KEGG   PATHWAY: syb00860
Entry
syb00860                    Pathway                                
Name
Porphyrin metabolism - Sphingobium sp. YBL2
Description
Porphyrins are a group of chemical compounds with the backbone ring structure consisting of four linked pyrrole units. Metal complexes of porphyrins, as well as those of corrinoids with the one-carbon shorter ring structure, play important biological roles. They include iron-containing heme, magnesium-containing chlorophyll, nickel-containing coenzyme F430 and cobalt-containing cobamide (such as vitamin B12 coenzyme) as shown in this map.
Class
Metabolism; Metabolism of cofactors and vitamins
Pathway map
syb00860  Porphyrin metabolism
syb00860

Module
syb_M00122  Cobalamin biosynthesis, cobyrinate a,c-diamide => cobalamin [PATH:syb00860]
syb_M00925  Cobalamin biosynthesis, aerobic, uroporphyrinogen III => precorrin 2 => cobyrinate a,c-diamide [PATH:syb00860]
Other DBs
GO: 0006778
Organism
Sphingobium sp. YBL2 [GN:syb]
Gene
TZ53_19105  5-aminolevulinate synthase [KO:K00643] [EC:2.3.1.37]
TZ53_15175  glutamyl-tRNA synthetase [KO:K01885] [EC:6.1.1.17]
TZ53_10210  glutamyl-tRNA ligase [KO:K01885] [EC:6.1.1.17]
TZ53_20035  delta-aminolevulinic acid dehydratase [KO:K01698] [EC:4.2.1.24]
TZ53_10230  porphobilinogen deaminase [KO:K01749] [EC:2.5.1.61]
TZ53_10225  uroporphyrinogen-III synthase [KO:K01719] [EC:4.2.1.75]
TZ53_04510  uroporphyrinogen decarboxylase [KO:K01599] [EC:4.1.1.37]
TZ53_02365  coproporphyrinogen III oxidase [KO:K00228] [EC:1.3.3.3]
TZ53_07890  coproporphyrinogen III oxidase [KO:K02495] [EC:1.3.98.3]
TZ53_04505  membrane protein [KO:K08973] [EC:1.3.99.-]
TZ53_13735  hemH; ferrochelatase [KO:K01772] [EC:4.98.1.1 4.99.1.9]
TZ53_01305  siroheme synthase [KO:K02302] [EC:2.1.1.107 1.3.1.76 4.99.1.4]
TZ53_01235  uroporphyrin-III methyltransferase [KO:K02303] [EC:2.1.1.107]
TZ53_15745  uroporphyrin-III methyltransferase [KO:K02303] [EC:2.1.1.107]
TZ53_11985  protoheme IX farnesyltransferase [KO:K02257] [EC:2.5.1.141]
TZ53_11250  heme A synthase [KO:K02259] [EC:1.17.99.9]
TZ53_06725  precorrin-2 C20-methyltransferase [KO:K03394] [EC:2.1.1.130 2.1.1.151]
TZ53_06715  cobalamin biosynthesis protein CobG [KO:K02229] [EC:1.14.13.83]
TZ53_06730  precorrin-3B C17-methyltransferase [KO:K05934] [EC:2.1.1.131 2.1.1.272]
TZ53_06750  precorrin-4 C11-methyltransferase [KO:K05936] [EC:2.1.1.133 2.1.1.271]
TZ53_06745  precorrin methylase [KO:K02189] [EC:3.7.1.12]
TZ53_06760  precorrin 6A synthase [KO:K02228] [EC:2.1.1.152]
TZ53_06735  cobalt-precorrin-6X reductase [KO:K05895] [EC:1.3.1.54 1.3.1.106]
TZ53_06740  precorrin-6Y methyltransferase [KO:K00595] [EC:2.1.1.132 2.1.1.289 2.1.1.196]
TZ53_06720  cobH; precorrin-8X methylmutase [KO:K06042] [EC:5.4.99.61 5.4.99.60]
TZ53_06755  cobyrinic acid a,c-diamide synthase [KO:K02224] [EC:6.3.5.9 6.3.5.11]
TZ53_06700  cobalamin biosynthesis protein CobN [KO:K02230] [EC:6.6.1.2]
TZ53_10050  cobalamin biosynthesis protein CobS [KO:K09882] [EC:6.6.1.2]
TZ53_10035  cobalt chelatase [KO:K09883] [EC:6.6.1.2]
TZ53_13000  cob(I)yrinic acid a c-diamide adenosyltransferase [KO:K00798] [EC:2.5.1.17]
TZ53_06705  cobinamide adenolsyltransferase [KO:K19221] [EC:2.5.1.17]
TZ53_19325  cobalamin biosynthesis protein CobQ [KO:K02232] [EC:6.3.5.10]
TZ53_06815  adenosylcobinamide-phosphate synthase [KO:K02227] [EC:6.3.1.10]
TZ53_06820  aminotransferase [KO:K02225]
TZ53_06810  cobalamin biosynthesis protein [KO:K02231] [EC:2.7.1.156 2.7.7.62]
TZ53_06825  cobalamin synthase [KO:K02233] [EC:2.7.8.26]
TZ53_06835  nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase [KO:K00768] [EC:2.4.2.21]
TZ53_06830  phosphoglycerate mutase [KO:K02226] [EC:3.1.3.73]
TZ53_21585  phosphoglycerate mutase [KO:K22316] [EC:3.1.26.4 3.1.3.73]
TZ53_15055  bacterioferritin [KO:K03594] [EC:1.16.3.1]
Compound
C00025  L-Glutamate
C00032  Heme
C00037  Glycine
C00188  L-Threonine
C00194  Cobamide coenzyme
C00430  5-Aminolevulinate
C00486  Bilirubin
C00500  Biliverdin
C00524  Cytochrome c
C00541  Cob(II)alamin
C00748  Siroheme
C00853  Cob(I)alamin
C00931  Porphobilinogen
C00992  Aquacob(III)alamin
C01024  Hydroxymethylbilane
C01051  Uroporphyrinogen III
C01079  Protoporphyrinogen IX
C01708  Hemoglobin
C02139  Chlorophyllide
C02191  Protoporphyrin
C02463  Precorrin 2
C02469  Uroporphyrin III
C02800  4,5-Dioxopentanoate
C02823  Cyanocobalamin
C02880  Protochlorophyllide
C02987  L-Glutamyl-tRNA(Glu)
C03029  Transferrin[Fe(II)]2
C03114  Dimethylbenzimidazole
C03179  Transferrin[Fe(III)]2
C03194  (R)-1-Aminopropan-2-ol
C03263  Coproporphyrinogen III
C03373  Aminoimidazole ribotide
C03516  Magnesium protoporphyrin
C03741  (S)-4-Amino-5-oxopentanoate
C04122  D-1-Aminopropan-2-ol O-phosphate
C04536  Magnesium protoporphyrin monomethyl ester
C04778  N1-(5-Phospho-alpha-D-ribosyl)-5,6-dimethylbenzimidazole
C05306  Chlorophyll a
C05307  Chlorophyll b
C05766  Uroporphyrinogen I
C05767  Uroporphyrin I
C05768  Coproporphyrinogen I
C05769  Coproporphyrin I
C05770  Coproporphyrin III
C05772  Precorrin 3A
C05773  Cobyrinate
C05774  Cobinamide
C05775  alpha-Ribazole
C05777  Coenzyme F430
C05778  Sirohydrochlorin
C05779  Apoferritin
C05780  Apotransferrin
C05781  Oxyhemoglobin
C05782  Myoglobin
C05783  Cytochrome a
C05784  Catalase
C05785  Peroxidase
C05786  (3Z)-Phycocyanobilin
C05787  Bilirubin beta-diglucuronide
C05789  L-Urobilinogen
C05790  I-Urobilinogen
C05791  D-Urobilinogen
C05793  L-Urobilin
C05794  Urobilin
C05795  D-Urobilin
C05797  Pheophytin a
C05798  Bacteriopheophytin
C05912  (3Z)-Phycoerythrobilin
C05913  (3Z)-Phytochromobilin
C06319  Precorrin 6Y
C06320  Precorrin 6X
C06399  Hydrogenobyrinate
C06406  Precorrin 3B
C06407  Precorrin 4
C06408  Precorrin 8X
C06416  Precorrin 5
C06503  Hydrogenobyrinate a,c diamide
C06504  Cob(II)yrinate a,c diamide
C06505  Cob(I)yrinate a,c diamide
C06506  Adenosyl cobyrinate a,c diamide
C06507  Adenosyl cobyrinate hexaamide
C06508  Adenosyl cobinamide
C06509  Adenosyl cobinamide phosphate
C06510  Adenosine-GDP-cobinamide
C11242  Bacteriochlorophyll a
C11243  Bacteriochlorophyll b
C11538  Cobalt-sirohydrochlorin
C11540  Cobalt-precorrin 4
C11542  Cobalt-precorrin 6
C11543  Cobalt-dihydro-precorrin 6
C11545  Cobalt-precorrin 8
C11630  15,16-Dihydrobiliverdin
C11829  13(1)-Hydroxy-magnesium-protoporphyrin IX 13-monomethyl ester
C11830  13(1)-Oxo-magnesium-protoporphyrin IX 13-monomethyl ester
C11831  Divinylprotochlorophyllide
C11832  Divinyl chlorophyllide a
C11850  Divinylchlorophyll a
C11851  Zn-Bacteriochlorophyll a
C12147  L-Threonine O-3-phosphate
C14818  Fe2+
C14819  Fe3+
C15670  Heme A
C15672  Heme O
C16242  Cobalt-precorrin 5A
C16243  Cobalt-precorrin 5B
C16244  Cobalt-precorrin 7
C16540  7(1)-Hydroxychlorophyllide a
C16541  Chlorophyllide b
C17401  Cobalt-factor III
C18021  Pheophorbide a
C18022  Red chlorophyll catabolite
C18064  Pyropheophorbide a
C18098  Primary fluorescent chlorophyll catabolite
C18151  7(1)-Hydroxychlorophyll a
C18152  3-Vinylbacteriochlorophyllide a
C18153  3-Hydroxyethylbacteriochlorophyllide a
C18154  3-Hydroxyethylchlorophyllide a
C18155  Bacteriochlorophyllide a
C18156  Bacteriochlorophyllide b
C18157  8-Ethyl-12-methyl-3-vinylbacteriochlorophyllide d
C18160  Bacteriochlorophyllide d
C18161  Bacteriochlorophyllide c
C18162  Bacteriochlorophyll d
C18163  Bacteriochlorophyll c
C19608  Ferritin
C20666  5-Oxo-delta-bilirubin
C21217  Geranylgeranyl bacteriochlorophyllide a
C21284  Fe-coproporphyrin III
C21427  8,12-Diethyl-3-vinylbacteriochlorophyllide d
C21428  12-Ethyl-8-propyl-3-vinylbacteriochlorophyllide d
C21429  12-Ethyl-8-isobutyl-3-vinylbacteriochlorophyllide d
C21431  8-Ethyl-12-methylbacteriochlorophyllide d
C21432  8,12-Diethylbacteriochlorophyllide d
C21433  12-Ethyl-8-propylbacteriochlorophyllide d
C21434  12-Ethyl-8-isobutylbacteriochlorophyllide d
C21435  Geranylgeranyl bacteriochlorophyllide b
C21510  Nickel-sirohydrochlorin
C21511  Nickel-sirohydrochlorin a,c-diamide
C21512  15,17(3)-Seco-F430-17(3)-acid
C21582  Bacteriochlorophyllide e
C21723  Biliverdin-IX-delta
C21724  Biliverdin-IX-beta
C21764  5-Hydroxybenzimidazole
C21835  12,18-Didecarboxysiroheme
C22338  Dihydro-heme d1
C22339  Heme d1
C22450  5-Methoxybenzimidazole
C22451  5-Methoxy-6-methylbenzimidazole
Reference
PMID:9461500
  Authors
Woodcock SC, Raux E, Levillayer F, Thermes C, Rambach A, Warren MJ.
  Title
Effect of mutations in the transmethylase and dehydrogenase/chelatase domains of sirohaem synthase (CysG) on sirohaem and cobalamin biosynthesis.
  Journal
Biochem J 330:121-9 (1998)
DOI:10.1042/bj3300121
Reference
PMID:10217486
  Authors
Johansson P, Hederstedt L
  Title
Organization of genes for tetrapyrrole biosynthesis in gram--positive bacteria.
  Journal
Microbiology 145 ( Pt 3):529-38 (1999)
DOI:10.1099/13500872-145-3-529
Reference
PMID:10518530
  Authors
Maggio-Hall LA, Escalante-Semerena JC.
  Title
In vitro synthesis of the nucleotide loop of cobalamin by Salmonella typhimurium enzymes.
  Journal
Proc Natl Acad Sci USA 96:11798-803 (1999)
DOI:10.1073/pnas.96.21.11798
Reference
PMID:11007789
  Authors
Roper JM, Raux E, Brindley AA, Schubert HL, Gharbia SE, Shah HN, Warren MJ.
  Title
The enigma of cobalamin (Vitamin B12) biosynthesis in Porphyromonas gingivalis. Identification and characterization of a functional corrin pathway.
  Journal
J Biol Chem 275:40316-23 (2000)
DOI:10.1074/jbc.M007146200
Reference
PMID:12196148
  Authors
Scott AI, Roessner CA.
  Title
Biosynthesis of cobalamin (vitamin B(12)).
  Journal
Biochem Soc Trans 30:613-20 (2002)
DOI:10.1042/bst0300613
Reference
PMID:12195810
  Authors
Warren MJ, Raux E, Schubert HL, Escalante-Semerena JC.
  Title
The biosynthesis of adenosylcobalamin (vitamin B12).
  Journal
Nat Prod Rep 19:390-412 (2002)
DOI:10.1039/b108967f
Reference
PMID:12055304
  Authors
Roessner CA, Huang KX, Warren MJ, Raux E, Scott AI.
  Title
Isolation and characterization of 14 additional genes specifying the anaerobic biosynthesis of cobalamin (vitamin B12) in Propionibacterium freudenreichii (P. shermanii).
  Journal
Microbiology 148:1845-53 (2002)
DOI:10.1099/00221287-148-6-1845
Reference
PMID:11283349
  Authors
Frankenberg N, Mukougawa K, Kohchi T, Lagarias JC.
  Title
Functional genomic analysis of the HY2 family of ferredoxin-dependent bilin reductases from oxygenic photosynthetic organisms.
  Journal
Plant Cell 13:965-78 (2001)
DOI:10.1105/tpc.13.4.965
Reference
PMID:17506685
  Authors
Chew AG, Bryant DA
  Title
Chlorophyll biosynthesis in bacteria: the origins of structural and functional diversity.
  Journal
Annu Rev Microbiol 61:113-29 (2007)
DOI:10.1146/annurev.micro.61.080706.093242
Reference
PMID:16245042
  Authors
Frigaard NU, Chew AG, Li H, Maresca JA, Bryant DA
  Title
Chlorobium tepidum: insights into the structure, physiology, and metabolism of a green sulfur bacterium derived from the complete genome sequence.
  Journal
Photosynth Res 78:93-117 (2003)
DOI:10.1023/B:PRES.0000004310.96189.b4
Reference
PMID:23042036
  Authors
Deery E, Schroeder S, Lawrence AD, Taylor SL, Seyedarabi A, Waterman J, Wilson KS, Brown D, Geeves MA, Howard MJ, Pickersgill RW, Warren MJ
  Title
An enzyme-trap approach allows isolation of intermediates in cobalamin biosynthesis.
  Journal
Nat Chem Biol 8:933-40 (2012)
DOI:10.1038/nchembio.1086
Reference
PMID:23922391
  Authors
Moore SJ, Lawrence AD, Biedendieck R, Deery E, Frank S, Howard MJ, Rigby SE, Warren MJ
  Title
Elucidation of the anaerobic pathway for the corrin component of cobalamin (vitamin B12).
  Journal
Proc Natl Acad Sci U S A 110:14906-11 (2013)
DOI:10.1073/pnas.1308098110
Related
pathway
syb00230  Purine metabolism
syb00250  Alanine, aspartate and glutamate metabolism
syb00260  Glycine, serine and threonine metabolism
syb00740  Riboflavin metabolism
KO pathway
ko00860   
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