KEGG   PATHWAY: rde00260
Entry
rde00260                    Pathway                                
Name
Glycine, serine and threonine metabolism - Roseobacter denitrificans
Description
Serine is derived from 3-phospho-D-glycerate, an intermediate of glycolysis [MD:M00020], and glycine is derived from serine. Threonine is an essential amino acid, which animals cannot synthesize. In bacteria and plants, threonine is derived from aspartate [MD:M00018].
Class
Metabolism; Amino acid metabolism
Pathway map
rde00260  Glycine, serine and threonine metabolism
rde00260

Module
rde_M00020  Serine biosynthesis, glycerate-3P => serine [PATH:rde00260]
rde_M00555  Betaine biosynthesis, choline => betaine [PATH:rde00260]
rde_M00621  Glycine cleavage system [PATH:rde00260]
Other DBs
GO: 0006544 0006563 0070178 0006566
Organism
Roseobacter denitrificans [GN:rde]
Gene
RD1_0003  [KO:K00605] [EC:2.1.2.10]
RD1_0019  [KO:K00315] [EC:1.5.8.4]
RD1_0127  hemA; 5-aminolevulinic acid synthase [KO:K00643] [EC:2.3.1.37]
RD1_0195  serB; phosphoserine phosphatase, putative [KO:K01079] [EC:3.1.3.3]
RD1_0196  serC; phosphoserine aminotransferase [KO:K00831] [EC:2.6.1.52]
RD1_0197  serA; D-3-phosphoglycerate dehydrogenase [KO:K00058] [EC:1.1.1.95 1.1.1.399]
RD1_0198  tdh; L-threonine 3-dehydrogenase [KO:K00060] [EC:1.1.1.103]
RD1_0199  kbl; 2-amino-3-ketobutyrate coenzyme A ligase [KO:K00639] [EC:2.3.1.29]
RD1_0306  asd; aspartate-semialdehyde dehydrogenase [KO:K00133] [EC:1.2.1.11]
RD1_0335  gpmI; 2,3-bisphosphoglycerate-independent phosphoglycerate mutase [KO:K15633] [EC:5.4.2.12]
RD1_0416  ilvA; threonine dehydratase [KO:K01754] [EC:4.3.1.19]
RD1_0535  [KO:K00274] [EC:1.4.3.4]
RD1_0607  [KO:K00315] [EC:1.5.8.4]
RD1_0929  cln; creatinase [KO:K08688] [EC:3.5.3.3]
RD1_1165  glyA; serine hydroxymethyltransferase [KO:K00600] [EC:2.1.2.1]
RD1_1204  [KO:K12972] [EC:1.1.1.79 1.1.1.81]
RD1_1222  gcvT; aminomethyltransferase [KO:K00605] [EC:2.1.2.10]
RD1_1223  gcvH; glycine cleavage system H protein [KO:K02437]
RD1_1225  gcvP; glycine dehydrogenase [KO:K00281] [EC:1.4.4.2]
RD1_1345  [KO:K00315] [EC:1.5.8.4]
RD1_1472  gatM; glycine amidinotransferase [KO:K00613] [EC:2.1.4.1]
RD1_1576  hemA; 5-aminolevulinic acid synthase [KO:K00643] [EC:2.3.1.37]
RD1_1603  lpdA; dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
RD1_1701  soxB; sarcosine oxidase, beta subunit [KO:K00303] [EC:1.5.3.24 1.5.3.1]
RD1_1702  soxD; sarcosine oxidase, delta subunit [KO:K00304] [EC:1.5.3.24 1.5.3.1]
RD1_1704  soxA; sarcosine oxidase, alpha subunit [KO:K00302] [EC:1.5.3.24 1.5.3.1]
RD1_1705  soxG; sarcosine oxidase, gamma subunit, putative [KO:K00305] [EC:1.5.3.24 1.5.3.1]
RD1_1750  sgaA; serine--glyoxylate aminotransferase, putative [KO:K00830] [EC:2.6.1.44 2.6.1.45 2.6.1.51]
RD1_1917  sdaA; L-serine ammonia-lyase [KO:K01752] [EC:4.3.1.17]
RD1_1981  ttuD; hydroxypyruvate reductase [KO:K11529] [EC:2.7.1.165]
RD1_2023  betB; betaine aldehyde dehydrogenase [KO:K00130] [EC:1.2.1.8]
RD1_2024  betA; choline dehydrogenase [KO:K00108] [EC:1.1.99.1]
RD1_2141  thrC; threonine synthase [KO:K01733] [EC:4.2.3.1]
RD1_2157  [KO:K00928] [EC:2.7.2.4]
RD1_2538  hom; homoserine dehydrogenase [KO:K00003] [EC:1.1.1.3]
RD1_2827  hemA; 5-aminolevulinic acid synthase [KO:K00643] [EC:2.3.1.37]
RD1_2995  lpdA; dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
RD1_3093  [KO:K00315] [EC:1.5.8.4]
RD1_3431  ectC; ectoine synthase, putative [KO:K06720] [EC:4.2.1.108]
RD1_3434  [KO:K00315] [EC:1.5.8.4]
RD1_3474  [KO:K15783] [EC:3.5.4.44]
RD1_3475  [KO:K15784] [EC:3.5.1.125]
RD1_3525  ltaE; low-specificity L-threonine aldolase [KO:K01620] [EC:4.1.2.48]
RD1_3633  serA; D-3-phosphoglycerate dehydrogenase, putative [KO:K00058] [EC:1.1.1.95 1.1.1.399]
RD1_3670  [KO:K00382] [EC:1.8.1.4]
RD1_3778  hemA; 5-aminolevulinic acid synthase [KO:K00643] [EC:2.3.1.37]
RD1_3858  [KO:K00605] [EC:2.1.2.10]
RD1_3895  trpA; tryptophan synthase, alpha subunit [KO:K01695] [EC:4.2.1.20]
RD1_3906  trpB; tryptophan synthase, beta subunit [KO:K01696] [EC:4.2.1.20]
RD1_3931  [KO:K01754] [EC:4.3.1.19]
RD1_3991  glyA; serine hydroxymethyltransferase [KO:K00600] [EC:2.1.2.1]
RD1_4241  [KO:K11529] [EC:2.7.1.165]
RD1_4249  glyA; serine hydroxymethyltransferase [KO:K00600] [EC:2.1.2.1]
Compound
C00011  CO2
C00014  Ammonia
C00022  Pyruvate
C00037  Glycine
C00048  Glyoxylate
C00049  L-Aspartate
C00065  L-Serine
C00078  L-Tryptophan
C00097  L-Cysteine
C00101  Tetrahydrofolate
C00109  2-Oxobutanoate
C00114  Choline
C00143  5,10-Methylenetetrahydrofolate
C00168  Hydroxypyruvate
C00188  L-Threonine
C00197  3-Phospho-D-glycerate
C00213  Sarcosine
C00258  D-Glycerate
C00263  L-Homoserine
C00300  Creatine
C00430  5-Aminolevulinate
C00441  L-Aspartate 4-semialdehyde
C00546  Methylglyoxal
C00576  Betaine aldehyde
C00581  Guanidinoacetate
C00631  2-Phospho-D-glycerate
C00719  Betaine
C00740  D-Serine
C00986  1,3-Diaminopropane
C01005  O-Phospho-L-serine
C01026  N,N-Dimethylglycine
C01102  O-Phospho-L-homoserine
C01242  [Protein]-S8-aminomethyldihydrolipoyllysine
C01888  Aminoacetone
C02051  Lipoylprotein
C02291  L-Cystathionine
C02737  Phosphatidylserine
C02972  Dihydrolipoylprotein
C03082  4-Phospho-L-aspartate
C03194  (R)-1-Aminopropan-2-ol
C03232  3-Phosphonooxypyruvate
C03283  L-2,4-Diaminobutanoate
C03508  L-2-Amino-3-oxobutanoic acid
C05519  L-Allothreonine
C06231  Ectoine
C06442  N(gamma)-Acetyldiaminobutyrate
C16432  5-Hydroxyectoine
C19929  N(alpha)-Acetyl-L-2,4-diaminobutyrate
Reference
  Authors
Nishizuka Y, Seyama Y, Ikai A, Ishimura Y, Kawaguchi A (eds).
  Title
[Cellular Functions and Metabolic Maps] (In Japanese)
  Journal
Tokyo Kagaku Dojin (1997)
Reference
PMID:11823218
  Authors
Kuhlmann AU, Bremer E.
  Title
Osmotically regulated synthesis of the compatible solute ectoine in Bacillus pasteurii and related Bacillus spp.
  Journal
Appl Environ Microbiol 68:772-83 (2002)
DOI:10.1128/AEM.68.2.772-783.2002
Reference
PMID:10473374
  Authors
Canovas D, Borges N, Vargas C, Ventosa A, Nieto JJ, Santos H.
  Title
Role of Ngamma-acetyldiaminobutyrate as an enzyme stabilizer and an intermediate in the biosynthesis of hydroxyectoine.
  Journal
Appl Environ Microbiol 65:3774-9 (1999)
DOI:10.1128/AEM.65.9.3774-3779.1999
Reference
PMID:17636255
  Authors
Bursy J, Pierik AJ, Pica N, Bremer E.
  Title
Osmotically induced synthesis of the compatible solute hydroxyectoine is mediated by an evolutionarily conserved ectoine hydroxylase.
  Journal
J Biol Chem 282:31147-55 (2007)
DOI:10.1074/jbc.M704023200
Reference
PMID:16707670
  Authors
Garcia-Estepa R, Argandona M, Reina-Bueno M, Capote N, Iglesias-Guerra F, Nieto JJ, Vargas C.
  Title
The ectD gene, which is involved in the synthesis of the compatible solute hydroxyectoine, is essential for thermoprotection of the halophilic bacterium Chromohalobacter salexigens.
  Journal
J Bacteriol 188:3774-84 (2006)
DOI:10.1128/JB.00136-06
Reference
PMID:15470257
  Authors
Arevalo-Rodriguez M, Pan X, Boeke JD, Heitman J
  Title
FKBP12 controls aspartate pathway flux in Saccharomyces cerevisiae to prevent toxic intermediate accumulation.
  Journal
Eukaryot Cell 3:1287-96 (2004)
DOI:10.1128/EC.3.5.1287-1296.2004
Reference
PMID:7639721
  Authors
Rees WD, Hay SM
  Title
The biosynthesis of threonine by mammalian cells: expression of a complete bacterial biosynthetic pathway in an animal cell.
  Journal
Biochem J 309 ( Pt 3):999-1007 (1995)
DOI:10.1042/bj3090999
Reference
PMID:11341914
  Authors
Jacques SL, Nieman C, Bareich D, Broadhead G, Kinach R, Honek JF, Wright GD
  Title
Characterization of yeast homoserine dehydrogenase, an antifungal target: the invariant histidine 309 is important for enzyme integrity.
  Journal
Biochim Biophys Acta 1544:28-41 (2001)
DOI:10.1016/S0167-4838(00)00203-X
Reference
PMID:15520012
  Authors
Chen X, Jhee KH, Kruger WD
  Title
Production of the neuromodulator H2S by cystathionine beta-synthase via the condensation of cysteine and homocysteine.
  Journal
J Biol Chem 279:52082-6 (2004)
DOI:10.1074/jbc.C400481200
Related
pathway
rde00010  Glycolysis / Gluconeogenesis
rde00020  Citrate cycle (TCA cycle)
rde00230  Purine metabolism
rde00250  Alanine, aspartate and glutamate metabolism
rde00270  Cysteine and methionine metabolism
rde00290  Valine, leucine and isoleucine biosynthesis
rde00300  Lysine biosynthesis
rde00330  Arginine and proline metabolism
rde00460  Cyanoamino acid metabolism
rde00470  D-Amino acid metabolism
rde00564  Glycerophospholipid metabolism
rde00600  Sphingolipid metabolism
rde00620  Pyruvate metabolism
rde00630  Glyoxylate and dicarboxylate metabolism
rde00640  Propanoate metabolism
rde00680  Methane metabolism
rde00860  Porphyrin metabolism
rde00920  Sulfur metabolism
KO pathway
ko00260   

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