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Conserved domains on  [gi|83700220|ref|NP_001032354|]
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geranylgeranyl pyrophosphate synthase isoform A [Homo sapiens]

Protein Classification

FPP/GGPP synthase family protein( domain architecture ID 11092413)

FPP/GGPP synthase family protein such as farnesyl/geranylgeranyl diphosphate synthases, which are key enzymes in isoprenoid biosynthesis, catalyzing the formation of farnesyl diphosphate (FPP) and geranylgeranyl diphosphate (GGPP), respectively

CATH:  1.10.600.10
EC:  2.5.1.-
Gene Ontology:  GO:0004659|GO:0046872|GO:0008299
PubMed:  8003978|11111076
SCOP:  4001453

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
polyprenyl_synt pfam00348
Polyprenyl synthetase;
9-250 3.32e-97

Polyprenyl synthetase;


:

Pssm-ID: 459773  Cd Length: 251  Bit Score: 286.32  E-value: 3.32e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220     9 QRILLEPYKYLLQLPGKQVRTKLSQAFNHWLKVPED--KLQIIIEVTEMLHNASLLIDDIEDNSKLRRGFPVAHSIYGIP 86
Cdd:pfam00348   1 EKLLYEPLDYLVSAGGKRIRPLLVLLSAEALGGPEDleKAIVLAWAVELLHAASLVHDDIMDNSDLRRGQPTWHRIFGNA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220    87 SVINSANYVYFLGLEKVLTL-DHPDAVKLFTRQLLELHQGQGLDIYWRDNYTCP-TEEEYKAMVLQKTGGLFGLAVGLMQ 164
Cdd:pfam00348  81 IAINDGDYLYALAFQLLAKLfPNPELLELFSEVTLQTAEGQGLDLLWRNDDDLScTEEEYLEIVKYKTAYLFALAVKLGA 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220   165 LFS----DYKEDLKPLLNTLGLFFQIRDDYANLHSKEYSENKSFCEDLTEGKFSFPTIHAIWSRPE-STQVQNILRQRTE 239
Cdd:pfam00348 161 ILSgaddEVIEALKDYGLNLGLAFQIQDDYLDLFGDPEVLGKPAGTDITEGKCTWPVIHALERTPEqRKILLEIYGKRPE 240
                         250
                  ....*....|.
gi 83700220   240 NIDIKKYCVHY 250
Cdd:pfam00348 241 DVEKVKEAYEL 251
 
Name Accession Description Interval E-value
polyprenyl_synt pfam00348
Polyprenyl synthetase;
9-250 3.32e-97

Polyprenyl synthetase;


Pssm-ID: 459773  Cd Length: 251  Bit Score: 286.32  E-value: 3.32e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220     9 QRILLEPYKYLLQLPGKQVRTKLSQAFNHWLKVPED--KLQIIIEVTEMLHNASLLIDDIEDNSKLRRGFPVAHSIYGIP 86
Cdd:pfam00348   1 EKLLYEPLDYLVSAGGKRIRPLLVLLSAEALGGPEDleKAIVLAWAVELLHAASLVHDDIMDNSDLRRGQPTWHRIFGNA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220    87 SVINSANYVYFLGLEKVLTL-DHPDAVKLFTRQLLELHQGQGLDIYWRDNYTCP-TEEEYKAMVLQKTGGLFGLAVGLMQ 164
Cdd:pfam00348  81 IAINDGDYLYALAFQLLAKLfPNPELLELFSEVTLQTAEGQGLDLLWRNDDDLScTEEEYLEIVKYKTAYLFALAVKLGA 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220   165 LFS----DYKEDLKPLLNTLGLFFQIRDDYANLHSKEYSENKSFCEDLTEGKFSFPTIHAIWSRPE-STQVQNILRQRTE 239
Cdd:pfam00348 161 ILSgaddEVIEALKDYGLNLGLAFQIQDDYLDLFGDPEVLGKPAGTDITEGKCTWPVIHALERTPEqRKILLEIYGKRPE 240
                         250
                  ....*....|.
gi 83700220   240 NIDIKKYCVHY 250
Cdd:pfam00348 241 DVEKVKEAYEL 251
Trans_IPPS_HT cd00685
Trans-Isoprenyl Diphosphate Synthases, head-to-tail; These trans-Isoprenyl Diphosphate ...
10-293 3.84e-73

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: 225.51  E-value: 3.84e-73
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220  10 RILLEPYKYLLQLPGKQVRTKLSQAFNHWLKVPE-DKLQIIIEVTEMLHNASLLIDDIEDNSKLRRGFPVAHSIYGIPSV 88
Cdd:cd00685   4 ELLREALRYLLLAGGKRLRPLLVLLAARALGGPElEAALRLAAAIELLHTASLVHDDVMDNSDLRRGKPTVHKVFGNATA 83
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220  89 INSANYVYFLGLEKVLTLDH---PDAVKLFTRQLLELHQGQGLDIYWRDNyTCPTEEEYKAMVLQKTGGLFGLAVGLMQL 165
Cdd:cd00685  84 ILAGDYLLARAFELLARLGNpyyPRALELFSEAILELVEGQLLDLLSEYD-TDVTEEEYLRIIRLKTAALFAAAPLLGAL 162
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220 166 FS----DYKEDLKPLLNTLGLFFQIRDDYANLHSKEYSENKSFCEDLTEGKFSFPTIHAIwsrpestqvqnilrqrteni 241
Cdd:cd00685 163 LAgadeEEAEALKRFGRNLGLAFQIQDDILDLFGDPETLGKPVGSDLREGKCTLPVLLAL-------------------- 222
                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*
gi 83700220 242 dikkycvhyledvgsfeytRNTLKELEAKAYKQIDARGGNPE---LVALVKHLSK 293
Cdd:cd00685 223 -------------------RELAREYEEKALEALKALPESPAreaLRALADFILE 258
IspA COG0142
Geranylgeranyl pyrophosphate synthase [Coenzyme transport and metabolism]; Geranylgeranyl ...
12-287 4.43e-39

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: 139.59  E-value: 4.43e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220  12 LLEPYKYLLQLPGKQVRTKLSQAFNHWLKVPEDKLQIIIEVTEMLHNASLLIDDIEDNSKLRRGFPVAHSIYGIPSVINS 91
Cdd:COG0142  33 LAEAMRYLLLAGGKRLRPLLVLLAARALGGDPEAALRAAAAVELIHTASLVHDDVMDDDDLRRGKPTVHARFGEATAILA 112
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220  92 ANYVYFLGLEKVLTLDHPD----AVKLFTRQLLELHQGQGLDIYWRDNYTcPTEEEYKAMVLQKTGGLFGLAVGLMQLFS 167
Cdd:COG0142 113 GDALLALAFELLAELGDPErrlrALRILARAARGMCEGQALDLEAEGRLD-VTLEEYLRVIRLKTAALFAAALRLGAILA 191
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220 168 DYKEDLKPLLNT----LGLFFQIRDDYANLHSKEYSENKSFCEDLTEGKFSFPTIHAIW--SRPESTQVQNILRQRTENI 241
Cdd:COG0142 192 GADEEQVEALRRygrnLGLAFQIRDDILDVTGDPEVLGKPAGSDLREGKPTLPLLLALEraDPEERAELRELLGKPDLDE 271
                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*.
gi 83700220 242 DIKKYCVHYLEDVGSFEYTRNTLKELEAKAYKQIDARGGNPELVAL 287
Cdd:COG0142 272 EDLAEVRALLRESGALEYARELARELAEEALAALAALPDSEAREAL 317
preA CHL00151
prenyl transferase; Reviewed
11-271 1.76e-18

prenyl transferase; Reviewed


Pssm-ID: 164542  Cd Length: 323  Bit Score: 84.07  E-value: 1.76e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220   11 ILLEPYKYLLQLPGKQVRTKL----SQAF--NHWLKVPEDKLQiiiEVTEMLHNASLLIDDIEDNSKLRRGFPVAHSIYG 84
Cdd:CHL00151  32 ILYAAAKHLFSAGGKRIRPAIvllvAKATggNMEIKTSQQRLA---EITEIIHTASLVHDDVIDECSIRRGIPTVHKIFG 108
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220   85 IPSVINSANYVYFLGLEKVLTLDHPDAVKLFTRQLLELHQG---QGLDIYwrdnYTCPTEEEYKAMVLQKTGGLFGLAVG 161
Cdd:CHL00151 109 TKIAVLAGDFLFAQSSWYLANLNNLEVVKLISKVITDFAEGeirQGLVQF----DTTLSILNYIEKSFYKTASLIAASCK 184
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220  162 LMQLFSDYKE-DLKPLLN---TLGLFFQIRDDYANLHSKEYSENKSFCEDLTEGKFSFPTIHAIwsRPESTQVQNILRQR 237
Cdd:CHL00151 185 AAALLSDADEkDHNDFYLygkHLGLAFQIIDDVLDITSSTESLGKPIGSDLKNGNLTAPVLFAL--TQNSKLAKLIEREF 262
                        250       260       270
                 ....*....|....*....|....*....|....
gi 83700220  238 TENIDIkKYCVHYLEDVGSFEYTRNTLKELEAKA 271
Cdd:CHL00151 263 CETKDI-SQALQIIKETNGIEKAKDLALEHMQAA 295
hexpp_archaea NF040936
hexaprenyl pyrophosphate synthase;
12-200 2.23e-11

hexaprenyl pyrophosphate synthase;


Pssm-ID: 468868  Cd Length: 275  Bit Score: 63.16  E-value: 2.23e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220   12 LLEPYKYLLQlPGKQVRTKLSQAFNHWLKVPEDKLQIIIEVTEMLHNASLLIDDIEDNSKLRRGFPVAHSIYGIPSVINS 91
Cdd:NF040936  30 LLEMSKYIMK-DGKRFRGTLMFLFTEALGGEEKDAYKGALATEILHSASLALDDIVDYDLTRRGDKSAWAVYTNRRVIFV 108
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220   92 ANYVYFLGLeKVLTLDHPDAVKLFTRQLLELHQGQGLDIYWRDnytcpteEEYKAMVLQKTGGLFGLAVGLMQLFSDYKE 171
Cdd:NF040936 109 SNYLIPTAL-NIISSYGEDALKISIELWKDTAVGALKDMYGNK-------EDYFKTIELKTASLFKLSTMLASFSSRREE 180
                        170       180       190
                 ....*....|....*....|....*....|..
gi 83700220  172 DLKPLLNT---LGLFFQIRDDYANLHSKEYSE 200
Cdd:NF040936 181 LLDELLDAgkyLGIIYQLIDDYVDCVKYEREE 212
 
Name Accession Description Interval E-value
polyprenyl_synt pfam00348
Polyprenyl synthetase;
9-250 3.32e-97

Polyprenyl synthetase;


Pssm-ID: 459773  Cd Length: 251  Bit Score: 286.32  E-value: 3.32e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220     9 QRILLEPYKYLLQLPGKQVRTKLSQAFNHWLKVPED--KLQIIIEVTEMLHNASLLIDDIEDNSKLRRGFPVAHSIYGIP 86
Cdd:pfam00348   1 EKLLYEPLDYLVSAGGKRIRPLLVLLSAEALGGPEDleKAIVLAWAVELLHAASLVHDDIMDNSDLRRGQPTWHRIFGNA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220    87 SVINSANYVYFLGLEKVLTL-DHPDAVKLFTRQLLELHQGQGLDIYWRDNYTCP-TEEEYKAMVLQKTGGLFGLAVGLMQ 164
Cdd:pfam00348  81 IAINDGDYLYALAFQLLAKLfPNPELLELFSEVTLQTAEGQGLDLLWRNDDDLScTEEEYLEIVKYKTAYLFALAVKLGA 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220   165 LFS----DYKEDLKPLLNTLGLFFQIRDDYANLHSKEYSENKSFCEDLTEGKFSFPTIHAIWSRPE-STQVQNILRQRTE 239
Cdd:pfam00348 161 ILSgaddEVIEALKDYGLNLGLAFQIQDDYLDLFGDPEVLGKPAGTDITEGKCTWPVIHALERTPEqRKILLEIYGKRPE 240
                         250
                  ....*....|.
gi 83700220   240 NIDIKKYCVHY 250
Cdd:pfam00348 241 DVEKVKEAYEL 251
Trans_IPPS_HT cd00685
Trans-Isoprenyl Diphosphate Synthases, head-to-tail; These trans-Isoprenyl Diphosphate ...
10-293 3.84e-73

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: 225.51  E-value: 3.84e-73
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220  10 RILLEPYKYLLQLPGKQVRTKLSQAFNHWLKVPE-DKLQIIIEVTEMLHNASLLIDDIEDNSKLRRGFPVAHSIYGIPSV 88
Cdd:cd00685   4 ELLREALRYLLLAGGKRLRPLLVLLAARALGGPElEAALRLAAAIELLHTASLVHDDVMDNSDLRRGKPTVHKVFGNATA 83
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220  89 INSANYVYFLGLEKVLTLDH---PDAVKLFTRQLLELHQGQGLDIYWRDNyTCPTEEEYKAMVLQKTGGLFGLAVGLMQL 165
Cdd:cd00685  84 ILAGDYLLARAFELLARLGNpyyPRALELFSEAILELVEGQLLDLLSEYD-TDVTEEEYLRIIRLKTAALFAAAPLLGAL 162
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220 166 FS----DYKEDLKPLLNTLGLFFQIRDDYANLHSKEYSENKSFCEDLTEGKFSFPTIHAIwsrpestqvqnilrqrteni 241
Cdd:cd00685 163 LAgadeEEAEALKRFGRNLGLAFQIQDDILDLFGDPETLGKPVGSDLREGKCTLPVLLAL-------------------- 222
                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*
gi 83700220 242 dikkycvhyledvgsfeytRNTLKELEAKAYKQIDARGGNPE---LVALVKHLSK 293
Cdd:cd00685 223 -------------------RELAREYEEKALEALKALPESPAreaLRALADFILE 258
Trans_IPPS cd00867
Trans-Isoprenyl Diphosphate Synthases; Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of ...
27-221 1.01e-52

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: 172.53  E-value: 1.01e-52
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220  27 VRTKLSQAFNHWLKVPEDKLQIIIEVTEMLHNASLLIDDIEDNSKLRRGFPVAHSI-YGIPSVINSANYVYFLGLEKVLT 105
Cdd:cd00867   1 SRPLLVLLLARALGGDLEAALRLAAAVELLHAASLVHDDIVDDSDLRRGKPTAHLRrFGNALAILAGDYLLARAFQLLAR 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220 106 LDHPDAVKLFTRQLLELHQGQGLDIYWRDNyTCPTEEEYKAMVLQKTGGLFGLAVGLMQLFSD----YKEDLKPLLNTLG 181
Cdd:cd00867  81 LGYPRALELFAEALRELLEGQALDLEFERD-TYETLDEYLEYCRYKTAGLVGLLCLLGAGLSGaddeQAEALKDYGRALG 159
                       170       180       190       200
                ....*....|....*....|....*....|....*....|
gi 83700220 182 LFFQIRDDYANLHSKEYSENKsFCEDLTEGKFSFPTIHAI 221
Cdd:cd00867 160 LAFQLTDDLLDVFGDAEELGK-VGSDLREGRITLPVILAR 198
IspA COG0142
Geranylgeranyl pyrophosphate synthase [Coenzyme transport and metabolism]; Geranylgeranyl ...
12-287 4.43e-39

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: 139.59  E-value: 4.43e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220  12 LLEPYKYLLQLPGKQVRTKLSQAFNHWLKVPEDKLQIIIEVTEMLHNASLLIDDIEDNSKLRRGFPVAHSIYGIPSVINS 91
Cdd:COG0142  33 LAEAMRYLLLAGGKRLRPLLVLLAARALGGDPEAALRAAAAVELIHTASLVHDDVMDDDDLRRGKPTVHARFGEATAILA 112
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220  92 ANYVYFLGLEKVLTLDHPD----AVKLFTRQLLELHQGQGLDIYWRDNYTcPTEEEYKAMVLQKTGGLFGLAVGLMQLFS 167
Cdd:COG0142 113 GDALLALAFELLAELGDPErrlrALRILARAARGMCEGQALDLEAEGRLD-VTLEEYLRVIRLKTAALFAAALRLGAILA 191
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220 168 DYKEDLKPLLNT----LGLFFQIRDDYANLHSKEYSENKSFCEDLTEGKFSFPTIHAIW--SRPESTQVQNILRQRTENI 241
Cdd:COG0142 192 GADEEQVEALRRygrnLGLAFQIRDDILDVTGDPEVLGKPAGSDLREGKPTLPLLLALEraDPEERAELRELLGKPDLDE 271
                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*.
gi 83700220 242 DIKKYCVHYLEDVGSFEYTRNTLKELEAKAYKQIDARGGNPELVAL 287
Cdd:COG0142 272 EDLAEVRALLRESGALEYARELARELAEEALAALAALPDSEAREAL 317
Isoprenoid_Biosyn_C1 cd00385
Isoprenoid Biosynthesis enzymes, Class 1; Superfamily of trans-isoprenyl diphosphate synthases ...
41-277 4.59e-37

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: 132.23  E-value: 4.59e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220  41 VPEDKLQIIIEVTEMLHNASLLIDDIEDNSKLRRGFPVAH---SIYGIPSVINSANYVYFLGLEKVLTLDHPDAVKLFTR 117
Cdd:cd00385   7 LLEPEASRLRAAVEKLHAASLVHDDIVDDSGTRRGLPTAHlavAIDGLPEAILAGDLLLADAFEELAREGSPEALEILAE 86
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220 118 QLLELHQGQGLDIYWRDNYtCPTEEEYKAMVLQKTGGLFGLAVGLMQLFSDYK----EDLKPLLNTLGLFFQIRDDYANL 193
Cdd:cd00385  87 ALLDLLEGQLLDLKWRREY-VPTLEEYLEYCRYKTAGLVGALCLLGAGLSGGEaellEALRKLGRALGLAFQLTNDLLDY 165
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220 194 HSKeysenksfcEDLTEGKFSFPTIHAIWSRPESTQVQNIlrqrtenidikkycvhylEDVGSFEYTRNTLKELEAKAYK 273
Cdd:cd00385 166 EGD---------AERGEGKCTLPVLYALEYGVPAEDLLLV------------------EKSGSLEEALEELAKLAEEALK 218

                ....
gi 83700220 274 QIDA 277
Cdd:cd00385 219 ELNE 222
preA CHL00151
prenyl transferase; Reviewed
11-271 1.76e-18

prenyl transferase; Reviewed


Pssm-ID: 164542  Cd Length: 323  Bit Score: 84.07  E-value: 1.76e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220   11 ILLEPYKYLLQLPGKQVRTKL----SQAF--NHWLKVPEDKLQiiiEVTEMLHNASLLIDDIEDNSKLRRGFPVAHSIYG 84
Cdd:CHL00151  32 ILYAAAKHLFSAGGKRIRPAIvllvAKATggNMEIKTSQQRLA---EITEIIHTASLVHDDVIDECSIRRGIPTVHKIFG 108
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220   85 IPSVINSANYVYFLGLEKVLTLDHPDAVKLFTRQLLELHQG---QGLDIYwrdnYTCPTEEEYKAMVLQKTGGLFGLAVG 161
Cdd:CHL00151 109 TKIAVLAGDFLFAQSSWYLANLNNLEVVKLISKVITDFAEGeirQGLVQF----DTTLSILNYIEKSFYKTASLIAASCK 184
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220  162 LMQLFSDYKE-DLKPLLN---TLGLFFQIRDDYANLHSKEYSENKSFCEDLTEGKFSFPTIHAIwsRPESTQVQNILRQR 237
Cdd:CHL00151 185 AAALLSDADEkDHNDFYLygkHLGLAFQIIDDVLDITSSTESLGKPIGSDLKNGNLTAPVLFAL--TQNSKLAKLIEREF 262
                        250       260       270
                 ....*....|....*....|....*....|....
gi 83700220  238 TENIDIkKYCVHYLEDVGSFEYTRNTLKELEAKA 271
Cdd:CHL00151 263 CETKDI-SQALQIIKETNGIEKAKDLALEHMQAA 295
PRK10888 PRK10888
octaprenyl diphosphate synthase; Provisional
18-288 5.17e-17

octaprenyl diphosphate synthase; Provisional


Pssm-ID: 182813  Cd Length: 323  Bit Score: 79.89  E-value: 5.17e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220   18 YLLQLPGKQVRTKLSQAFNHWLKVPEDKLQIIIEVTEMLHNASLLIDDIEDNSKLRRGFPVAHSIYGIPSVINSANYVYF 97
Cdd:PRK10888  38 YIISGGGKRIRPMIAVLAARAVGYQGNAHVTIAALIEFIHTATLLHDDVVDESDMRRGKATANAAFGNAASVLVGDFIYT 117
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220   98 LGLEKVLTLDHPDAVKLFTRQLLELHQGQGLDIYwrdNYTCP--TEEEYKAMVLQKTGGLFGLAVGLMQLFSDYKEDLKP 175
Cdd:PRK10888 118 RAFQMMTSLGSLKVLEVMSEAVNVIAEGEVLQLM---NVNDPdiTEENYMRVIYSKTARLFEAAAQCSGILAGCTPEQEK 194
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220  176 LLNT----LGLFFQIRDDYANLHSKEYSENKSFCEDLTEGKFSFPTIHAIW-SRPESTQvqnILRQRTENIDIKkycvHY 250
Cdd:PRK10888 195 GLQDygryLGTAFQLIDDLLDYSADGETLGKNVGDDLNEGKPTLPLLHAMHhGTPEQAA---MIRTAIEQGNGR----HL 267
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 83700220  251 LEDV-------GSFEYTRNTLKELEAKAYKQIDARGGNPELVALV 288
Cdd:PRK10888 268 LEPVleamnacGSLEWTRQRAEEEADKAIAALQVLPDTPWREALI 312
PLN02857 PLN02857
octaprenyl-diphosphate synthase
51-226 8.86e-12

octaprenyl-diphosphate synthase


Pssm-ID: 215462  Cd Length: 416  Bit Score: 65.25  E-value: 8.86e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220   51 EVTEMLHNASLLIDDIEDNSKLRRGFPVAHSIYGIPSVINSANYVYFLGLEKVLTLDHPDAVKLFTrQLL------ELHQ 124
Cdd:PLN02857 168 EITEMIHTASLIHDDVLDESDMRRGKETVHQLYGTRVAVLAGDFMFAQSSWYLANLDNLEVIKLIS-QVIkdfasgEIKQ 246
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220  125 GQGLdiywrdnYTCPTE-EEYKAMVLQKTGGLFGLAVGLMQLFSDYKEDLKPLL----NTLGLFFQIRDDYANLHSKEYS 199
Cdd:PLN02857 247 ASSL-------FDCDVTlDEYLLKSYYKTASLIAASTKSAAIFSGVDSSVKEQMyeygKNLGLAFQVVDDILDFTQSTEQ 319
                        170       180
                 ....*....|....*....|....*..
gi 83700220  200 ENKSFCEDLTEGKFSFPTIHAIWSRPE 226
Cdd:PLN02857 320 LGKPAGSDLAKGNLTAPVIFALEKEPE 346
hexpp_archaea NF040936
hexaprenyl pyrophosphate synthase;
12-200 2.23e-11

hexaprenyl pyrophosphate synthase;


Pssm-ID: 468868  Cd Length: 275  Bit Score: 63.16  E-value: 2.23e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220   12 LLEPYKYLLQlPGKQVRTKLSQAFNHWLKVPEDKLQIIIEVTEMLHNASLLIDDIEDNSKLRRGFPVAHSIYGIPSVINS 91
Cdd:NF040936  30 LLEMSKYIMK-DGKRFRGTLMFLFTEALGGEEKDAYKGALATEILHSASLALDDIVDYDLTRRGDKSAWAVYTNRRVIFV 108
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220   92 ANYVYFLGLeKVLTLDHPDAVKLFTRQLLELHQGQGLDIYWRDnytcpteEEYKAMVLQKTGGLFGLAVGLMQLFSDYKE 171
Cdd:NF040936 109 SNYLIPTAL-NIISSYGEDALKISIELWKDTAVGALKDMYGNK-------EDYFKTIELKTASLFKLSTMLASFSSRREE 180
                        170       180       190
                 ....*....|....*....|....*....|..
gi 83700220  172 DLKPLLNT---LGLFFQIRDDYANLHSKEYSE 200
Cdd:NF040936 181 LLDELLDAgkyLGIIYQLIDDYVDCVKYEREE 212
PLN02890 PLN02890
geranyl diphosphate synthase
47-277 5.01e-09

geranyl diphosphate synthase


Pssm-ID: 178478  Cd Length: 422  Bit Score: 56.86  E-value: 5.01e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220   47 QIIIEVTEMLHNASLLIDDIEDNSKLRRGFPVAHSIYGIPSVINSANYVYFLGLEKVLTLDHPDAVKLFTRQLLELHQGQ 126
Cdd:PLN02890 164 QNIAEITEMIHVASLLHDDVLDDADTRRGVGSLNVVMGNKLSVLAGDFLLSRACVALAALKNTEVVSLLATAVEHLVTGE 243
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83700220  127 GLDIYWRDNYTCpTEEEYKAMVLQKTGGLFGLAVGLMQLFSDYKEDLKPLL----NTLGLFFQIRDDYANLHSKEYSENK 202
Cdd:PLN02890 244 TMQITSSREQRR-SMDYYMQKTYYKTASLISNSCKAVAILAGQTAEVAVLAfeygRNLGLAFQLIDDVLDFTGTSASLGK 322
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 83700220  203 SFCEDLTEGKFSFPTIHAIWSRPESTQVQNILRQRTENIDIkkyCVHYLEDVGSFEYTRNTLKELEAKAYKQIDA 277
Cdd:PLN02890 323 GSLSDIRHGVITAPILFAMEEFPQLREVVDRGFDNPANVDI---ALEYLGKSRGIQRTRELAREHANLAAAAIES 394
 
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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