1FPS,1UBX,1UBY


Conserved Protein Domain Family
Trans_IPPS_HT

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cd00685: Trans_IPPS_HT 
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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.
Statistics
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PSSM-Id: 173833
View PSSM: cd00685
Aligned: 153 rows
Threshold Bit Score: 166.573
Threshold Setting Gi: 29249983
Created: 6-Mar-2002
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
  next features
Conserved site includes 22 residues -Click on image for an interactive view with Cn3D
Feature 1:substrate binding pocket [chemical binding site]
Evidence:
  • Comment:Binding studies indicate that the active site contains distinct allylic (aspartate-rich region 1) and homoallylic (aspartate-rich region 2) binding regions.
  • Structure:1UBX; Gallus gallus Farnesyl diphosphate synthase binds Farnesyl Diphosphate (FPP)
    View structure with Cn3D
  • Citation:PMID 8086404
  • Citation:PMID 8986756

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                          #  ### ### ##
1FPS         35 DAVARLKEVLQyn---apGGKCNRGLTVVAAYRELSgpgqkd---------aeslrcALAVGWCIELFQAFFLVADDIMD 102 chicken
1UBX         54 DAVARLKEVLQyn---apGGKCNRGLTVVAAYRELSgpgqkd---------aeslrcALAVGWCIELFQAASLVADDIMD 121 chicken
T51127       66 AQYGQLWDSLThm---atGGKLIRPRMLLDAHAALGgrd---------------ehaAVDAACAMQLLHIALVIHDDVID 127 Brevibacterium l...
NP_216689    25 SDYDGLIADLEdfv--lgGGKRLRPLFAYWGWHAVAsrep--------------dpdVLLLFSALELLHAWALVHDDLID 88  Mycobacterium tu...
NP_624521    61 FARELADRLAAlt---arGGKRLRTAFAHCGWRAAGgsgd--------------ataVLRTGAALELLQACALVHDDVMD 123 Streptomyces coe...
NP_624878    33 DAALAPVADQLrka--agHGKRLRAAFCYWGWRAAGqpe---------------sdaLVRAAASMELVHAAAVVHDDLID 95  Streptomyces coe...
BAB99565     43 APVTDAVAHLRsfv--lnGGKRIRPLYAWAGFLAAQghknss----------eklesVLDAAASLEFIQACALIHDDIID 110 Corynebacterium ...
AAM94362     36 ADYRRLWAAARda---asGGKRIRPRLVLGAYDALAaqgapasgreradaepaaaaeAVALAAAFELLHTAFLVHDDVID 112 Agromyces mediol...
ZP_00056752  36 AEWEPVLAALEam---isGGKRLRPAFCYWGWRGAGgge---------------epgLYTAAAALELLQACALIHDDVID 97  Thermobifida fusca
NP_696587    46 ALKPVMEQVVDqaasssqGGKRLRALLALDAFDILAgdvtp-----------drrdaMIDLACAIEVFQTAALVHDDIID 114 Bifidobacterium ...
Feature 1           ##                                                                          
1FPS        103 QSLTRRGQLCWYKKEGv----------------gLDAINDSFLLESSVYRVLKKycrqr---pyyvhLLELFLQTAYQTE 163 chicken
1UBX        122 QSLTRRGQLCWYKKEGv----------------gLDAINDSFLLESSVYRVLKKycrqr---pyyvhLLELFLQTAYQTE 182 chicken
T51127      128 NDTIRRGEATISGEFAseamsrgalrrdanawgiATSILGGDLILTLSHSLLARldied---tkrraILDIFDDTVVESA 204 Brevibacterium l...
NP_216689    89 RSATRRGRPTAQLRYAalhrdrdwr-gspdqfgmSAAILLGDLAQVWADDIVSKvcqsalapdaqrrVHRVWADIRNEVL 167 Mycobacterium tu...
NP_624521   124 GSVQRRGAPALHVDLArghwaagmh-gssesfgtSAAVLTGDLALAWADDLLTEtalgt---phgprLHGEWRAMRTEMV 199 Streptomyces coe...
NP_624878    96 DSRLRHGLPTAHVALEavlardgr--pdartaarSLAMLVGDQLMVLAGLLFTTsglpa---aylarARDLWAVLARELV 170 Streptomyces coe...
BAB99565    111 SSDTRRGAPTVHRAVEadhrannfe-gdpehfgvSVSILAGDMALVWAEDMLQDsglsa---ealarTRDAWRGMRTEVI 186 Corynebacterium ...
AAM94362    113 RDLVRRGEPNVAGRFAldaalrglereradaygqASAILAGDLLIAAAHSVAAAstcrs---sagepSSPSLTKCVFAAA 189 Agromyces mediol...
ZP_00056752  98 NSDTRRGQPAVHRRLAalhresgwh-gdpdefgrGAAILLGDLCLAWCEDMYQSsalpa---ealaaGRGPFDLMRTEVV 173 Thermobifida fusca
NP_696587   115 ESDLRRGKPSAHHALEqavhs--------gaigrGLGLMLGDILATACIEITRRsasrl---pntdaLNEAFLTMQREVE 183 Bifidobacterium ...
Feature 1         #  #                         ##  #                                       ##  #
1FPS        164 LGQMLDLitapvskvdlshfseERYKAIVKYKTAFYSFYLPVAAAMymvg-idskEEHEnAKAILLEMGEYFQIQDDYLD 242 chicken
1UBX        183 LGQMLDLitapvskvdlshfseERYKAIVKYKTAFYSFYLPVAAAMymvg-idskEEHEnAKAILLEMGEYFQIQDDYLD 261 chicken
T51127      205 AGEHSDVwlslhl----egansPDVLAMVDQKTAVYSFQAPLLIAAvlag-adsgLIDD-LANISRQIGVIYQLRDDVLG 278 Brevibacterium l...
NP_216689   168 GGQYLDIvaeas-----aaesiESAMNVATLKTACYTVSRPLQLGTaaaa-drsdVAAI-FEHFGADLGVAFQLRDDVLG 240 Mycobacterium tu...
NP_624521   200 AGQYRDLhaqaa-----rssgvDEALAIATLKSALYTVARPLALGAvlagaadgdALEA-LRAAGRCAGLAFQLRDDLLG 273 Streptomyces coe...
NP_624878   171 AGECLEIlhtgg------ppdtGTSLKVVRYKTAKYTVEHPLLIGGllag-aapaLRDT-YRAYALPLGEAFQLRDDLLG 242 Streptomyces coe...
BAB99565    187 GGQLLDIylesh-----anesvELADSVNRFKTAAYTIARPLHLGAsiag-gspqLIDA-LLHYGHDIGIAFQLRDDLLG 259 Corynebacterium ...
AAM94362    190 AGEHADVrhaag-----vrpgeADILAMIEDKTACYSFSAPLRAGAllag-apraTVER-LGEIGRRLGVAFQLQDDVLG 262 Agromyces mediol...
ZP_00056752 174 AGQYLDLveqar-----gadtvEAALRVMRFKSAKYTIEQPLHLGAalag-ryaeLAPA-YTAYGIPLGIAFQLRDDVLG 246 Thermobifida fusca
NP_696587   184 IGQVLDLavemtpl-snpealaNASLNVFRWKTASYTTIAPLLLALlaag-espdQARHcALAVGRPLGLAFQLADDLLD 261 Bifidobacterium ...
Feature 1                #    #    #                                                            
1FPS        243 CFGDpaltgK-VGTDiqDNKCSWLVVQCLqrvtpeqrqllednygrk--------epekvakvkelyeavgmRAAFQQYE 313 chicken
1UBX        262 CFGDpaltgK-VGTDiqDNKCSWLVVQCLqrvtpeqrqllednygrk--------epekvakvkelyeavgmRAAFQQYE 332 chicken
T51127      279 LFGDeretgKsNVSDlrEGKETLLITFARsdpswpevhtlfgdrmlsn-----adgdrlrkvieesgalvfvESMITQRC 353 Brevibacterium l...
NP_216689   241 VFGDpavtgKpSGDDlkSGKRTVLVAEAVeladrsdplaakllrtsigtrltdaqvrelrtvieavgaraaaESRIAALT 320 Mycobacterium tu...
NP_624521   274 AFGDpaltgKpADDDlrSRKLTYLLAVAVrladaaddhlaaaalapdadpksekavrqvrsalvrtgardlvETKIGELT 353 Streptomyces coe...
NP_624878   243 LFGDpertgKaSLDDlrAHRPTALLAETWkaadasqrqwlrrllgrddld--athlhdvrrlmrelnapqrvEQMIADRV 320 Streptomyces coe...
BAB99565    260 VFGDpaitgKpAGDDirEGKRTVLLALALqradkqspeaatairagvgkvtspediavitehiratgaeeevEQRISQLT 339 Corynebacterium ...
AAM94362    263 VYGDervtgKtALGDlrEGKETLLIAYARghaawvaasgafgrpdlde-----agarplraaieasgararvEARIAEEA 337 Agromyces mediol...
ZP_00056752 247 VFGDpeetgKpAGDDlrEGKRTVLVAETLrraaaddaeqfrrllgdpelg--aeeiawmrsvivdsgaleacEARIADYV 324 Thermobifida fusca
NP_696587   262 VVGSsrntgKpVGGDirEGKRTVLLADALsaadtadkadliaifeedcrn--dnqvartielftstgaldrsRERIAALW 339 Bifidobacterium ...
Feature 1                                        
1FPS        314 ESSYRRLQELIekhsnrlpkeIFLGLAQKIYKR 346 chicken
1UBX        333 ESSYRRLQELIekhsnrlpkeIFLGLAQKIYKR 365 chicken
T51127      354 ENLYRLIGEAAlppa---lsnQLIQLTSDASSR 383 Brevibacterium linens
NP_216689   321 QRALATLASAPinat---akaGLSELAMMAANR 350 Mycobacterium tuberculosis H37Rv
NP_624521   354 DMSLAHFDRCGar-------pAVRHEFAALIGR 379 Streptomyces coelicolor A3(2)
NP_624878   321 ERATRALDGAGtpph---arrALRELAQQATDR 350 Streptomyces coelicolor A3(2)
BAB99565    340 ESGLAHLDDVDipde---vraQLRALAIRSTER 369 Corynebacterium glutamicum ATCC 13032
AAM94362    338 AAARTAIAAAGlpaa---leaELLGLAAEATRR 367 Agromyces mediolanus
ZP_00056752 325 ADATQALENDViadd---arsALADLIVAATAR 354 Thermobifida fusca
NP_696587   340 GESRKAIAGLElnse--aqrrLTEACARFVPES 370 Bifidobacterium longum NCC2705

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