KEGG   PATHWAY: rphi00270
Entry
rphi00270                   Pathway                                
Name
Cysteine and methionine metabolism - Ruditapes philippinarum (Manila clam)
Description
Cysteine and methionine are sulfur-containing amino acids. Cysteine is synthesized from serine through different pathways in different organism groups. In bacteria and plants, cysteine is converted from serine (via acetylserine) by transfer of hydrogen sulfide [MD:M00021]. In animals, methionine-derived homocysteine is used as sulfur source and its condensation product with serine (cystathionine) is converted to cysteine [MD:M00338]. Cysteine is metabolized to pyruvate in multiple routes. Methionine is an essential amino acid, which animals cannot synthesize. In bacteria and plants, methionine is synthesized from aspartate [MD:M00017]. S-Adenosylmethionine (SAM), synthesized from methionine and ATP, is a methyl group donor in many important transfer reactions including DNA methylation for regulation of gene expression. SAM may also be used to regenerate methionine in the methionine salvage pathway [MD:M00034].
Class
Metabolism; Amino acid metabolism
Pathway map
rphi00270  Cysteine and methionine metabolism
rphi00270

Module
rphi_M00034  Methionine salvage pathway [PATH:rphi00270]
rphi_M00035  Methionine degradation [PATH:rphi00270]
rphi_M00338  Cysteine biosynthesis, homocysteine + serine => cysteine [PATH:rphi00270]
Other DBs
GO: 0006534 0006555
Organism
Ruditapes philippinarum (Manila clam) [GN:rphi]
Gene
132737677  uncharacterized protein LOC132737677 [KO:K01738] [EC:2.5.1.47]
132714579  cystathionine gamma-lyase-like [KO:K01758] [EC:4.4.1.1]
132713340  cystathionine beta-synthase-like isoform X1 [KO:K01697] [EC:4.2.1.22]
132749131  betaine--homocysteine S-methyltransferase 1-like isoform X1 [KO:K00544] [EC:2.1.1.5]
132749132  betaine--homocysteine S-methyltransferase 1-like [KO:K00544] [EC:2.1.1.5]
132734918  betaine--homocysteine S-methyltransferase 1-like isoform X1 [KO:K00544] [EC:2.1.1.5]
132738754  betaine--homocysteine S-methyltransferase 1-like [KO:K00544] [EC:2.1.1.5]
132738770  betaine--homocysteine S-methyltransferase 1-like [KO:K00544] [EC:2.1.1.5]
132746720  betaine--homocysteine S-methyltransferase 1-like [KO:K00544] [EC:2.1.1.5]
132747125  betaine--homocysteine S-methyltransferase 1-like [KO:K00544] [EC:2.1.1.5]
132738771  betaine--homocysteine S-methyltransferase 1-like [KO:K00547] [EC:2.1.1.10]
132731578  uncharacterized protein LOC132731578 isoform X1 [KO:K00547] [EC:2.1.1.10]
132747124  betaine--homocysteine S-methyltransferase 1-like [KO:K00547] [EC:2.1.1.10]
132747134  betaine--homocysteine S-methyltransferase 1-like [KO:K00547] [EC:2.1.1.10]
132719731  methionine synthase-like [KO:K00548] [EC:2.1.1.13]
132755138  S-adenosylmethionine synthase-like [KO:K00789] [EC:2.5.1.6]
132732546  methionine adenosyltransferase 2 subunit beta-like isoform X1 [KO:K00789] [EC:2.5.1.6]
132758343  S-adenosylmethionine decarboxylase proenzyme 1-like isoform X1 [KO:K01611] [EC:4.1.1.50]
132712977  spermidine synthase-like [KO:K00797] [EC:2.5.1.16]
132731361  spermidine synthase-like [KO:K00797] [EC:2.5.1.16]
132719804  methylthioribose kinase-like [KO:K00899] [EC:2.7.1.100]
132724542  S-methyl-5'-thioadenosine phosphorylase-like [KO:K00772] [EC:2.4.2.28]
132752319  methylthioribose-1-phosphate isomerase-like [KO:K08963] [EC:5.3.1.23]
132719675  methylthioribulose-1-phosphate dehydratase-like [KO:K08964] [EC:4.2.1.109]
132735409  methylthioribulose-1-phosphate dehydratase-like [KO:K08964] [EC:4.2.1.109]
132759741  methylthioribulose-1-phosphate dehydratase-like [KO:K08964] [EC:4.2.1.109]
132714246  enolase-phosphatase E1-like [KO:K09880] [EC:3.1.3.77]
132746841  acireductone dioxygenase-like [KO:K08967] [EC:1.13.11.53 1.13.11.54]
132713482  tyrosine aminotransferase-like isoform X1 [KO:K00815] [EC:2.6.1.5]
132732968  aplysianin-A-like isoform X1 [KO:K03334] [EC:1.4.3.2]
132739731  aplysianin-A-like [KO:K03334] [EC:1.4.3.2]
132717714  DNA (cytosine-5)-methyltransferase 1-like isoform X1 [KO:K00558] [EC:2.1.1.37]
132749997  DNA (cytosine-5)-methyltransferase 3A-like isoform X1 [KO:K17398] [EC:2.1.1.37]
132750945  adenosylhomocysteinase A-like [KO:K01251] [EC:3.13.2.1]
132742973  adenosylhomocysteinase-like 1 [KO:K01251] [EC:3.13.2.1]
132758621  adenosylhomocysteinase A-like [KO:K01251] [EC:3.13.2.1]
132760504  S-adenosylhomocysteine hydrolase-like protein 1 [KO:K01251] [EC:3.13.2.1]
132733840  branched-chain-amino-acid aminotransferase-like isoform X1 [KO:K00826] [EC:2.6.1.42]
132737157  alanine--glyoxylate aminotransferase 2, mitochondrial-like [KO:K00827] [EC:2.6.1.44 2.6.1.40]
132725346  alanine--glyoxylate aminotransferase 2, mitochondrial-like [KO:K00827] [EC:2.6.1.44 2.6.1.40]
132757496  glutamate--cysteine ligase catalytic subunit-like [KO:K11204] [EC:6.3.2.2]
132755630  glutamate--cysteine ligase regulatory subunit-like [KO:K11205]
132747858  glutathione synthetase-like [KO:K21456] [EC:6.3.2.3]
132723695  glutathione synthetase-like [KO:K21456] [EC:6.3.2.3]
132731580  glutathione synthetase-like isoform X1 [KO:K21456] [EC:6.3.2.3]
132712695  cysteine dioxygenase type 1-like [KO:K00456] [EC:1.13.11.20]
132725025  aspartate aminotransferase, cytoplasmic-like [KO:K14454] [EC:2.6.1.1]
132753655  aspartate aminotransferase, cytoplasmic-like [KO:K14454] [EC:2.6.1.1]
132743486  aspartate aminotransferase, mitochondrial-like [KO:K14455] [EC:2.6.1.1]
132719822  thiosulfate sulfurtransferase-like [KO:K01011] [EC:2.8.1.1 2.8.1.2]
132748192  thiosulfate sulfurtransferase-like [KO:K01011] [EC:2.8.1.1 2.8.1.2]
132737931  3-mercaptopyruvate sulfurtransferase-like [KO:K01011] [EC:2.8.1.1 2.8.1.2]
132740104  thiosulfate sulfurtransferase-like [KO:K01011] [EC:2.8.1.1 2.8.1.2]
132731178  thiosulfate sulfurtransferase-like [KO:K01011] [EC:2.8.1.1 2.8.1.2]
132731188  thiosulfate sulfurtransferase-like [KO:K01011] [EC:2.8.1.1 2.8.1.2]
132731199  thiosulfate sulfurtransferase-like isoform X1 [KO:K01011] [EC:2.8.1.1 2.8.1.2]
132718655  thiosulfate sulfurtransferase-like [KO:K01011] [EC:2.8.1.1 2.8.1.2]
132733530  uncharacterized protein LOC132733530 [KO:K05396] [EC:4.4.1.15]
132722539  uncharacterized protein LOC132722539 [KO:K05396] [EC:4.4.1.15]
132722540  uncharacterized protein LOC132722540 [KO:K05396] [EC:4.4.1.15]
132752517  uncharacterized protein LOC132752517 [KO:K05396] [EC:4.4.1.15]
132728620  uncharacterized protein LOC132728620 isoform X1 [KO:K22207] [EC:4.4.1.28]
132758918  uncharacterized protein LOC132758918 [KO:K22207] [EC:4.4.1.28]
132713368  malate dehydrogenase, cytoplasmic-like [KO:K00025] [EC:1.1.1.37]
132743616  malate dehydrogenase, cytoplasmic-like [KO:K00025] [EC:1.1.1.37]
132749638  malate dehydrogenase, mitochondrial-like [KO:K00026] [EC:1.1.1.37]
132723489  serine dehydratase-like [KO:K17989] [EC:4.3.1.17 4.3.1.19]
132723516  serine dehydratase-like [KO:K17989] [EC:4.3.1.17 4.3.1.19]
132739070  serine dehydratase-like [KO:K17989] [EC:4.3.1.17 4.3.1.19]
132739071  L-serine dehydratase/L-threonine deaminase-like [KO:K17989] [EC:4.3.1.17 4.3.1.19]
132724981  D-3-phosphoglycerate dehydrogenase-like [KO:K00058] [EC:1.1.1.95 1.1.1.399]
132738973  phosphoserine aminotransferase-like [KO:K00831] [EC:2.6.1.52]
Compound
C00019  S-Adenosyl-L-methionine
C00021  S-Adenosyl-L-homocysteine
C00022  Pyruvate
C00041  L-Alanine
C00049  L-Aspartate
C00051  Glutathione
C00059  Sulfate
C00065  L-Serine
C00073  L-Methionine
C00094  Sulfite
C00097  L-Cysteine
C00109  2-Oxobutanoate
C00155  L-Homocysteine
C00170  5'-Methylthioadenosine
C00197  3-Phospho-D-glycerate
C00263  L-Homoserine
C00283  Hydrogen sulfide
C00409  Methanethiol
C00441  L-Aspartate 4-semialdehyde
C00491  L-Cystine
C00506  L-Cysteate
C00606  3-Sulfino-L-alanine
C00793  D-Cysteine
C00957  Mercaptopyruvate
C00979  O-Acetyl-L-serine
C01005  O-Phospho-L-serine
C01077  O-Acetyl-L-homoserine
C01118  O-Succinyl-L-homoserine
C01137  S-Adenosylmethioninamine
C01180  4-Methylthio-2-oxobutanoic acid
C01234  1-Aminocyclopropane-1-carboxylate
C01817  L-Homocystine
C01962  Thiocysteine
C02218  Dehydroalanine
C02291  L-Cystathionine
C02356  (S)-2-Aminobutanoate
C02989  L-Methionine S-oxide
C03082  4-Phospho-L-aspartate
C03089  5-Methylthio-D-ribose
C03145  N-Formylmethionine
C03232  3-Phosphonooxypyruvate
C03431  S-Inosyl-L-homocysteine
C03539  S-Ribosyl-L-homocysteine
C04188  S-Methyl-5-thio-D-ribose 1-phosphate
C04582  S-Methyl-5-thio-D-ribulose 1-phosphate
C05324  Nicotianamine
C05524  Aminoacyl-L-methionine
C05526  S-Glutathionyl-L-cysteine
C05527  3-Sulfinylpyruvate
C05528  3-Sulfopyruvate
C05823  3-Mercaptolactate
C05824  S-Sulfo-L-cysteine
C06547  Ethylene
C08276  3-(Methylthio)propanoate
C09306  Sulfur dioxide
C11437  1-Deoxy-D-xylulose 5-phosphate
C11481  HSO3-
C11499  (S)-3-Sulfolactate
C11537  (2R)-3-Sulfolactate
C15606  1,2-Dihydroxy-5-(methylthio)pent-1-en-3-one
C15650  2,3-Diketo-5-methylthiopentyl-1-phosphate
C15651  2-Hydroxy-3-keto-5-methylthiopentenyl-1-phosphate
C18049  N-Acyl-L-homoserine lactone
C19787  5'-S-Methyl-5'-thioinosine
C21015  gamma-L-Glutamyl-L-2-aminobutyrate
C21016  Ophthalmate
C22359  S-Methyl-1-thio-D-xylulose 5-phosphate
Reference
  Authors
Sekowska A, Denervaud V, Ashida H, Michoud K, Haas D, Yokota A, Danchin A
  Title
Bacterial variations on the methionine salvage pathway.
  Journal
BMC Microbiol 4:9 (2004)
DOI:10.1186/1471-2180-4-9
Reference
  Authors
Ashida H, Saito Y, Kojima C, Kobayashi K, Ogasawara N, Yokota A.
  Title
A functional link between RuBisCO-like protein of Bacillus and photosynthetic RuBisCO.
  Journal
Science 302:286-90 (2003)
DOI:10.1126/science.1086997
Reference
  Authors
Sekowska A, Danchin A.
  Title
The methionine salvage pathway in Bacillus subtilis.
  Journal
BMC Microbiol 2:8 (2002)
DOI:10.1186/1471-2180-2-8
Reference
  Authors
Berger BJ, English S, Chan G, Knodel MH.
  Title
Methionine regeneration and aminotransferases in Bacillus subtilis, Bacillus cereus, and Bacillus anthracis.
  Journal
J Bacteriol 185:2418-31 (2003)
DOI:10.1128/JB.185.8.2418-2431.2003
Reference
  Authors
Goyer A, Collakova E, Shachar-Hill Y, Hanson AD
  Title
Functional characterization of a methionine gamma-lyase in Arabidopsis and its implication in an alternative to the reverse trans-sulfuration pathway.
  Journal
Plant Cell Physiol 48:232-42 (2007)
DOI:10.1093/pcp/pcl055
Reference
  Authors
Rebeille F, Jabrin S, Bligny R, Loizeau K, Gambonnet B, Van Wilder V, Douce R, Ravanel S
  Title
Methionine catabolism in Arabidopsis cells is initiated by a gamma-cleavage process and leads to S-methylcysteine and isoleucine syntheses.
  Journal
Proc Natl Acad Sci U S A 103:15687-92 (2006)
DOI:10.1073/pnas.0606195103
Reference
  Authors
Pirkov I, Norbeck J, Gustafsson L, Albers E
  Title
A complete inventory of all enzymes in the eukaryotic methionine salvage pathway.
  Journal
FEBS J 275:4111-20 (2008)
DOI:10.1111/j.1742-4658.2008.06552.x
Reference
  Authors
Ashida H, Saito Y, Kojima C, Yokota A
  Title
Enzymatic characterization of 5-methylthioribulose-1-phosphate dehydratase of the methionine salvage pathway in Bacillus subtilis.
  Journal
Biosci Biotechnol Biochem 72:959-67 (2008)
DOI:10.1271/bbb.70651
Reference
  Authors
Kitabatake M, So MW, Tumbula DL, Soll D
  Title
Cysteine biosynthesis pathway in the archaeon Methanosarcina barkeri encoded by acquired bacterial genes?
  Journal
J Bacteriol 182:143-5 (2000)
DOI:10.1128/JB.182.1.143-145.2000
Reference
  Authors
Mino K, Ishikawa K
  Title
Characterization of a novel thermostable O-acetylserine sulfhydrylase from Aeropyrum pernix K1.
  Journal
J Bacteriol 185:2277-84 (2003)
DOI:10.1128/JB.185.7.2277-2284.2003
Reference
  Authors
Tanabe S
  Title
Development of assay methods for endogenous inorganic sulfur compounds and sulfurtransferases and evaluation of the physiological functions of bound sulfur.
  Journal
Yakugaku Zasshi 128:881-900 (2008)
DOI:10.1248/yakushi.128.881
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
  Authors
Gutierrez JA, Crowder T, Rinaldo-Matthis A, Ho MC, Almo SC, Schramm VL
  Title
Transition state analogs of 5'-methylthioadenosine nucleosidase disrupt quorum sensing.
  Journal
Nat Chem Biol 5:251-7 (2009)
DOI:10.1038/nchembio.153
Related
pathway
rphi00010  Glycolysis / Gluconeogenesis
rphi00250  Alanine, aspartate and glutamate metabolism
rphi00260  Glycine, serine and threonine metabolism
rphi00290  Valine, leucine and isoleucine biosynthesis
rphi00430  Taurine and hypotaurine metabolism
rphi00480  Glutathione metabolism
rphi00620  Pyruvate metabolism
rphi00640  Propanoate metabolism
rphi00770  Pantothenate and CoA biosynthesis
rphi00900  Terpenoid backbone biosynthesis
rphi00920  Sulfur metabolism
KO pathway
ko00270   
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