KEGG   PATHWAY: vum00260
Entry
vum00260                    Pathway                                
Name
Glycine, serine and threonine metabolism - Vigna umbellata (ricebean)
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
vum00260  Glycine, serine and threonine metabolism
vum00260

Module
vum_M00018  Threonine biosynthesis, aspartate => homoserine => threonine [PATH:vum00260]
vum_M00020  Serine biosynthesis, glycerate-3P => serine [PATH:vum00260]
vum_M00555  Betaine biosynthesis, choline => betaine [PATH:vum00260]
vum_M00621  Glycine cleavage system [PATH:vum00260]
Other DBs
GO: 0006544 0006563 0070178 0006566
Organism
Vigna umbellata (ricebean) [GN:vum]
Gene
124841104  aspartokinase 2, chloroplastic-like isoform X1 [KO:K00928] [EC:2.7.2.4]
124823890  bifunctional aspartokinase/homoserine dehydrogenase 2, chloroplastic-like [KO:K12524] [EC:2.7.2.4 1.1.1.3]
124839709  bifunctional aspartokinase/homoserine dehydrogenase, chloroplastic-like isoform X1 [KO:K12524] [EC:2.7.2.4 1.1.1.3]
124832055  bifunctional aspartokinase/homoserine dehydrogenase 2, chloroplastic-like [KO:K12524] [EC:2.7.2.4 1.1.1.3]
124822302  LOW QUALITY PROTEIN: aspartate-semialdehyde dehydrogenase-like [KO:K00133] [EC:1.2.1.11]
124825296  homoserine kinase-like [KO:K00872] [EC:2.7.1.39]
124837163  homoserine kinase [KO:K00872] [EC:2.7.1.39]
124823553  threonine synthase 1, chloroplastic-like [KO:K01733] [EC:4.2.3.1]
124843320  threonine synthase, chloroplastic-like [KO:K01733] [EC:4.2.3.1]
124834461  low-specificity L-threonine aldolase 1 [KO:K01620] [EC:4.1.2.48]
124830124  low-specificity L-threonine aldolase 1-like [KO:K01620] [EC:4.1.2.48]
124843998  serine hydroxymethyltransferase 4 [KO:K00600] [EC:2.1.2.1]
124821686  serine hydroxymethyltransferase, mitochondrial-like [KO:K00600] [EC:2.1.2.1]
124846059  serine hydroxymethyltransferase 7-like [KO:K00600] [EC:2.1.2.1]
124825936  serine hydroxymethyltransferase 3, chloroplastic-like [KO:K00600] [EC:2.1.2.1]
124826150  serine hydroxymethyltransferase, mitochondrial [KO:K00600] [EC:2.1.2.1]
124837964  serine hydroxymethyltransferase 3, chloroplastic-like [KO:K00600] [EC:2.1.2.1]
124827959  serine hydroxymethyltransferase 4-like [KO:K00600] [EC:2.1.2.1]
124841160  serine hydroxymethyltransferase 7-like [KO:K00600] [EC:2.1.2.1]
124835222  serine--glyoxylate aminotransferase [KO:K00830] [EC:2.6.1.44 2.6.1.45 2.6.1.51]
124838214  glycerate dehydrogenase HPR, peroxisomal-like [KO:K15893] [EC:1.1.1.29]
124838222  glycerate dehydrogenase [KO:K15893] [EC:1.1.1.29]
124847022  glyoxylate/hydroxypyruvate reductase HPR3-like [KO:K15919] [EC:1.1.1.79 1.1.1.81]
124833478  2,3-bisphosphoglycerate-dependent phosphoglycerate mutase 1-like [KO:K01834] [EC:5.4.2.11]
124845456  2,3-bisphosphoglycerate-dependent phosphoglycerate mutase 1-like [KO:K01834] [EC:5.4.2.11]
124842110  2,3-bisphosphoglycerate-dependent phosphoglycerate mutase 1-like [KO:K01834] [EC:5.4.2.11]
124826577  phosphoglycerate mutase-like protein 4 isoform X1 [KO:K15634] [EC:5.4.2.11]
124826579  phosphoglycerate mutase-like protein 4 isoform X1 [KO:K15634] [EC:5.4.2.11]
124847842  2,3-bisphosphoglycerate-independent phosphoglycerate mutase [KO:K15633] [EC:5.4.2.12]
124828575  D-glycerate 3-kinase, chloroplastic [KO:K15918] [EC:2.7.1.31]
124832150  D-3-phosphoglycerate dehydrogenase 1, chloroplastic [KO:K00058] [EC:1.1.1.95 1.1.1.399]
124831684  D-3-phosphoglycerate dehydrogenase 2, chloroplastic-like [KO:K00058] [EC:1.1.1.95 1.1.1.399]
124821422  phosphoserine aminotransferase 2, chloroplastic-like [KO:K00831] [EC:2.6.1.52]
124843593  phosphoserine aminotransferase 1, chloroplastic-like [KO:K00831] [EC:2.6.1.52]
124843596  phosphoserine aminotransferase 1, chloroplastic-like [KO:K00831] [EC:2.6.1.52]
124820669  phosphoserine phosphatase, chloroplastic-like [KO:K01079] [EC:3.1.3.3]
124820670  phosphoserine phosphatase, chloroplastic-like [KO:K01079] [EC:3.1.3.3]
124845772  copper methylamine oxidase-like isoform X1 [KO:K00276] [EC:1.4.3.21]
124822796  primary amine oxidase 2-like [KO:K00276] [EC:1.4.3.21]
124822804  LOW QUALITY PROTEIN: primary amine oxidase 2-like [KO:K00276] [EC:1.4.3.21]
124822812  primary amine oxidase-like [KO:K00276] [EC:1.4.3.21]
124822821  primary amine oxidase 1 [KO:K00276] [EC:1.4.3.21]
124835471  primary amine oxidase-like [KO:K00276] [EC:1.4.3.21]
124823883  primary amine oxidase-like isoform X1 [KO:K00276] [EC:1.4.3.21]
124847846  copper methylamine oxidase-like [KO:K00276] [EC:1.4.3.21]
124819667  primary amine oxidase-like [KO:K00276] [EC:1.4.3.21]
124826076  glycine dehydrogenase (decarboxylating), mitochondrial-like [KO:K00281] [EC:1.4.4.2]
124839478  glycine dehydrogenase (decarboxylating), mitochondrial isoform X1 [KO:K00281] [EC:1.4.4.2]
124833662  aminomethyltransferase, mitochondrial [KO:K00605] [EC:2.1.2.10]
124835379  leghemoglobin reductase [KO:K00382] [EC:1.8.1.4]
124847262  dihydrolipoyl dehydrogenase 2, chloroplastic [KO:K00382] [EC:1.8.1.4]
124836797  dihydrolipoyl dehydrogenase 1, chloroplastic-like [KO:K00382] [EC:1.8.1.4]
124823478  glycine cleavage system H protein 3, mitochondrial [KO:K02437]
124838271  glycine cleavage system H protein 2, mitochondrial-like [KO:K02437]
124829135  glycine cleavage system H protein 2, mitochondrial-like [KO:K02437]
124841619  alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial [KO:K00827] [EC:2.6.1.44 2.6.1.40]
124831983  alanine--glyoxylate aminotransferase 2 homolog 3, mitochondrial-like [KO:K00827] [EC:2.6.1.44 2.6.1.40]
124833860  glutamate--glyoxylate aminotransferase 2 isoform X1 [KO:K14272] [EC:2.6.1.4 2.6.1.2 2.6.1.44]
124839013  choline monooxygenase, chloroplastic isoform X1 [KO:K00499] [EC:1.14.15.7]
124826641  aminoaldehyde dehydrogenase 2, peroxisomal [KO:K00130] [EC:1.2.1.8]
124843589  aminoaldehyde dehydrogenase 1, peroxisomal [KO:K00130] [EC:1.2.1.8]
124819683  LOW QUALITY PROTEIN: aldehyde dehydrogenase family 7 member A1 [KO:K14085] [EC:1.2.1.31 1.2.1.8 1.2.1.3]
124838129  LOW QUALITY PROTEIN: probable sarcosine oxidase [KO:K00306] [EC:1.5.3.1 1.5.3.7]
124831818  threonine dehydratase biosynthetic, chloroplastic [KO:K01754] [EC:4.3.1.19]
124835168  serine racemase isoform X1 [KO:K12235] [EC:5.1.1.18]
124835820  tryptophan synthase alpha chain-like isoform X1 [KO:K01695] [EC:4.2.1.20]
124829684  tryptophan synthase alpha chain-like isoform X1 [KO:K01695] [EC:4.2.1.20]
124820894  tryptophan synthase beta chain 1 [KO:K01696] [EC:4.2.1.20]
124839581  LOW QUALITY PROTEIN: tryptophan synthase beta chain 2 [KO:K06001] [EC:4.2.1.20]
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
vum00010  Glycolysis / Gluconeogenesis
vum00020  Citrate cycle (TCA cycle)
vum00230  Purine metabolism
vum00250  Alanine, aspartate and glutamate metabolism
vum00270  Cysteine and methionine metabolism
vum00290  Valine, leucine and isoleucine biosynthesis
vum00300  Lysine biosynthesis
vum00330  Arginine and proline metabolism
vum00460  Cyanoamino acid metabolism
vum00470  D-Amino acid metabolism
vum00564  Glycerophospholipid metabolism
vum00600  Sphingolipid metabolism
vum00620  Pyruvate metabolism
vum00630  Glyoxylate and dicarboxylate metabolism
vum00640  Propanoate metabolism
vum00860  Porphyrin metabolism
vum00920  Sulfur metabolism
KO pathway
ko00260   
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