EC 1.1.1.261     
Accepted name: sn-glycerol-1-phosphate dehydrogenase
Reaction: sn-glycerol 1-phosphate + NAD(P)+ = glycerone phosphate + NAD(P)H + H+
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): glycerol-1-phosphate dehydrogenase [NAD(P)+]; sn-glycerol-1-phosphate:NAD+ oxidoreductase; G-1-P dehydrogenase; Gro1PDH; AraM
Systematic name: sn-glycerol-1-phosphate:NAD(P)+ 2-oxidoreductase
Comments: This enzyme is found primarily as a Zn2+-dependent form in archaea but a Ni2+-dependent form has been found in Gram-positive bacteria [6]. The Zn2+-dependent metalloenzyme is responsible for the formation of archaea-specific sn-glycerol-1-phosphate, the first step in the biosynthesis of polar lipids in archaea. It is the enantiomer of sn-glycerol 3-phosphate, the form of glycerophosphate found in bacteria and eukaryotes. The other enzymes involved in the biosynthesis of polar lipids in archaea are EC 2.5.1.41 (phosphoglycerol geranylgeranyltransferase) and EC 2.5.1.42 (geranylgeranylglycerol-phosphate geranylgeranyltransferase), which together alkylate the hydroxy groups of glycerol 1-phosphate to give unsaturated archaetidic acid, which is acted upon by EC 2.7.7.67 (CDP-archaeol synthase) to form CDP-unsaturated archaeol. The final step in the pathway involves the addition of L-serine, with concomitant removal of CMP, leading to the production of unsaturated archaetidylserine [4]. Activity of the enzyme is stimulated by K+ [2].
References:
1.  Nishihara, M. and Koga, Y. sn-Glycerol-1-phosphate dehydrogenase in Methanobacterium thermoautotrophicum: key enzyme in biosynthesis of the enantiomeric glycerophosphate backbone of ether phospholipids of archaebacteria. J. Biochem. 117 (1995) 933–935. [PMID: 8586635]
2.  Nishihara, M. and Koga, Y. Purification and properties of sn-glycerol-1-phosphate dehydrogenase from Methanobacterium thermoautotrophicum: characterization of the biosynthetic enzyme for the enantiomeric glycerophosphate backbone of ether polar lipids of Archaea. J. Biochem. 122 (1997) 572–576. [PMID: 9348086]
3.  Koga, Y., Kyuragi, T., Nishihara, M. and Sone, N. Did archaeal and bacterial cells arise independently from noncellular precursors? A hypothesis stating that the advent of membrane phospholipid with enantiomeric glycerophosphate backbones caused the separation of the two lines of descent. J. Mol. Evol. 46 (1998) 54–63. [PMID: 9419225]
4.  Morii, H., Nishihara, M. and Koga, Y. CTP:2,3-di-O-geranylgeranyl-sn-glycero-1-phosphate cytidyltransferase in the methanogenic archaeon Methanothermobacter thermoautotrophicus. J. Biol. Chem. 275 (2000) 36568–36574. [PMID: 10960477]
5.  Han, J.S. and Ishikawa, K. Active site of Zn2+-dependent sn-glycerol-1-phosphate dehydrogenase from Aeropyrum pernix K1. Archaea 1 (2005) 311–317. [PMID: 15876564]
6.  Guldan, H., Sterner, R. and Babinger, P. Identification and characterization of a bacterial glycerol-1-phosphate dehydrogenase: Ni(2+)-dependent AraM from Bacillus subtilis. Biochemistry 47 (2008) 7376–7384. [PMID: 18558723]
[EC 1.1.1.261 created 2000, modified 2009]
 
 
EC 1.3.1.101     
Accepted name: 2,3-bis-O-geranylgeranyl-sn-glycerol 1-phosphate reductase [NAD(P)H]
Reaction: 2,3-bis-(O-phytanyl)-sn-glycerol 1-phosphate + 8 NAD(P)+ = 2,3-bis-(O-geranylgeranyl)-sn-glycerol 1-phosphate + 8 NAD(P)H + 8 H+
Glossary: phytanol = (7R,11R,15R)-3,7,11,15-tetramethylhexadecan-1-ol
Other name(s): digeranylgeranylglycerophospholipid reductase; Ta0516m (gene name); DGGGPL reductase; 2,3-digeranylgeranylglycerophospholipid reductase
Systematic name: 2,3-bis-(O-phytany)l-sn-glycerol 1-phosphate:NAD(P)+ oxidoreductase
Comments: A flavoprotein (FAD). The enzyme from the archaeon Thermoplasma acidophilum is involved in the biosynthesis of membrane lipids. In vivo the reaction occurs in the reverse direction with the formation of 2,3-bis-O-phytanyl-sn-glycerol 1-phosphate. cf. EC 1.3.7.11, 2,3-bis-O-geranylgeranyl-sn-glycero-phospholipid reductase.
References:
1.  Nishimura, Y. and Eguchi, T. Biosynthesis of archaeal membrane lipids: digeranylgeranylglycerophospholipid reductase of the thermoacidophilic archaeon Thermoplasma acidophilum. J. Biochem. 139 (2006) 1073–1081. [PMID: 16788058]
2.  Nishimura, Y. and Eguchi, T. Stereochemistry of reduction in digeranylgeranylglycerophospholipid reductase involved in the biosynthesis of archaeal membrane lipids from Thermoplasma acidophilum. Bioorg. Chem. 35 (2007) 276–283. [PMID: 17275067]
3.  Xu, Q., Eguchi, T., Mathews, I.I., Rife, C.L., Chiu, H.J., Farr, C.L., Feuerhelm, J., Jaroszewski, L., Klock, H.E., Knuth, M.W., Miller, M.D., Weekes, D., Elsliger, M.A., Deacon, A.M., Godzik, A., Lesley, S.A. and Wilson, I.A. Insights into substrate specificity of geranylgeranyl reductases revealed by the structure of digeranylgeranylglycerophospholipid reductase, an essential enzyme in the biosynthesis of archaeal membrane lipids. J. Mol. Biol. 404 (2010) 403–417. [PMID: 20869368]
[EC 1.3.1.101 created 2013]
 
 
EC 1.3.7.11     
Accepted name: 2,3-bis-O-geranylgeranyl-sn-glycero-phospholipid reductase
Reaction: a 2,3-bis-(O-phytanyl)-sn-glycero-phospholipid + 16 oxidized ferredoxin [iron-sulfur] cluster = a 2,3-bis-(O-geranylgeranyl)-sn-glycero-phospholipid + 16 reduced ferredoxin [iron-sulfur] cluster + 16 H+
Glossary: phytanol = 3,7,11,15-tetramethylhexadecan-1-ol
Other name(s): AF0464 (gene name); 2,3-bis-O-geranylgeranyl-sn-glycerol 1-phosphate reductase (donor)
Systematic name: 2,3-bis-(O-phytanyl)-sn-glycero-phospholipid:ferredoxin oxidoreductase
Comments: A flavoprotein (FAD). The enzyme is involved in the biosynthesis of archaeal membrane lipids. It catalyses the reduction of all 8 double bonds in 2,3-bis-O-geranylgeranyl-sn-glycero-phospholipids and all 4 double bonds in 3-O-geranylgeranyl-sn-glycerol phospholipids with comparable activity. Unlike EC 1.3.1.101, 2,3-bis-O-geranylgeranyl-sn-glycerol 1-phosphate reductase [NAD(P)H], this enzyme shows no activity with NADPH, and requires a dedicated ferredoxin [4].
References:
1.  Murakami, M., Shibuya, K., Nakayama, T., Nishino, T., Yoshimura, T. and Hemmi, H. Geranylgeranyl reductase involved in the biosynthesis of archaeal membrane lipids in the hyperthermophilic archaeon Archaeoglobus fulgidus. FEBS J. 274 (2007) 805–814. [PMID: 17288560]
2.  Sato, S., Murakami, M., Yoshimura, T. and Hemmi, H. Specific partial reduction of geranylgeranyl diphosphate by an enzyme from the thermoacidophilic archaeon Sulfolobus acidocaldarius yields a reactive prenyl donor, not a dead-end product. J. Bacteriol. 190 (2008) 3923–3929. [PMID: 18375567]
3.  Sasaki, D., Fujihashi, M., Iwata, Y., Murakami, M., Yoshimura, T., Hemmi, H. and Miki, K. Structure and mutation analysis of archaeal geranylgeranyl reductase. J. Mol. Biol. 409 (2011) 543–557. [PMID: 21515284]
4.  Isobe, K., Ogawa, T., Hirose, K., Yokoi, T., Yoshimura, T. and Hemmi, H. Geranylgeranyl reductase and ferredoxin from Methanosarcina acetivorans are required for the synthesis of fully reduced archaeal membrane lipid in Escherichia coli cells. J. Bacteriol. 196 (2014) 417–423. [PMID: 24214941]
[EC 1.3.7.11 created 2013 as EC 1.3.99.34, transferred 2015 to EC 1.3.7.11 ]
 
 
EC 1.3.99.34      
Transferred entry: 2,3-bis-O-geranylgeranyl-sn-glycerol 1-phosphate reductase (donor). Now classified as EC 1.3.7.11, 2,3-bis-O-geranylgeranyl-sn-glycero-phospholipid reductase.
[EC 1.3.99.34 created 2013, deleted 2015]
 
 
EC 2.5.1.41     
Accepted name: phosphoglycerol geranylgeranyltransferase
Reaction: geranylgeranyl diphosphate + sn-glycerol 1-phosphate = diphosphate + 3-(O-geranylgeranyl)-sn-glycerol 1-phosphate
Glossary: sn-glycerol 1-phosphate = sn-glyceryl phosphate = (S)-2,3-dihydroxypropyl dihydrogen phosphate
Other name(s): glycerol phosphate geranylgeranyltransferase; geranylgeranyl-transferase (ambiguous); prenyltransferase (ambiguous); (S)-3-O-geranylgeranylglyceryl phosphate synthase; (S)-geranylgeranylglyceryl phosphate synthase; GGGP synthase; (S)-GGGP synthase; GGGPS; geranylgeranyl diphosphate:sn-glyceryl phosphate geranylgeranyltransferase; geranylgeranyl diphosphate:sn-glycerol-1-phosphate geranylgeranyltransferase
Systematic name: geranylgeranyl-diphosphate:sn-glycerol-1-phosphate geranylgeranyltransferase
Comments: This cytosolic enzyme catalyses the first pathway-specific step in the biosynthesis of the core membrane diether lipids in archaebacteria [2]. Requires Mg2+ for maximal activity [2]. It catalyses the alkylation of the primary hydroxy group in sn-glycerol 1-phosphate by geranylgeranyl diphosphate (GGPP) in a prenyltransfer reaction where a hydroxy group is the nucleophile in the acceptor substrate [2]. The other enzymes involved in the biosynthesis of polar lipids in Archaea are EC 1.1.1.261 (sn-glycerol-1-phosphate dehydrogenase), EC 2.5.1.42 (geranylgeranylglycerol-phosphate geranylgeranyltransferase) and EC 2.7.7.67 (CDP-archaeol synthase), which lead to the formation of CDP-unsaturated archaeol. The final step in the pathway involves the addition of L-serine, with concomitant removal of CMP, leading to the production of unsaturated archaetidylserine [5].
References:
1.  Zhang, D.-L., Daniels, L. and Poulter, C.D. Biosynthesis of archaebacterial membranes. Formation of isoprene ethers by a prenyl transfer reaction. J. Am. Chem. Soc. 112 (1990) 1264–1265.
2.  Chen, A., Zhang, D. and Poulter, C.D. (S)-Geranylgeranylglyceryl phosphate synthase. Purification and characterization of the first pathway-specific enzyme in archaebacterial membrane lipid biosynthesis. J. Biol. Chem. 268 (1993) 21701–21705. [PMID: 8408023]
3.  Nemoto, N., Oshima, T. and Yamagishi, A. Purification and characterization of geranylgeranylglyceryl phosphate synthase from a thermoacidophilic archaeon, Thermoplasma acidophilum. J. Biochem. 133 (2003) 651–657. [PMID: 12801917]
4.  Payandeh, J., Fujihashi, M., Gillon, W. and Pai, E.F. The crystal structure of (S)-3-O-geranylgeranylglyceryl phosphate synthase reveals an ancient fold for an ancient enzyme. J. Biol. Chem. 281 (2006) 6070–6078. [PMID: 16377641]
5.  Morii, H., Nishihara, M. and Koga, Y. CTP:2,3-di-O-geranylgeranyl-sn-glycero-1-phosphate cytidyltransferase in the methanogenic archaeon Methanothermobacter thermoautotrophicus. J. Biol. Chem. 275 (2000) 36568–36574. [PMID: 10960477]
[EC 2.5.1.41 created 1992, modified 2009]
 
 
EC 2.5.1.42     
Accepted name: geranylgeranylglycerol-phosphate geranylgeranyltransferase
Reaction: geranylgeranyl diphosphate + 3-(O-geranylgeranyl)-sn-glycerol 1-phosphate = diphosphate + 2,3-bis-(O-geranylgeranyl)-sn-glycerol 1-phosphate
Other name(s): geranylgeranyloxyglycerol phosphate geranylgeranyltransferase; geranylgeranyltransferase II; (S)-2,3-di-O-geranylgeranylglyceryl phosphate synthase; DGGGP synthase; DGGGPS; geranylgeranyl diphosphate:sn-3-O-(geranylgeranyl)glycerol 1-phosphate geranylgeranyltransferase
Systematic name: geranylgeranyl diphosphate:3-(O-geranylgeranyl)-sn-glycerol 1-phosphate geranylgeranyltransferase
Comments: This enzyme is an integral-membrane protein that carries out the second prenyltransfer reaction involved in the formation of polar membrane lipids in Archaea. Requires a divalent metal cation, such as Mg2+ or Mn2+, for activity [2]. 4-Hydroxybenzoate, 1,4-dihydroxy 2-naphthoate, homogentisate and α-glycerophosphate cannot act as prenyl-acceptor substrates [2]. The other enzymes involved in the biosynthesis of polar lipids in Archaea are EC 1.1.1.261 (sn-glycerol-1-phosphate dehydrogenase), EC 2.5.1.41 (phosphoglycerol geranylgeranyltransferase), which, together with this enzyme, alkylates the hydroxy groups of glycerol 1-phosphate to yield unsaturated archaetidic acid, which is acted upon by EC 2.7.7.67 (CDP-archaeol synthase) to form CDP-unsaturated archaeol. The final step in the pathway involves the addition of L-serine, with concomitant removal of CMP, leading to the production of unsaturated archaetidylserine [3]. Belongs in the UbiA prenyltransferase family [2].
References:
1.  Zhang, D.-L., Daniels, L. and Poulter, C.D. Biosynthesis of archaebacterial membranes. Formation of isoprene ethers by a prenyl transfer reaction. J. Am. Chem. Soc. 112 (1990) 1264–1265.
2.  Hemmi, H., Shibuya, K., Takahashi, Y., Nakayama, T. and Nishino, T. (S)-2,3-Di-O-geranylgeranylglyceryl phosphate synthase from the thermoacidophilic archaeon Sulfolobus solfataricus. Molecular cloning and characterization of a membrane-intrinsic prenyltransferase involved in the biosynthesis of archaeal ether-linked membrane lipids. J. Biol. Chem. 279 (2004) 50197–50203. [PMID: 15356000]
3.  Morii, H., Nishihara, M. and Koga, Y. CTP:2,3-di-O-geranylgeranyl-sn-glycero-1-phosphate cytidyltransferase in the methanogenic archaeon Methanothermobacter thermoautotrophicus. J. Biol. Chem. 275 (2000) 36568–36574. [PMID: 10960477]
[EC 2.5.1.42 created 1992, modified 2009]
 
 
EC 2.5.1.145     
Accepted name: phosphatidylglycerol—prolipoprotein diacylglyceryl transferase
Reaction: L-1-phosphatidyl-sn-glycerol + a [prolipoprotein]-L-cysteine = sn-glycerol 1-phosphate + an [prolipoprotein]-S-1,2-diacyl-sn-glyceryl-L-cysteine
Other name(s): lgt (gene name)
Systematic name: L-1-phosphatidyl-sn-glycerol:[prolipoprotein]-L-cysteine diacyl-sn-glyceryltransferase
Comments: This bacterial enzyme, which is associated with the membrane, catalyses the transfer of an sn-1,2-diacylglyceryl group from phosphatidylglycerol to the sulfhydryl group of the prospective N-terminal cysteine of a prolipoprotein, the first step in the formation of mature triacylated lipoproteins.
References:
1.  Sankaran, K. and Wu, H.C. Lipid modification of bacterial prolipoprotein. Transfer of diacylglyceryl moiety from phosphatidylglycerol. J. Biol. Chem. 269 (1994) 19701–19706. [PMID: 8051048]
2.  Qi, H.Y., Sankaran, K., Gan, K. and Wu, H.C. Structure-function relationship of bacterial prolipoprotein diacylglyceryl transferase: functionally significant conserved regions. J. Bacteriol. 177 (1995) 6820–6824. [PMID: 7592473]
3.  Gan, K., Sankaran, K., Williams, M.G., Aldea, M., Rudd, K.E., Kushner, S.R. and Wu, H.C. The umpA gene of Escherichia coli encodes phosphatidylglycerol:prolipoprotein diacylglyceryl transferase (lgt) and regulates thymidylate synthase levels through translational coupling. J. Bacteriol. 177 (1995) 1879–1882. [PMID: 7896715]
4.  Sankaran, K., Gan, K., Rash, B., Qi, H.Y., Wu, H.C. and Rick, P.D. Roles of histidine-103 and tyrosine-235 in the function of the prolipoprotein diacylglyceryl transferase of Escherichia coli. J. Bacteriol. 179 (1997) 2944–2948. [PMID: 9139912]
5.  Pailler, J., Aucher, W., Pires, M. and Buddelmeijer, N. Phosphatidylglycerol::prolipoprotein diacylglyceryl transferase (Lgt) of Escherichia coli has seven transmembrane segments, and its essential residues are embedded in the membrane. J. Bacteriol. 194 (2012) 2142–2151. [PMID: 22287519]
[EC 2.5.1.145 created 2018]
 
 
EC 2.7.7.67     
Accepted name: CDP-2,3-bis-(O-geranylgeranyl)-sn-glycerol synthase
Reaction: CTP + 2,3-bis-(O-geranylgeranyl)-sn-glycerol 1-phosphate = diphosphate + CDP-2,3-bis-(O-geranylgeranyl)-sn-glycerol
Glossary: 2,3-bis-(O-geranylgeranyl)-sn-glycerol 1-phosphate = 2,3-bis-(O-geranylgeranyl)-glycerophosphate ether = unsaturated archaetidic acid
CDP-unsaturated archaeol = CDP-2,3-bis-(O-geranylgeranyl)-sn-glycerol
Other name(s): carS (gene name); CDP-2,3-di-O-geranylgeranyl-sn-glycerol synthase; CTP:2,3-GG-GP ether cytidylyltransferase; CTP:2,3-di-O-geranylgeranyl-sn-glycero-1-phosphate cytidyltransferase; CDP-2,3-bis-O-(geranylgeranyl)-sn-glycerol synthase; CTP:2,3-bis-O-(geranylgeranyl)-sn-glycero-1-phosphate cytidylyltransferase; CDP-unsaturated archaeol synthase; CDP-archaeol synthase (incorrect)
Systematic name: CTP:2,3-bis-(O-geranylgeranyl)-sn-glycerol 1-phosphate cytidylyltransferase
Comments: This enzyme catalyses one of the steps in the biosynthesis of polar lipids in archaea, which are characterized by having an sn-glycerol 1-phosphate backbone rather than an sn-glycerol 3-phosphate backbone as is found in bacteria and eukaryotes [1]. The enzyme requires Mg2+ and K+ for maximal activity [1].
References:
1.  Morii, H., Nishihara, M. and Koga, Y. CTP:2,3-di-O-geranylgeranyl-sn-glycero-1-phosphate cytidyltransferase in the methanogenic archaeon Methanothermobacter thermoautotrophicus. J. Biol. Chem. 275 (2000) 36568–36574. [PMID: 10960477]
2.  Morii, H. and Koga, Y. CDP-2,3-di-O-geranylgeranyl-sn-glycerol:L-serine O-archaetidyltransferase (archaetidylserine synthase) in the methanogenic archaeon Methanothermobacter thermautotrophicus. J. Bacteriol. 185 (2003) 1181–1189. [PMID: 12562787]
3.  Jain, S., Caforio, A., Fodran, P., Lolkema, J.S., Minnaard, A.J. and Driessen, A.J. Identification of CDP-archaeol synthase, a missing link of ether lipid biosynthesis in Archaea. Chem. Biol. 21 (2014) 1392–1401. [PMID: 25219966]
[EC 2.7.7.67 created 2009, modified 2014]
 
 
EC 3.1.3.21     
Accepted name: glycerol-1-phosphatase
Reaction: glycerol 1-phosphate + H2O = glycerol + phosphate
Other name(s): α-glycerophosphatase; α-glycerol phosphatase; glycerol 3-phosphatase; glycerol-3-phosphate phosphatase; glycerol 3-phosphate phosphohydrolase
Systematic name: glycerol-1-phosphate phosphohydrolase
Comments: The Dunaliella enzyme acts more rapidly on sn-glycerol 1-phosphate than on the 3-phosphate. The enzyme from yeast also acts on propane-1,2-diol 1-phosphate, but not on a variety of other phosphate esters.
References:
1.  Sussman, I. and Avron, M. Characterization and partial purification of DL-glycerol-1-phosphatase from Dunaliella salina. Biochim. Biophys. Acta 661 (1981) 199–204.
[EC 3.1.3.21 created 1972, modified 1986]
 
 


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