The SEED: an Annotation/Analysis Tool Provided by FIG
[ Subsystem Forum | Essentiality Data | FIG Tutorials | Peer-to-peer Updates | (New) Clearinghouse | SEED Control Panel | NMPDR | SEED Wiki]
[GOLD | "Complete" Genomes in SEED | ExPASy | IMG | KEGG | NCBI | TIGR cmr | UniProt | Report "Bugz"]

SEED version cvs.1555556707 (3/17/2019 22:5:7) on aspen.cels.anl.gov
 The SEED

Subsystem: Archaeal_lipids

Author: gjo


Functional Roles
Column Abbrev Functional Role GO Pre-Computed Publication(s) Relevant Publication(s)
1 23-dGGGPS (S)-2,3-di-O-geranylgeranylglyceryl phosphate synthase Add Publication(s)
2 3-GGGPS (S)-3-O-geranylgeranylglyceryl phosphate synthase Add Publication(s)
3 ACAT Acetyl-CoA acetyltransferase (EC 2.3.1.9) 25 Publication(s) Add Publication(s)
4 DGGGPLR Digeranylgeranylglycerophospholipid reductase Add Publication(s)
5 DMAT Dimethylallyltransferase (EC 2.5.1.1) Add Publication(s)
6 DPM_decarb Diphosphomevalonate decarboxylase (EC 4.1.1.33) Add Publication(s)
7 5PPS Farnesylgeranyl pyrophosphate synthetase Add Publication(s)
8 4PPS Geranylgeranyl pyrophosphate synthetase (EC 2.5.1.29) Add Publication(s)
9 3PPT (2E,6E)-farnesyl diphosphate synthase (EC 2.5.1.10) Add Publication(s)
10 GPDH Glycerol-1-phosphate dehydrogenase [NAD(P)] (EC 1.1.1.261) 2 Publication(s)
11 6PPP Hexaprenyl pyrophosphate synthetase Add Publication(s)
12 HMG-CoA_red Hydroxymethylglutaryl-CoA reductase (EC 1.1.1.34) Add Publication(s)
13 HMP-CoA_syn Hydroxymethylglutaryl-CoA synthase (EC 2.3.3.10) Add Publication(s)
14 IPP_kin Isopentenyl phosphate kinase Add Publication(s)
15 IPDPI Isopentenyl-diphosphate delta-isomerase (EC 5.3.3.2) Add Publication(s)
16 IPDPI-FMN Isopentenyl-diphosphate delta-isomerase, FMN-dependent (EC 5.3.3.2) Add Publication(s)
17 Mev_kin Mevalonate kinase (EC 2.7.1.36) Add Publication(s)
18 PM_kin Phosphomevalonate kinase (EC 2.7.4.2) Add Publication(s)
19 MJ0861 Putative Zn-dependent hydrolase in polyisoprenoid biosynthetic cluster Add Publication(s)

Show Phylogenetic Tree
Basic Spreadsheet
Genome ID Organism Variant Code 23-dGGGPS 3-GGGPS ACAT DGGGPLR DMAT DPM_decarb 5PPS 4PPS 3PPT GPDH 6PPP HMG-CoA_red HMP-CoA_syn IPP_kin IPDPI IPDPI-FMN Mev_kin PM_kin MJ0861
644279.4 Staphylococcus aureus subsp. aureus 132 [B] 1   2058 422, 650     667     1673     2696 2697     2489 666 668  
585143.3 Staphylococcus aureus subsp. aureus 55/2053 [B] 1   2462 627, 1091     1107     2055     46 47     822 1106 1108  
585144.3 Staphylococcus aureus subsp. aureus 58-424 [B] 1   2478 519, 1448     1464     2080     21 22     811 1463 1465  
585145.3 Staphylococcus aureus subsp. aureus 65-1322 [B] 1   2464 333, 1081     1097     1784     820 821     620 1096 1098  
585146.3 Staphylococcus aureus subsp. aureus 68-397 [B] 1   2444 945, 1086     1102     2052     451 452     191 1101 1103  
585147.3 Staphylococcus aureus subsp. aureus A017934/97 [B] 1   1444 134, 2681     150     1128     2174 2175     1904 149 151  
762962.3 Staphylococcus aureus subsp. aureus ATCC 51811 [B] 1   2496 118, 1467     101     464     1960 1959     2164 102 100  
585148.3 Staphylococcus aureus subsp. aureus Btn1260 [B] 1   1502 102, 1870     118     1105     2332 2333     2130 117 119  
585149.6 Staphylococcus aureus subsp. aureus C101 [B] 1   2085 507, 707     723     1692     22 23     2522 722 724  
585150.3 Staphylococcus aureus subsp. aureus C160 [B] 1   2511 443, 1127     1143     1780     942 943     739 1142 1144  
Genome ID Organism Variant Code 23-dGGGPS 3-GGGPS ACAT DGGGPLR DMAT DPM_decarb 5PPS 4PPS 3PPT GPDH 6PPP HMG-CoA_red HMP-CoA_syn IPP_kin IPDPI IPDPI-FMN Mev_kin PM_kin MJ0861
585151.3 Staphylococcus aureus subsp. aureus C427 [B] 1   1599 195, 2235     211     739     2535 2536     2332 210 212  
93062.19 Staphylococcus aureus subsp. aureus COL [B] 1   1921 410, 606     622     1523     2491 2492     2287 621 623  
93062.4 Staphylococcus aureus subsp. aureus COL [B] 1   106 884, 115     130     1799     2606 2607     2401 129 131  
585152.3 Staphylococcus aureus subsp. aureus D139 [B] 1   1882 265, 493     508     1513     2536 2537     2327 507 509  
585153.3 Staphylococcus aureus subsp. aureus E1410 [B] 1   2533 343, 1139     1155     1799     823 824     620 1154 1156  
681288.4 Staphylococcus aureus subsp. aureus ED98 [B] 1   1942 327, 529     545     1512     2575 2576     2374 544 546  
585154.3 Staphylococcus aureus subsp. aureus EMRSA16 [B] 1   1949 308, 538     554     1221     2610 2611     2411 553 555  
585155.3 Staphylococcus aureus subsp. aureus H19 [B] 1   2500 590, 1119     1135     1741     95 96     892 1134 1136  
359787.11 Staphylococcus aureus subsp. aureus JH1 [B] 1   2046 440, 641     657     1648     2672 2673     2473 656 658  
Genome ID Organism Variant Code 23-dGGGPS 3-GGGPS ACAT DGGGPLR DMAT DPM_decarb 5PPS 4PPS 3PPT GPDH 6PPP HMG-CoA_red HMP-CoA_syn IPP_kin IPDPI IPDPI-FMN Mev_kin PM_kin MJ0861
359787.3 Staphylococcus aureus subsp. aureus JH1 [B] 1   2664 550, 2432     2417     1371     1035 1036     1862 2418 2416  
359786.13 Staphylococcus aureus subsp. aureus JH9 [B] 1   2075 447, 651     667     1671     2710 2711     2510 666 668  
359786.3 Staphylococcus aureus subsp. aureus JH9 [B] 1   544 2513, 2195     2453     165     1938 1939     1387 2454 2506  
585156.3 Staphylococcus aureus subsp. aureus M1015 [B] 1   1462 103, 1932     119     1073     2226 2227     1902 118 120  
585157.3 Staphylococcus aureus subsp. aureus M809 [B] 1   1113 22, 267     283     1252     2224 2225     2019 282 284  
585158.3 Staphylococcus aureus subsp. aureus M876 [B] 1   2450 122, 1077     1093     2040     599 600     399 1092 1094  
585159.3 Staphylococcus aureus subsp. aureus M899 [B] 1   1977 497, 692     709     1596     21 22     2455 708 710  
548470.3 Staphylococcus aureus subsp. aureus MN8 [B] 1   1947 537, 1520     1503     2321     800 799     996 1504 1502  
282458.4 Staphylococcus aureus subsp. aureus MRSA252 [B] 1   2010 357, 588     604     1603     2654 2655     2453 603 605  
Genome ID Organism Variant Code 23-dGGGPS 3-GGGPS ACAT DGGGPLR DMAT DPM_decarb 5PPS 4PPS 3PPT GPDH 6PPP HMG-CoA_red HMP-CoA_syn IPP_kin IPDPI IPDPI-FMN Mev_kin PM_kin MJ0861
282458.1 Staphylococcus aureus subsp. aureus MRSA252 [B] 1   1888 331, 552     568     1513     2487 2488     2302 567 569  
282459.5 Staphylococcus aureus subsp. aureus MSSA476 [B] 1   1906 347, 556     572     1520     2533 2534     2327 571 573  
282459.1 Staphylococcus aureus subsp. aureus MSSA476 [B] 1   1813 322, 529     545     1446     2411 2412     2216 544 546  
196620.5 Staphylococcus aureus subsp. aureus MW2 [B] 1   1921 349, 560     576     1540     2548 2549     2344 575 577  
196620.1 Staphylococcus aureus subsp. aureus MW2 [B] 1   1847 330, 531     546     1474     2466 2467     2267 545 547  
418127.6 Staphylococcus aureus subsp. aureus Mu3 [B] 1   1945 357, 579     595     1546     2594 2595     2394 594 596  
418127.4 Staphylococcus aureus subsp. aureus Mu3 [B] 1   1763 329, 542     553     1404     2334 2335     2151 552 554  
158878.14 Staphylococcus aureus subsp. aureus Mu50 [B] 1   1973 358, 582     598     1568     2637 2638     2429 597 599  
585891.3 Staphylococcus aureus subsp. aureus Mu50-omega [B] 1   1971 357, 581     597     1565     2627 2628     2425 596 598  
Genome ID Organism Variant Code 23-dGGGPS 3-GGGPS ACAT DGGGPLR DMAT DPM_decarb 5PPS 4PPS 3PPT GPDH 6PPP HMG-CoA_red HMP-CoA_syn IPP_kin IPDPI IPDPI-FMN Mev_kin PM_kin MJ0861
158878.1 Staphylococcus aureus subsp. aureus Mu50 [B] 1   1906 354, 576     591     1521     2545 2546     2346 590 592  
158879.11 Staphylococcus aureus subsp. aureus N315 [B] 1   1858 358, 560     576     1457     2530 2531     2320 575 577  
158879.1 Staphylococcus aureus subsp. aureus N315 [B] 1   1775 349, 548     563     1397     2418 2419     2221 562 564  
93061.5 Staphylococcus aureus subsp. aureus NCTC 8325 [B] 1   1927 307, 504     520     1472     2584 2585     2372 519 521  
93061.3 Staphylococcus aureus subsp. aureus NCTC 8325 [B] 1   2007 340, 544     558     1524     2707 2708     2476 557 561  
548474.3 Staphylococcus aureus subsp. aureus TCH130 [B] 1   2572 1652, 1754     1636     788     331 330     530 1637 1635  
548473.3 Staphylococcus aureus subsp. aureus TCH60 [B] 1   2604 464, 1351     1335     1752     972 971     244 1336 1334  
548475.3 Staphylococcus aureus subsp. aureus TCH70 [B] 1   2500 863, 2063     879     511     1624 1623     1823 878 880  
367830.3 Staphylococcus aureus subsp. aureus USA300 [B] 1   1944 640, 252     653     2311     1426 1427     2580 652 759  
Genome ID Organism Variant Code 23-dGGGPS 3-GGGPS ACAT DGGGPLR DMAT DPM_decarb 5PPS 4PPS 3PPT GPDH 6PPP HMG-CoA_red HMP-CoA_syn IPP_kin IPDPI IPDPI-FMN Mev_kin PM_kin MJ0861
451515.3 Staphylococcus aureus subsp. aureus USA300_FPR3757 [B] 1   2011 418, 624     640     1608     2658 2659     2448 639 641  
451516.9 Staphylococcus aureus subsp. aureus USA300_TCH1516 [B] 1   2001 408, 614     630     1613     2651 2652     2437 629 631  
450394.6 Staphylococcus aureus subsp. aureus USA300_TCH959 [B] 1   2425 1131, 2120     1147     776     1546 1547     1847 1146 1148  
585160.3 Staphylococcus aureus subsp. aureus WBG10049 [B] 1   1447 100, 1887     116     1062     2366 2367     2162 115 117  
585161.3 Staphylococcus aureus subsp. aureus WW2703/97 [B] 1   1749 89, 441     458     1237     2414 2415     2217 457 459  
505321.3 Staphylococcus aureus subsp. aureus str. CF-Marseille [B] 1   2466 2079, 2172     2156     345     1587, 1588 1586     132 2157 2155  
546342.3 Staphylococcus aureus subsp. aureus str. JKD6008 [B] 1   2108 2233, 2532     2250     810     978 979     1036 2249 2251  
546343.3 Staphylococcus aureus subsp. aureus str. JKD6009 [B] 1   368 1919, 2724     1935     62     1462 1463     1309 1934 1936  
426430.8 Staphylococcus aureus subsp. aureus str. Newman [B] 1   2006 380, 586     602     1553     2654 2655     2445 601 603  
Genome ID Organism Variant Code 23-dGGGPS 3-GGGPS ACAT DGGGPLR DMAT DPM_decarb 5PPS 4PPS 3PPT GPDH 6PPP HMG-CoA_red HMP-CoA_syn IPP_kin IPDPI IPDPI-FMN Mev_kin PM_kin MJ0861
426430.6 Staphylococcus aureus subsp. aureus str. Newman [B] 1   1793 538, 349     549     1386     2362 2363     2176 548 550  

Spreadsheet Options


















notes

Archaeal membrane lipids are characterized by 
(S)-2,3-di-O-geranylgeranylglyceryl phosphate, and variations.

Grochowski, L. L., Xu, H., and White, R. H.  2006.  Methanocaldococcus 
jannaschii uses a modified mevalonate pathway for biosynthesis of isopentenyl 
diphosphate.  J. Bacteriol. 188: 3192-8.

PMID: 16621811 

  Acetyl-CoA

     |

     |  Acetyl-CoA

     |/

     |  Acetyl-CoA acetyltransferase (EC 2.3.1.9)

     |\

     |  CoA

     |

Acetoacetyl-CoA

     |

     |  Acetyl-CoA

     |/

     |  Hydroxymethylglutaryl-CoA synthase (EC 2.3.3.10)

     |\

     |  CoA

     |

     Hydroxymethylglutaryl-CoA

     |

     |  2 NADPH

     |/

     |  Hydroxymethylglutaryl-CoA reductase (EC 1.1.1.34)

     |\

     |  2 NADP+ + CoA

     |

Mevalonate

     |

     |  ATP

     |/

     |  Mevalonate kinase (EC 2.7.1.36)

     |\

     |  ADP

     |

Mevalonate phosphate

     |

     |  Phosphomevalonate decarboxylase - hypothetical

     |\

     |  H2O

     |

Isopentenyl phosphate

     |

     |  ATP

     |/

     |  Isopentenyl phosphate kinase

     |\

     |  ADP

     |

Isopentenyl diphosphate

Bacterial version of Mevalonate phosphate to Isopentenyl diphosphate

Mevalonate phosphate

     |

     |  ATP

     |/

     |  Mevalonate phosphate kinase

     |\

     |  ADP

     |

Diphosphomevalonate

     |

     |  Diphosphomevalonate decarboxylase (EC 4.1.1.33)

     |\

     |  CO2

     |

Isopentenyl diphosphate

Dimethylallyl diphosphate

     |

     |  Isopentenyl-diphosphate delta-isomerase (EC 5.3.3.2)

     |    or

     |  Isopentenyl-diphosphate delta-isomerase, FMN-dependent (EC 5.3.3.2)

     |

Isopentenyl diphosphate

Polyisoprenoids:

                    Glycerol-1-phosphate

                                   |

                                   |  Geranylgeranyl pyrophosphate

                                   |/

                                   |  (S)-3-O-geranylgeranylglyceryl phosphate 
synthase

                                   |\

                                   |  PPi

                                   |

  (S)-3-O-geranylgeranylglyceryl phosphate

                                   |

                                   |  Geranylgeranyl pyrophosphate

                                   |/

                                   |  (S)-2,3-di-O-geranylgeranylglyceryl 
phosphate synthase

                                   |\

                                   |  PPi

                                   |

(S)-2,3-di-O-geranylgeranylglyceryl phosphate

----

(S)-3-O-geranylgeranylglyceryl phosphate synthase:

Identified in Methanothermobacter thermautotrophicus str. Delta H:

Soderberg, T., Chen, A., and Poulter, C. D.  2001.  Geranylgeranylglyceryl 
phosphate synthase. Characterization of the recombinant enzyme from 
Methanobacterium thermoautotrophicum.  Biochemistry 40: 14847-54.

Similar to 

----

(S)-2,3-di-O-geranylgeranylglyceryl phosphate synthase:

Identified in.

Similar to PcrB gene of low-G+C gram positive bacteria (e.g., B. subtilis), a 
gene of unknown function.

Crystalized from Archaeoglobus fulgidus DSM 4304:

Payandeh, J., Fujihashi, M., Gillon, W., and Pai, E. F.	2006.  The crystal 
structure of (S)-3-O-geranylgeranylglyceryl phosphate synthase reveals an 
ancient fold for an ancient enzyme.  J. Biol. Chem. 281: 6070-8.

###############################

LITERATURE