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Conserved domains on  [gi|924355403|ref|WP_053488454|]
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MULTISPECIES: polyprenyl synthetase family protein [Priestia]

Protein Classification

inner membrane-spanning protein YciB; polyprenyl synthetase family protein( domain architecture ID 1903478)

inner membrane-spanning protein YciB plays a role in cell envelope biogenesis, maintenance of cell envelope integrity and membrane homeostasis| polyprenyl synthetase family protein such as farnesyl/geranylgeranyl diphosphate synthase, which is a key enzyme in isoprenoid biosynthesis, catalyzing the formation of farnesyl diphosphate (FPP) and geranylgeranyl diphosphate (GGPP), respectively

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
IspA super family cl43038
Geranylgeranyl pyrophosphate synthase [Coenzyme transport and metabolism]; Geranylgeranyl ...
 146-294 4.36e-14

Geranylgeranyl pyrophosphate synthase [Coenzyme transport and metabolism]; Geranylgeranyl pyrophosphate synthase is part of the Pathway/BioSystem: Isoprenoid biosynthesis


The actual alignment was detected with superfamily member COG0142:

Pssm-ID: 439912 [Multi-domain]  Cd Length: 329  Bit Score: 71.79  E-value: 4.36e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924355403 146 GEWKDLHFRFSINkrviPTEEEYFKLIKQKSGKLTE-------IISQAiDPSQL-ILKKITYYIGIAGQLRNDAADVLND 217
Cdd:COG0142  150 GQALDLEAEGRLD----VTLEEYLRVIRLKTAALFAaalrlgaILAGA-DEEQVeALRRYGRNLGLAFQIRDDILDVTGD 224

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924355403 218 KK-------SDLRDLKAYLPFLKAYEYSCEVQDEFFHKLKDEEIMTsPLKRQLIREYIEQSGSIDYCHILSRFYYMRAFK 290
Cdd:COG0142  225 PEvlgkpagSDLREGKPTLPLLLALERADPEERAELRELLGKPDLD-EEDLAEVRALLRESGALEYARELARELAEEALA 303


                 ....
gi 924355403 291 LLEE 294
Cdd:COG0142  304 ALAA 307
 
Name Accession Description Interval E-value
IspA COG0142
Geranylgeranyl pyrophosphate synthase [Coenzyme transport and metabolism]; Geranylgeranyl ...
 146-294 4.36e-14

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: 71.79  E-value: 4.36e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924355403 146 GEWKDLHFRFSINkrviPTEEEYFKLIKQKSGKLTE-------IISQAiDPSQL-ILKKITYYIGIAGQLRNDAADVLND 217
Cdd:COG0142  150 GQALDLEAEGRLD----VTLEEYLRVIRLKTAALFAaalrlgaILAGA-DEEQVeALRRYGRNLGLAFQIRDDILDVTGD 224

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924355403 218 KK-------SDLRDLKAYLPFLKAYEYSCEVQDEFFHKLKDEEIMTsPLKRQLIREYIEQSGSIDYCHILSRFYYMRAFK 290
Cdd:COG0142  225 PEvlgkpagSDLREGKPTLPLLLALERADPEERAELRELLGKPDLD-EEDLAEVRALLRESGALEYARELARELAEEALA 303


                 ....
gi 924355403 291 LLEE 294
Cdd:COG0142  304 ALAA 307
Trans_IPPS cd00867
Trans-Isoprenyl Diphosphate Synthases; Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of ...
 78-265 3.78e-12

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: 65.06  E-value: 3.78e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924355403  78 IECIFLSADIVDDICDLDD-----PNLPTFQNEDRYLILISQYLLAKGFFYLRPVSDSYEDNCLFSLIMDSGCGEWKDLH 152
Cdd:cd00867   27 VELLHAASLVHDDIVDDSDlrrgkPTAHLRRFGNALAILAGDYLLARAFQLLARLGYPRALELFAEALRELLEGQALDLE 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924355403 153 FRFsinkRVIPTEEEYFKLIKQKSGKLTE-------IISQAIDPSQLILKKITYYIGIAGQLRNDAADVLNDKK------ 219
Cdd:cd00867  107 FER----DTYETLDEYLEYCRYKTAGLVGllcllgaGLSGADDEQAEALKDYGRALGLAFQLTDDLLDVFGDAEelgkvg 182

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 924355403 220 SDLRDLKAYLPFLKAYEYSCEVQDEFFHKLKDEEIMTSPLKRQLIR 265
Cdd:cd00867  183 SDLREGRITLPVILARERAAEYAEEAYAALEALPPSLPRARRALIA 228
polyprenyl_synt pfam00348
Polyprenyl synthetase;
110-240 1.80e-08

Polyprenyl synthetase;


Pssm-ID: 459773  Cd Length: 251  Bit Score: 54.43  E-value: 1.80e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924355403  110 ILISQYLLAKGFFYLRPVSDSYEDNCLFS-LIMDSGCGEWKDLHFRFSINkrVIPTEEEYFKLIKQKSGKLTE------- 181
Cdd:pfam00348  83 INDGDYLYALAFQLLAKLFPNPELLELFSeVTLQTAEGQGLDLLWRNDDD--LSCTEEEYLEIVKYKTAYLFAlavklga 160

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 924355403  182 IISQAIDPSQLILKKITYYIGIAGQLRNDAADVLNDKK-------SDLRDLKAYLPFLKAYEYSCE 240
Cdd:pfam00348 161 ILSGADDEVIEALKDYGLNLGLAFQIQDDYLDLFGDPEvlgkpagTDITEGKCTWPVIHALERTPE 226
PRK10888 PRK10888
octaprenyl diphosphate synthase; Provisional
 164-270 1.07e-04

octaprenyl diphosphate synthase; Provisional


Pssm-ID: 182813  Cd Length: 323  Bit Score: 43.29  E-value: 1.07e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924355403 164 TEEEYFKLIKQKSGKLTE-------IISQAIDPSQLILKKITYYIGIAGQLRNDAADVLNDKKS-------DLRDLKAYL 229
Cdd:PRK10888 159 TEENYMRVIYSKTARLFEaaaqcsgILAGCTPEQEKGLQDYGRYLGTAFQLIDDLLDYSADGETlgknvgdDLNEGKPTL 238

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 924355403 230 PFLKAYEYScevqdeffhklkdeeimtSPLKRQLIREYIEQ 270
Cdd:PRK10888 239 PLLHAMHHG------------------TPEQAAMIRTAIEQ 261
 
Name Accession Description Interval E-value
IspA COG0142
Geranylgeranyl pyrophosphate synthase [Coenzyme transport and metabolism]; Geranylgeranyl ...
 146-294 4.36e-14

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: 71.79  E-value: 4.36e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924355403 146 GEWKDLHFRFSINkrviPTEEEYFKLIKQKSGKLTE-------IISQAiDPSQL-ILKKITYYIGIAGQLRNDAADVLND 217
Cdd:COG0142  150 GQALDLEAEGRLD----VTLEEYLRVIRLKTAALFAaalrlgaILAGA-DEEQVeALRRYGRNLGLAFQIRDDILDVTGD 224

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924355403 218 KK-------SDLRDLKAYLPFLKAYEYSCEVQDEFFHKLKDEEIMTsPLKRQLIREYIEQSGSIDYCHILSRFYYMRAFK 290
Cdd:COG0142  225 PEvlgkpagSDLREGKPTLPLLLALERADPEERAELRELLGKPDLD-EEDLAEVRALLRESGALEYARELARELAEEALA 303


                 ....
gi 924355403 291 LLEE 294
Cdd:COG0142  304 ALAA 307
Trans_IPPS cd00867
Trans-Isoprenyl Diphosphate Synthases; Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of ...
 78-265 3.78e-12

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: 65.06  E-value: 3.78e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924355403  78 IECIFLSADIVDDICDLDD-----PNLPTFQNEDRYLILISQYLLAKGFFYLRPVSDSYEDNCLFSLIMDSGCGEWKDLH 152
Cdd:cd00867   27 VELLHAASLVHDDIVDDSDlrrgkPTAHLRRFGNALAILAGDYLLARAFQLLARLGYPRALELFAEALRELLEGQALDLE 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924355403 153 FRFsinkRVIPTEEEYFKLIKQKSGKLTE-------IISQAIDPSQLILKKITYYIGIAGQLRNDAADVLNDKK------ 219
Cdd:cd00867  107 FER----DTYETLDEYLEYCRYKTAGLVGllcllgaGLSGADDEQAEALKDYGRALGLAFQLTDDLLDVFGDAEelgkvg 182

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 924355403 220 SDLRDLKAYLPFLKAYEYSCEVQDEFFHKLKDEEIMTSPLKRQLIR 265
Cdd:cd00867  183 SDLREGRITLPVILARERAAEYAEEAYAALEALPPSLPRARRALIA 228
Isoprenoid_Biosyn_C1 cd00385
Isoprenoid Biosynthesis enzymes, Class 1; Superfamily of trans-isoprenyl diphosphate synthases ...
 78-271 5.67e-12

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: 64.44  E-value: 5.67e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924355403  78 IECIFLSADIVDDICDLDD--PNLPTFQNE-----DRYLILISQYLLAKGFFYLRPVSDSYEDNCLFSLIMDSGCGEWKD 150
Cdd:cd00385   19 VEKLHAASLVHDDIVDDSGtrRGLPTAHLAvaidgLPEAILAGDLLLADAFEELAREGSPEALEILAEALLDLLEGQLLD 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924355403 151 LHFRFsinkRVIPTEEEYFKLIKQKSGKLTE-------IISQAIDPSQLILKKITYYIGIAGQLRNDAADVLNDKKSDLR 223
Cdd:cd00385   99 LKWRR----EYVPTLEEYLEYCRYKTAGLVGalcllgaGLSGGEAELLEALRKLGRALGLAFQLTNDLLDYEGDAERGEG 174

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 924355403 224 dlKAYLPFLKAYEYSCEVQDEFFHKLKDEEIMTsplkRQLIREYIEQS 271
Cdd:cd00385  175 --KCTLPVLYALEYGVPAEDLLLVEKSGSLEEA----LEELAKLAEEA 216
polyprenyl_synt pfam00348
Polyprenyl synthetase;
110-240 1.80e-08

Polyprenyl synthetase;


Pssm-ID: 459773  Cd Length: 251  Bit Score: 54.43  E-value: 1.80e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924355403  110 ILISQYLLAKGFFYLRPVSDSYEDNCLFS-LIMDSGCGEWKDLHFRFSINkrVIPTEEEYFKLIKQKSGKLTE------- 181
Cdd:pfam00348  83 INDGDYLYALAFQLLAKLFPNPELLELFSeVTLQTAEGQGLDLLWRNDDD--LSCTEEEYLEIVKYKTAYLFAlavklga 160

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 924355403  182 IISQAIDPSQLILKKITYYIGIAGQLRNDAADVLNDKK-------SDLRDLKAYLPFLKAYEYSCE 240
Cdd:pfam00348 161 ILSGADDEVIEALKDYGLNLGLAFQIQDDYLDLFGDPEvlgkpagTDITEGKCTWPVIHALERTPE 226
PRK10888 PRK10888
octaprenyl diphosphate synthase; Provisional
 164-270 1.07e-04

octaprenyl diphosphate synthase; Provisional


Pssm-ID: 182813  Cd Length: 323  Bit Score: 43.29  E-value: 1.07e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924355403 164 TEEEYFKLIKQKSGKLTE-------IISQAIDPSQLILKKITYYIGIAGQLRNDAADVLNDKKS-------DLRDLKAYL 229
Cdd:PRK10888 159 TEENYMRVIYSKTARLFEaaaqcsgILAGCTPEQEKGLQDYGRYLGTAFQLIDDLLDYSADGETlgknvgdDLNEGKPTL 238

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 924355403 230 PFLKAYEYScevqdeffhklkdeeimtSPLKRQLIREYIEQ 270
Cdd:PRK10888 239 PLLHAMHHG------------------TPEQAAMIRTAIEQ 261
 
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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