd00685   77 --VFGNATAILAGDYLLA 92
IspA COG0142
Geranylgeranyl pyrophosphate synthase [Coenzyme transport and metabolism]; Geranylgeranyl ...
 111-199 1.19e-06

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: 48.30  E-value: 1.19e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767943184 111 LRGLVVLLISKAAGPSSVNTscqnydmvsgiyscqRSLAEITELIHIALLVH----------RGIVNLNElqssdgplkd 180
Cdd:COG0142   48 LRPLLVLLAARALGGDPEAA---------------LRAAAAVELIHTASLVHddvmddddlrRGKPTVHA---------- 102

                         90
                 ....*....|....*....
gi 767943184 181 mQFGNKIAILSGDFLLANA 199
Cdd:COG0142  103 -RFGEATAILAGDALLALA 120
 
Name Accession Description Interval E-value
preA CHL00151
prenyl transferase; Reviewed
 68-208 3.81e-16

prenyl transferase; Reviewed


Pssm-ID: 164542  Cd Length: 323  Bit Score: 75.98  E-value: 3.81e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767943184  68 SLRCLLSDELSNIAMQVRKLVGTQHPLLT-TARGLVhdSWNSLQLRGLVVLLISKAAGpssvntscQNYDMVSGiyscQR 146
Cdd:CHL00151   6 NLLTPIEEELLILEDNLKKLIGSGHPILYaAAKHLF--SAGGKRIRPAIVLLVAKATG--------GNMEIKTS----QQ 71

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767943184 147 SLAEITELIHIALLVHRGIVNLNELQSSDgPLKDMQFGNKIAILSGDFLLANACNGLALLQN 208
Cdd:CHL00151  72 RLAEITEIIHTASLVHDDVIDECSIRRGI-PTVHKIFGTKIAVLAGDFLFAQSSWYLANLNN 132
PLN02890 PLN02890
geranyl diphosphate synthase
 72-214 1.24e-15

geranyl diphosphate synthase


Pssm-ID: 178478  Cd Length: 422  Bit Score: 75.35  E-value: 1.24e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767943184  72 LLSDELSNIAMQVRKLVGTQHPLLTTA------RGLvhdswNSLQLRGLVVLLISKAAG-PSSVNTSCQNYDMV-SGIYS 143
Cdd:PLN02890  87 LVADELSLLANKLRSMVVAEVPKLASAaeyffkVGV-----EGKRFRPTVLLLMATALNvPLPESTEGGVLDIVaSELRT 161

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767943184 144 CQRSLAEITELIHIALLVHRGIVNLNELQSSDGPLkDMQFGNKIAILSGDFLLANACNGLALLQNTKSFSF 214
Cdd:PLN02890 162 RQQNIAEITEMIHVASLLHDDVLDDADTRRGVGSL-NVVMGNKLSVLAGDFLLSRACVALAALKNTEVVSL 231
PLN02857 PLN02857
octaprenyl-diphosphate synthase
 15-208 6.75e-13

octaprenyl-diphosphate synthase


Pssm-ID: 215462  Cd Length: 416  Bit Score: 67.18  E-value: 6.75e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767943184  15 GASGSPRRLWWSPSlDTISSVGSWRGRSSKSPAHWN------------------------QVVSEAEKIVGYPTSFMSLR 70
Cdd:PLN02857  20 SSNASSRRRVVRNG-ATPVCKSCSRSYASSLVTSRRdigrcrvvspspetslvngigqgpTVALDLKAESKEPISLSELF 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767943184  71 CLLSDELSNIAMQVRKLVGTQHPLLTTARGLVHDSWNSlQLRGLVVLLISKAagpssvntSCQNYDMvSGIYSCQRSLAE 150
Cdd:PLN02857  99 EPVADDLQQLNDNLQSIVGAENPVLMSAAEQIFGAGGK-RMRPALVFLVSRA--------TAELAGL-KELTTEHRRLAE 168

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 767943184 151 ITELIHIALLVHRGIVNLNELQSSDGPLKDMqFGNKIAILSGDFLLANACNGLALLQN 208
Cdd:PLN02857 169 ITEMIHTASLIHDDVLDESDMRRGKETVHQL-YGTRVAVLAGDFMFAQSSWYLANLDN 225
polyprenyl_synt pfam00348
Polyprenyl synthetase;
110-199 3.07e-08

Polyprenyl synthetase;


Pssm-ID: 459773  Cd Length: 251  Bit Score: 52.89  E-value: 3.07e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767943184  110 QLRGLVVLLISKAagpssvntsCQNYDmvsgIYSCQRSLAEITELIHIALLVH----------RGI--VNLnelqssdgp 177
Cdd:pfam00348  18 RIRPLLVLLSAEA---------LGGPE----DLEKAIVLAWAVELLHAASLVHddimdnsdlrRGQptWHR--------- 75

                          90       100
                  ....*....|....*....|..
gi 767943184  178 lkdmQFGNKIAILSGDFLLANA 199
Cdd:pfam00348  76 ----IFGNAIAINDGDYLYALA 93
Trans_IPPS_HT cd00685
Trans-Isoprenyl Diphosphate Synthases, head-to-tail; These trans-Isoprenyl Diphosphate ...
 110-197 9.06e-08

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: 51.40  E-value: 9.06e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767943184 110 QLRGLVVLLISKAAGPSSVNTscqnydmvsgiyscQRSLAEITELIHIALLVH----------RGIVNLNElqssdgplk 179
Cdd:cd00685   20 RLRPLLVLLAARALGGPELEA--------------ALRLAAAIELLHTASLVHddvmdnsdlrRGKPTVHK--------- 76

                         90
                 ....*....|....*...
gi 767943184 180 dmQFGNKIAILSGDFLLA 197
Cdd:cd00685   77 --VFGNATAILAGDYLLA 92
IspA COG0142
Geranylgeranyl pyrophosphate synthase [Coenzyme transport and metabolism]; Geranylgeranyl ...
 111-199 1.19e-06

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: 48.30  E-value: 1.19e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767943184 111 LRGLVVLLISKAAGPSSVNTscqnydmvsgiyscqRSLAEITELIHIALLVH----------RGIVNLNElqssdgplkd 180
Cdd:COG0142   48 LRPLLVLLAARALGGDPEAA---------------LRAAAAVELIHTASLVHddvmddddlrRGKPTVHA---------- 102

                         90
                 ....*....|....*....
gi 767943184 181 mQFGNKIAILSGDFLLANA 199
Cdd:COG0142  103 -RFGEATAILAGDALLALA 120
Trans_IPPS cd00867
Trans-Isoprenyl Diphosphate Synthases; Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of ...
 111-199 1.32e-03

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: 38.86  E-value: 1.32e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767943184 111 LRGLVVLLISKAAGpssvntscqnydmvsGIYSCQRSLAEITELIHIALLVHRGIVNlNELQSSDGP-LKDMQFGNKIAI 189
Cdd:cd00867    1 SRPLLVLLLARALG---------------GDLEAALRLAAAVELLHAASLVHDDIVD-DSDLRRGKPtAHLRRFGNALAI 64

                         90
                 ....*....|
gi 767943184 190 LSGDFLLANA 199
Cdd:cd00867   65 LAGDYLLARA 74
 
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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