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Conserved domains on  [gi|1013395206|ref|NP_001308907|]
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all trans-polyprenyl-diphosphate synthase PDSS1 isoform 2 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Trans_IPPS_HT cd00685
Trans-Isoprenyl Diphosphate Synthases, head-to-tail; These trans-Isoprenyl Diphosphate ...
 121-277 4.18e-56

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: 181.98  E-value: 4.18e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206 121 LKEMSEYYFDGKGKAFRPIIVALMARACnihhnnSRHVQASQRAIALIAEMIHTASLVHDDVIDDASSRRGKHTVNKIWG 200
Cdd:cd00685     6 LREALRYLLLAGGKRLRPLLVLLAARAL------GGPELEAALRLAAAIELLHTASLVHDDVMDNSDLRRGKPTVHKVFG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206 201 EKKAVLAGDLILSAASIALARIGNTT---VISILTQVIEDLVRGEFLQLGSKENENERFAHYLEKTFKKTASLIANSCKA 277
Cdd:cd00685    80 NATAILAGDYLLARAFELLARLGNPYyprALELFSEAILELVEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFAAAPLL 159
 
Name Accession Description Interval E-value
Trans_IPPS_HT cd00685
Trans-Isoprenyl Diphosphate Synthases, head-to-tail; These trans-Isoprenyl Diphosphate ...
 121-277 4.18e-56

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: 181.98  E-value: 4.18e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206 121 LKEMSEYYFDGKGKAFRPIIVALMARACnihhnnSRHVQASQRAIALIAEMIHTASLVHDDVIDDASSRRGKHTVNKIWG 200
Cdd:cd00685     6 LREALRYLLLAGGKRLRPLLVLLAARAL------GGPELEAALRLAAAIELLHTASLVHDDVMDNSDLRRGKPTVHKVFG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206 201 EKKAVLAGDLILSAASIALARIGNTT---VISILTQVIEDLVRGEFLQLGSKENENERFAHYLEKTFKKTASLIANSCKA 277
Cdd:cd00685    80 NATAILAGDYLLARAFELLARLGNPYyprALELFSEAILELVEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFAAAPLL 159
polyprenyl_synt pfam00348
Polyprenyl synthetase;
120-277 5.82e-54

Polyprenyl synthetase;


Pssm-ID: 459773  Cd Length: 251  Bit Score: 176.16  E-value: 5.82e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206 120 ELKEMSEYYFDGKGKAFRPIIVALMARACNIHHNNSRHvqasqRAIALIAEMIHTASLVHDDVIDDASSRRGKHTVNKIW 199
Cdd:pfam00348   3 LLYEPLDYLVSAGGKRIRPLLVLLSAEALGGPEDLEKA-----IVLAWAVELLHAASLVHDDIMDNSDLRRGQPTWHRIF 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206 200 GEKKAVLAGDLILSAASIALARI-GNTTVISILTQVIEDLVRGEFLQLGSKENENER--FAHYLEKTFKKTASLIANSCK 276
Cdd:pfam00348  78 GNAIAINDGDYLYALAFQLLAKLfPNPELLELFSEVTLQTAEGQGLDLLWRNDDDLSctEEEYLEIVKYKTAYLFALAVK 157


                  .
gi 1013395206 277 A 277
Cdd:pfam00348 158 L 158
PLN02890 PLN02890
geranyl diphosphate synthase
 6-278 3.23e-51

geranyl diphosphate synthase


Pssm-ID: 178478  Cd Length: 422  Bit Score: 174.34  E-value: 3.23e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206   6 WRWRRGCSWKPAARSPGPGSPGRAGPLGPSAAAevraqVHRRKGLDLSQIPYiNLVKHLTSACPNVCRISRFHHTTPDSK 85
Cdd:PLN02890    1 MLLSRRVARISATSGGGRGAYGCSQSLASSRAA-----LLGRHGHPLSQSTS-KVVGCRGTYSVSSRWLHGFQYQVRHQS 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206  86 THSGEKYTDPFKLGWRDLKGLYEDIRKELLISTSELKEMSEYYFD--GKGKAFRPIIVALMARACNIHHNNS-------- 155
Cdd:PLN02890   75 SSLVEEQLDPFSLVADELSLLANKLRSMVVAEVPKLASAAEYFFKvgVEGKRFRPTVLLLMATALNVPLPESteggvldi 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206 156 --RHVQASQRAIALIAEMIHTASLVHDDVIDDASSRRGKHTVNKIWGEKKAVLAGDLILSAASIALARIGNTTVISILTQ 233
Cdd:PLN02890  155 vaSELRTRQQNIAEITEMIHVASLLHDDVLDDADTRRGVGSLNVVMGNKLSVLAGDFLLSRACVALAALKNTEVVSLLAT 234

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 1013395206 234 VIEDLVRGEFLQLGSKENENERFAHYLEKTFKKTASLIANSCKAV 278
Cdd:PLN02890  235 AVEHLVTGETMQITSSREQRRSMDYYMQKTYYKTASLISNSCKAV 279
IspA COG0142
Geranylgeranyl pyrophosphate synthase [Coenzyme transport and metabolism]; Geranylgeranyl ...
 102-277 1.39e-47

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: 162.31  E-value: 1.39e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206 102 DLKGLYEDIRKEL---------LISTSE---LKEMSEYYFDGKGKAFRPIIVALMARACNIhhNNSRHVQAsqrAIALia 169
Cdd:COG0142     2 TLKDLLALLAEDLarveaaleeLLARSEpplLAEAMRYLLLAGGKRLRPLLVLLAARALGG--DPEAALRA---AAAV-- 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206 170 EMIHTASLVHDDVIDDASSRRGKHTVNKIWGEKKAVLAGDLILSAASIALARIGN----TTVISILTQVIEDLVRGEFLQ 245
Cdd:COG0142    75 ELIHTASLVHDDVMDDDDLRRGKPTVHARFGEATAILAGDALLALAFELLAELGDperrLRALRILARAARGMCEGQALD 154

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1013395206 246 LGSKENENERFAHYLEKTFKKTASLIANSCKA 277
Cdd:COG0142   155 LEAEGRLDVTLEEYLRVIRLKTAALFAAALRL 186
prenyl_cyano TIGR02749
solanesyl diphosphate synthase; Members of this family all are from cyanobacteria or ...
 102-277 2.42e-44

solanesyl diphosphate synthase; Members of this family all are from cyanobacteria or plastid-containing eukaryotes. A member from Arabidopsis (where both plastoquinone and ubiquinone contain the C(45) prenyl moiety) was characterized by heterologous expression as a solanesyl diphosphate synthase. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone]


Pssm-ID: 131796  Cd Length: 322  Bit Score: 153.75  E-value: 2.42e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206 102 DLKGLYEDIRKELLISTSELKEMSEYYFDGKGKAFRPIIVALMARACNihhnNSRHVQASQRAIALIAEMIHTASLVHDD 181
Cdd:TIGR02749  13 DLYLLTDNLKSLVGARHPILYAAAEHLFSAGGKRLRPAIVLLVSRATA----EQQELTPRHRRLAEITEMIHTASLVHDD 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206 182 VIDDASSRRGKHTVNKIWGEKKAVLAGDLILSAASIALARIGNTTVISILTQVIEDLVRGEFLQLGSKENENERFAHYLE 261
Cdd:TIGR02749  89 VIDESDTRRGIETVHSLFGTRVAVLAGDFLFAQASWYLANLENLEVVKLISKVITDFAEGEIKQGLNQFDSDLSLEDYLE 168

                         170
                  ....*....|....*.
gi 1013395206 262 KTFKKTASLIANSCKA 277
Cdd:TIGR02749 169 KSFYKTASLVAASSKA 184
 
Name Accession Description Interval E-value
Trans_IPPS_HT cd00685
Trans-Isoprenyl Diphosphate Synthases, head-to-tail; These trans-Isoprenyl Diphosphate ...
 121-277 4.18e-56

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: 181.98  E-value: 4.18e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206 121 LKEMSEYYFDGKGKAFRPIIVALMARACnihhnnSRHVQASQRAIALIAEMIHTASLVHDDVIDDASSRRGKHTVNKIWG 200
Cdd:cd00685     6 LREALRYLLLAGGKRLRPLLVLLAARAL------GGPELEAALRLAAAIELLHTASLVHDDVMDNSDLRRGKPTVHKVFG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206 201 EKKAVLAGDLILSAASIALARIGNTT---VISILTQVIEDLVRGEFLQLGSKENENERFAHYLEKTFKKTASLIANSCKA 277
Cdd:cd00685    80 NATAILAGDYLLARAFELLARLGNPYyprALELFSEAILELVEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFAAAPLL 159
polyprenyl_synt pfam00348
Polyprenyl synthetase;
120-277 5.82e-54

Polyprenyl synthetase;


Pssm-ID: 459773  Cd Length: 251  Bit Score: 176.16  E-value: 5.82e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206 120 ELKEMSEYYFDGKGKAFRPIIVALMARACNIHHNNSRHvqasqRAIALIAEMIHTASLVHDDVIDDASSRRGKHTVNKIW 199
Cdd:pfam00348   3 LLYEPLDYLVSAGGKRIRPLLVLLSAEALGGPEDLEKA-----IVLAWAVELLHAASLVHDDIMDNSDLRRGQPTWHRIF 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206 200 GEKKAVLAGDLILSAASIALARI-GNTTVISILTQVIEDLVRGEFLQLGSKENENER--FAHYLEKTFKKTASLIANSCK 276
Cdd:pfam00348  78 GNAIAINDGDYLYALAFQLLAKLfPNPELLELFSEVTLQTAEGQGLDLLWRNDDDLSctEEEYLEIVKYKTAYLFALAVK 157


                  .
gi 1013395206 277 A 277
Cdd:pfam00348 158 L 158
PLN02890 PLN02890
geranyl diphosphate synthase
 6-278 3.23e-51

geranyl diphosphate synthase


Pssm-ID: 178478  Cd Length: 422  Bit Score: 174.34  E-value: 3.23e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206   6 WRWRRGCSWKPAARSPGPGSPGRAGPLGPSAAAevraqVHRRKGLDLSQIPYiNLVKHLTSACPNVCRISRFHHTTPDSK 85
Cdd:PLN02890    1 MLLSRRVARISATSGGGRGAYGCSQSLASSRAA-----LLGRHGHPLSQSTS-KVVGCRGTYSVSSRWLHGFQYQVRHQS 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206  86 THSGEKYTDPFKLGWRDLKGLYEDIRKELLISTSELKEMSEYYFD--GKGKAFRPIIVALMARACNIHHNNS-------- 155
Cdd:PLN02890   75 SSLVEEQLDPFSLVADELSLLANKLRSMVVAEVPKLASAAEYFFKvgVEGKRFRPTVLLLMATALNVPLPESteggvldi 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206 156 --RHVQASQRAIALIAEMIHTASLVHDDVIDDASSRRGKHTVNKIWGEKKAVLAGDLILSAASIALARIGNTTVISILTQ 233
Cdd:PLN02890  155 vaSELRTRQQNIAEITEMIHVASLLHDDVLDDADTRRGVGSLNVVMGNKLSVLAGDFLLSRACVALAALKNTEVVSLLAT 234

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 1013395206 234 VIEDLVRGEFLQLGSKENENERFAHYLEKTFKKTASLIANSCKAV 278
Cdd:PLN02890  235 AVEHLVTGETMQITSSREQRRSMDYYMQKTYYKTASLISNSCKAV 279
IspA COG0142
Geranylgeranyl pyrophosphate synthase [Coenzyme transport and metabolism]; Geranylgeranyl ...
 102-277 1.39e-47

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: 162.31  E-value: 1.39e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206 102 DLKGLYEDIRKEL---------LISTSE---LKEMSEYYFDGKGKAFRPIIVALMARACNIhhNNSRHVQAsqrAIALia 169
Cdd:COG0142     2 TLKDLLALLAEDLarveaaleeLLARSEpplLAEAMRYLLLAGGKRLRPLLVLLAARALGG--DPEAALRA---AAAV-- 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206 170 EMIHTASLVHDDVIDDASSRRGKHTVNKIWGEKKAVLAGDLILSAASIALARIGN----TTVISILTQVIEDLVRGEFLQ 245
Cdd:COG0142    75 ELIHTASLVHDDVMDDDDLRRGKPTVHARFGEATAILAGDALLALAFELLAELGDperrLRALRILARAARGMCEGQALD 154

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1013395206 246 LGSKENENERFAHYLEKTFKKTASLIANSCKA 277
Cdd:COG0142   155 LEAEGRLDVTLEEYLRVIRLKTAALFAAALRL 186
prenyl_cyano TIGR02749
solanesyl diphosphate synthase; Members of this family all are from cyanobacteria or ...
 102-277 2.42e-44

solanesyl diphosphate synthase; Members of this family all are from cyanobacteria or plastid-containing eukaryotes. A member from Arabidopsis (where both plastoquinone and ubiquinone contain the C(45) prenyl moiety) was characterized by heterologous expression as a solanesyl diphosphate synthase. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone]


Pssm-ID: 131796  Cd Length: 322  Bit Score: 153.75  E-value: 2.42e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206 102 DLKGLYEDIRKELLISTSELKEMSEYYFDGKGKAFRPIIVALMARACNihhnNSRHVQASQRAIALIAEMIHTASLVHDD 181
Cdd:TIGR02749  13 DLYLLTDNLKSLVGARHPILYAAAEHLFSAGGKRLRPAIVLLVSRATA----EQQELTPRHRRLAEITEMIHTASLVHDD 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206 182 VIDDASSRRGKHTVNKIWGEKKAVLAGDLILSAASIALARIGNTTVISILTQVIEDLVRGEFLQLGSKENENERFAHYLE 261
Cdd:TIGR02749  89 VIDESDTRRGIETVHSLFGTRVAVLAGDFLFAQASWYLANLENLEVVKLISKVITDFAEGEIKQGLNQFDSDLSLEDYLE 168

                         170
                  ....*....|....*.
gi 1013395206 262 KTFKKTASLIANSCKA 277
Cdd:TIGR02749 169 KSFYKTASLVAASSKA 184
preA CHL00151
prenyl transferase; Reviewed
 110-277 1.66e-43

prenyl transferase; Reviewed


Pssm-ID: 164542  Cd Length: 323  Bit Score: 151.48  E-value: 1.66e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206 110 IRKELLISTSELKEM-----------SEYYFDGKGKAFRPIIVALMARACNihhnNSRHVQASQRAIALIAEMIHTASLV 178
Cdd:CHL00151   11 IEEELLILEDNLKKLigsghpilyaaAKHLFSAGGKRIRPAIVLLVAKATG----GNMEIKTSQQRLAEITEIIHTASLV 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206 179 HDDVIDDASSRRGKHTVNKIWGEKKAVLAGDLILSAASIALARIGNTTVISILTQVIEDLVRGEFLQLGSKENENERFAH 258
Cdd:CHL00151   87 HDDVIDECSIRRGIPTVHKIFGTKIAVLAGDFLFAQSSWYLANLNNLEVVKLISKVITDFAEGEIRQGLVQFDTTLSILN 166

                         170
                  ....*....|....*....
gi 1013395206 259 YLEKTFKKTASLIANSCKA 277
Cdd:CHL00151  167 YIEKSFYKTASLIAASCKA 185
PLN02857 PLN02857
octaprenyl-diphosphate synthase
 125-283 1.10e-40

octaprenyl-diphosphate synthase


Pssm-ID: 215462  Cd Length: 416  Bit Score: 146.14  E-value: 1.10e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206 125 SEYYFDGKGKAFRPIIVALMARA-CNIHHNNSRHVQasQRAIALIAEMIHTASLVHDDVIDDASSRRGKHTVNKIWGEKK 203
Cdd:PLN02857  127 AEQIFGAGGKRMRPALVFLVSRAtAELAGLKELTTE--HRRLAEITEMIHTASLIHDDVLDESDMRRGKETVHQLYGTRV 204

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206 204 AVLAGDLILSAASIALARIGNTTVISILTQVIEDLVRGEFLQLGSKENENERFAHYLEKTFKKTASLIANSCK--AVFPR 281
Cdd:PLN02857  205 AVLAGDFMFAQSSWYLANLDNLEVIKLISQVIKDFASGEIKQASSLFDCDVTLDEYLLKSYYKTASLIAASTKsaAIFSG 284


                  ..
gi 1013395206 282 NE 283
Cdd:PLN02857  285 VD 286
Trans_IPPS cd00867
Trans-Isoprenyl Diphosphate Synthases; Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of ...
 136-279 4.99e-40

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: 139.79  E-value: 4.99e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206 136 FRPIIVALMARACNIHHNnsrhvqaSQRAIALIAEMIHTASLVHDDVIDDASSRRGKHTVNKI-WGEKKAVLAGDLILSA 214
Cdd:cd00867     1 SRPLLVLLLARALGGDLE-------AALRLAAAVELLHAASLVHDDIVDDSDLRRGKPTAHLRrFGNALAILAGDYLLAR 73

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1013395206 215 ASIALARIGNTTVISILTQVIEDLVRGEFLQLGSKENENERFAHYLEKTFKKTASLIANSCKAVF 279
Cdd:cd00867    74 AFQLLARLGYPRALELFAEALRELLEGQALDLEFERDTYETLDEYLEYCRYKTAGLVGLLCLLGA 138
Isoprenoid_Biosyn_C1 cd00385
Isoprenoid Biosynthesis enzymes, Class 1; Superfamily of trans-isoprenyl diphosphate synthases ...
 136-279 2.30e-28

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: 109.51  E-value: 2.30e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206 136 FRPIIVALMARACnihhnnsrhvqasqrAIALIAEMIHTASLVHDDVIDDASSRRGKHTVNK---IWGEKKAVLAGDLIL 212
Cdd:cd00385     1 FRPLAVLLEPEAS---------------RLRAAVEKLHAASLVHDDIVDDSGTRRGLPTAHLavaIDGLPEAILAGDLLL 65

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1013395206 213 SAASIALARIGNTTVISILTQVIEDLVRGEFLQLGSKENENERFAHYLEKTFKKTASLIANSCKAVF 279
Cdd:cd00385    66 ADAFEELAREGSPEALEILAEALLDLLEGQLLDLKWRREYVPTLEEYLEYCRYKTAGLVGALCLLGA 132
PRK10888 PRK10888
octaprenyl diphosphate synthase; Provisional
 97-278 5.49e-25

octaprenyl diphosphate synthase; Provisional


Pssm-ID: 182813  Cd Length: 323  Bit Score: 102.23  E-value: 5.49e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206  97 KLGWRDLKGLYEDIRKELLISTSELKEMSEYYFDGKGKAFRPIIVALMARAcnIHHNNSRHVqasqrAIALIAEMIHTAS 176
Cdd:PRK10888    8 ELTAQDMAGVNAAILEQLNSDVQLINQLGYYIISGGGKRIRPMIAVLAARA--VGYQGNAHV-----TIAALIEFIHTAT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1013395206 177 LVHDDVIDDASSRRGKHTVNKIWGEKKAVLAGDLILSAASIALARIGNTTVISILTQVIEDLVRGEFLQLGSKENENERF 256
Cdd:PRK10888   81 LLHDDVVDESDMRRGKATANAAFGNAASVLVGDFIYTRAFQMMTSLGSLKVLEVMSEAVNVIAEGEVLQLMNVNDPDITE 160

                         170       180
                  ....*....|....*....|....
gi 1013395206 257 AHYLEKTFKKTASL--IANSCKAV 278
Cdd:PRK10888  161 ENYMRVIYSKTARLfeAAAQCSGI 184
PRK10581 PRK10581
(2E,6E)-farnesyl diphosphate synthase;
133-209 3.72e-06

(2E,6E)-farnesyl diphosphate synthase;


Pssm-ID: 182567  Cd Length: 299  Bit Score: 47.46  E-value: 3.72e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1013395206 133 GKAFRPIIVALMARACNIHhnnsrhvQASQRAIALIAEMIHTASLVHDDV--IDDASSRRGKHTVNKIWGEKKAVLAGD 209
Cdd:PRK10581   44 GKRLRPFLVYATGQMFGVS-------TNTLDAPAAAVECIHAYSLIHDDLpaMDDDDLRRGLPTCHVKFGEANAILAGD 115
 
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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