KEGG   PATHWAY: amq00860
Entry
amq00860                    Pathway                                
Name
Porphyrin metabolism - Amycolatopsis methanolica
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
amq00860  Porphyrin metabolism
amq00860

Module
amq_M00122  Cobalamin biosynthesis, cobyrinate a,c-diamide => cobalamin [PATH:amq00860]
amq_M00846  Siroheme biosynthesis, glutamyl-tRNA => siroheme [PATH:amq00860]
amq_M00926  Heme biosynthesis, bacteria, glutamyl-tRNA => coproporphyrin III => heme [PATH:amq00860]
Other DBs
GO: 0006778
Organism
Amycolatopsis methanolica [GN:amq]
Gene
AMETH_1518  gltX; glutamyl-tRNA synthetase [KO:K01885] [EC:6.1.1.17]
AMETH_0449  hemA; glutamyl-tRNA reductase [KO:K02492] [EC:1.2.1.70]
AMETH_0515  hemL; putative glutamate-1-semialdehyde-2,1-aminomutase [KO:K01845] [EC:5.4.3.8]
AMETH_3863  hemL; glutamate-1-semialdehyde 2,1-aminomutase [KO:K01845] [EC:5.4.3.8]
AMETH_0456  hemL; glutamate-1-semialdehyde 2,1-aminomutase [KO:K01845] [EC:5.4.3.8]
AMETH_0452  hemB; delta-aminolevulinic acid dehydratase [KO:K01698] [EC:4.2.1.24]
AMETH_0450  hemC; hydroxymethylbilane synthase [KO:K01749] [EC:2.5.1.61]
AMETH_1014  hemD; uroporphyrinogen-III synthase [KO:K01719] [EC:4.2.1.75]
AMETH_1022  hemD; Uroporphyrinogen III synthase HEM4 [KO:K01719] [EC:4.2.1.75]
AMETH_4745  hemE; Uroporphyrinogen decarboxylase [KO:K01599] [EC:4.1.1.37]
AMETH_4744  hemY; protoporphyrinogen oxidase [KO:K00231] [EC:1.3.3.4 1.3.3.15]
AMETH_3040  hemH; ferrochelatase [KO:K01772] [EC:4.98.1.1 4.99.1.9]
AMETH_4743  chlorite dismutase [KO:K00435] [EC:1.3.98.5]
AMETH_0451  hemD; uroporphyrinogen III synthase/methyltransferase [KO:K13542] [EC:2.1.1.107 4.2.1.75]
AMETH_2992  cysG; uroporphyrin-III C-methyltransferase/precorrin-2 dehydrogenase/sirohydrochlorin ferrochelatase [KO:K02302] [EC:2.1.1.107 1.3.1.76 4.99.1.4]
AMETH_4091  cyoE; protoheme IX farnesyltransferase [KO:K02257] [EC:2.5.1.141]
AMETH_4071  ctaA; Uncharacterized protein required for cytochrome oxidase assembly [KO:K02259] [EC:1.17.99.9]
AMETH_5464  cobI; precorrin-2 C20-methyltransferase [KO:K13540] [EC:2.1.1.130 2.1.1.131]
AMETH_5466  cobG; precorrin-3B synthase [KO:K02229] [EC:1.14.13.83]
AMETH_5459  cobM; precorrin-4 C11-methyltransferase [KO:K05936] [EC:2.1.1.133 2.1.1.271]
AMETH_5461  cobK; precorrin-6x reductase [KO:K05895] [EC:1.3.1.54 1.3.1.106]
AMETH_5460  cbiD; cobalt-precorrin-6A synthase (deacetylating) [KO:K02188] [EC:2.1.1.195]
AMETH_5458  cobL; precorrin-6Y C5,15-methyltransferase [KO:K00595] [EC:2.1.1.132 2.1.1.289 2.1.1.196]
AMETH_5465  cobH; precorrin-8X methylmutase [KO:K06042] [EC:5.4.99.61 5.4.99.60]
AMETH_5455  cobB; cobyrinic acid A,C-diamide synthase [KO:K02224] [EC:6.3.5.9 6.3.5.11]
AMETH_5490  cobN; cobaltochelatase CobN [KO:K02230] [EC:6.6.1.2]
AMETH_1361  ATP/cobalamin adenosyltransferase [KO:K00798] [EC:2.5.1.17]
AMETH_5456  cobO; cob(I)yrinic acid a,c-diamide adenosyltransferase [KO:K19221] [EC:2.5.1.17]
AMETH_5447  cobQ; cobyric acid synthase CobQ [KO:K02232] [EC:6.3.5.10]
AMETH_1051  cobD; cobalamin biosynthesis protein cobD/CbiB [KO:K02227] [EC:6.3.1.10]
AMETH_5448  cobD; cobalamin biosynthesis protein CobD [KO:K02227] [EC:6.3.1.10]
AMETH_5449  cobU; adenosylcobinamide kinase [KO:K02231] [EC:2.7.1.156 2.7.7.62]
AMETH_5451  cobS; cobalamin-5-phosphate synthase [KO:K02233] [EC:2.7.8.26]
AMETH_5450  cobT; nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase [KO:K00768] [EC:2.4.2.21]
AMETH_5137  cobU; nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase [KO:K00768] [EC:2.4.2.21]
AMETH_1057  fructose-2,6-bisphosphatase [KO:K22316] [EC:3.1.26.4 3.1.3.73]
AMETH_5457  chlD; magnesium chelatase subunit ChlD [KO:K03404] [EC:6.6.1.1]
AMETH_3576  chlI; magnesium chelatase subunit ChlI [KO:K03405] [EC:6.6.1.1]
AMETH_6239  Heme oxygenase [KO:K21480] [EC:1.14.15.20]
AMETH_0322  nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase [KO:K23825] [EC:1.3.98.-]
AMETH_0169  ferritin family protein [KO:K22336] [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
amq00230  Purine metabolism
amq00250  Alanine, aspartate and glutamate metabolism
amq00260  Glycine, serine and threonine metabolism
amq00740  Riboflavin metabolism
KO pathway
ko00860   
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