Information on EC 4.2.1.24 - porphobilinogen synthase

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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea

EC NUMBER
COMMENTARY hide
4.2.1.24
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RECOMMENDED NAME
GeneOntology No.
porphobilinogen synthase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
2 5-aminolevulinate = porphobilinogen + 2 H2O
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
condensation
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elimination
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of H2O, C-O bond clevage
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Knorr reaction
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Knorr pyrrole synthesis, C-C bond formation
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
tetrapyrrole biosynthesis I (from glutamate)
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tetrapyrrole biosynthesis II (from glycine)
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heme metabolism
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Porphyrin and chlorophyll metabolism
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Metabolic pathways
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Biosynthesis of secondary metabolites
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SYSTEMATIC NAME
IUBMB Comments
5-aminolevulinate hydro-lyase (adding 5-aminolevulinate and cyclizing; porphobilinogen-forming)
The enzyme catalyses the asymmetric condensation and cyclization of two 5-aminolevulinate molecules, which is the first common step in the biosynthesis of tetrapyrrole pigments such as porphyrin, chlorophyll, vitamin B12, siroheme, phycobilin, and cofactor F430. The enzyme is widespread, being essential in organisms that carry out respiration, photosynthesis, or methanogenesis. The enzymes from most organisms utilize metal ions (Zn2+, Mg2+, K+, and Na+) as cofactors that reside at multiple sites, including the active site and allosteric sites. Enzymes from archaea, yeast, and metazoa (including human) contain Zn2+ at the active site. In humans, the enzyme is a primary target for the environmental toxin Pb. The enzymes from some organisms utilize a dynamic equilibrium between architecturally distinct multimeric assemblies as a means for allosteric regulation.
CAS REGISTRY NUMBER
COMMENTARY hide
9036-37-7
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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Automatic Mining of ENzyme DAta
Acutodesmus obliquus
mutant strain C-2A'
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Manually annotated by BRENDA team
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Manually annotated by BRENDA team
Archaeoglobus sp.
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Manually annotated by BRENDA team
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
bat
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Automatic Mining of ENzyme DAta
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
Chlamydomonas sp.
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Manually annotated by BRENDA team
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Manually annotated by BRENDA team
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Manually annotated by BRENDA team
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Automatic Mining of ENzyme DAta
dogfish
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Automatic Mining of ENzyme DAta
Escherichia coli Rosetta(DE3)
Rosetta(DE3)
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Manually annotated by BRENDA team
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
Methanococcus sp.
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Manually annotated by BRENDA team
Methanothermus sp.
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Manually annotated by BRENDA team
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Automatic Mining of ENzyme DAta
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Manually annotated by BRENDA team
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
Physcomitrella sp.
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Manually annotated by BRENDA team
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
Propionibacterium sp.
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Manually annotated by BRENDA team
protozoa
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Automatic Mining of ENzyme DAta
quail
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Automatic Mining of ENzyme DAta
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1063905 A+, 1063906 A+, 1063909 A+, 1099693 A+, 1334350 A+, 1391560 A+, 1391572 A+, 1426456 A+, 1519769 A+, 1519897 A+, 1661544 A+, 1661607 A+, 1661725 A+, 1661734 A+, 1661785 A+, 1661814 A+, 1661816 A+, 1661819 A+, 1661827 A+, 1661840 A+, 1661855 A+, 1661863 A+, 1661869 A+, 1661878 A+, 1661884 A+, 2275017 A+, 2295632 A+, 2295666 A+, 2295688 A+, 2731753 A+, 2731762 A+, 2731799 A+, 2731801 A+, 2731806 A+, 2731809 A+, 2731851 A+, 2731880 A+, 2731890 A+, 2731898 A+, 2731902 A+, 691672 A+, 729333 A+, 967074 A+, 973277 A+, 973330 A+, 973435 A+, 1053281 A++, 1064193 A++, 1197418 A++, 1258256 A++, 1334384 A++, 1340295 A++, 1378521 A++, 1391546 A++, 1391555 A++, 1391579 A++, 1391587 A++, 1426352 A++, 1465636 A++, 1468911 A++, 1469267 A++, 1516944 A++, 1517212 A++, 1517839 A++, 1654415 A++, 1661541 A++, 1661552 A++, 1661553 A++, 1661561 A++, 1661564 A++, 1661565 A++, 1661569 A++, 1661571 A++, 1661573 A++, 1661577 A++, 1661578 A++, 1661580 A++, 1661585 A++, 1661588 A++, 1661591 A++, 1661595 A++, 1661598 A++, 1661599 A++, 1661604 A++, 1661617 A++, 1661626 A++, 1661630 A++, 1661636 A++, 1661650 A++, 1661656 A++, 1661658 A++, 1661659 A++, 1661660 A++, 1661662 A++, 1661665 A++, 1661668 A++, 1661678 A++, 1661686 A++, 1661700 A++, 1661703 A++, 1661717 A++, 1661719 A++, 1661726 A++, 1661728 A++, 1661747 A++, 1661750 A++, 1661753 A++, 1661762 A++, 1661786 A++, 1661795 A++, 1661803 A++, 1661806 A++, 1661817 A++, 1661828 A++, 1661843 A++, 1661846 A++, 2142071 A++, 2228111 A++, 2228115 A++, 2228128 A++, 2228136 A++, 2228142 A++, 2228146 A++, 2228148 A++, 2228149 A++, 2228166 A++, 2275006 A++, 2295627 A++, 2519094 A++, 2519099 A++, 2560681 A++, 2585457 A++, 2731774 A++, 2731777 A++, 2731785 A++, 2731792 A++, 2731794 A++, 2731795 A++, 2731808 A++, 2731814 A++, 2731848 A++, 2731866 A++, 677945 A++, 684809 A++, 783163 A++, 1075719 A++, 1334368 A++, 1391614 A++, 1475272 A++, 1639347 A++, 1661522 A++, 1661539 A++, 1661546 A++, 1661582 A++, 1661584 A++, 1661586 A++, 1661593 A++, 1661597 A++, 1661614 A++, 1661615 A++, 1661619 A++, 1661629 A++, 1661640 A++, 1661642 A++, 1661691 A++, 1661693 A++, 1661697 A++, 1661699 A++, 1661701 A++, 1661711 A++, 1661718 A++, 1661733 A++, 1661760 A++, 1661836 A++, 210716 A++, 2172740 A++, 2228113 A++, 2228114 A++, 2228130 A++, 2228132 A++, 2228143 A++, 2228156 A++, 2228174 A++, 2228191 A++, 2228192 A++, 2731758 A++, 2731786 A++, 2731796 A++, 2731843 A++, 2731846 A++, 2731884 A++, 2731886 A++, 653422 A++, 664767 A++, 666974 A++, 691169 A++, 783099 A++, 787635 A++, 883604 A++, 883690 A++, 973181 A++, 973185 A++, 973186 A++, 973187 A++, 973190 A++, 973199 A++, 973201 A++, 973222 A++, 973242 A++, 973245 A++, 973252 A++, 973291 A++, 973302 A++, 973308 A++, 973309 A++, 973312 A++, 973313 A++, 973315 A++, 973318 A++, 973319 A++, 973323 A++, 973325 A++, 973348 A++, 973362 A++, 973384 A++, 973417 A++, 973419 A++, 682119 A+++, 713007 A+++, 716429 A+++, 973445 A+++, 973449 A+++, 664768 A++++, 679087 A++++, 679181 A++++, 691205 A++++, 973179 A++++, 973180 A++++, 973188 A++++, 973216 A++++, 973228 A++++, 973229 A++++, 973238 A++++, 973240 A++++, 973249 A++++, 973250 A++++, 973306 A++++, 973307 A++++, 973310 A++++, 973328 A++++, 973341 A++++, 973355 A++++, 973368 A++++, 973374 A++++, 973398 A++++, 973403 A++++, 973406 A++++, 973424 A++++, 973427 A++++, 973436 A++++
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Automatic Mining of ENzyme DAta
Rattus norvegicus Sprague-Dawley
Sprague–Dawley
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Manually annotated by BRENDA team
animals infected with Trypanosoma evansi
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Automatic Mining of ENzyme DAta
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Manually annotated by BRENDA team
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
Schizosaccharomyces sp.
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Manually annotated by BRENDA team
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Automatic Mining of ENzyme DAta
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Manually annotated by BRENDA team
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
snake
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
toad
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Automatic Mining of ENzyme DAta
trout
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Automatic Mining of ENzyme DAta
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Manually annotated by BRENDA team
yeasts
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Automatic Mining of ENzyme DAta
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
metabolism
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2 5-aminolevulinate
porphobilinogen + 2 H2O
show the reaction diagram
5-aminolevulinate
?
show the reaction diagram
5-aminolevulinate
porphobilinogen + H2O
show the reaction diagram
5-aminolevulinate + 5-aminolevulinate
porphobilinogen + 2 H2O
show the reaction diagram
5-aminolevulinic acid + 5-aminolevulinic acid
porphobilinogen + 2 H2O
show the reaction diagram
additional information
?
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
2 5-aminolevulinate
porphobilinogen + 2 H2O
show the reaction diagram
5-aminolevulinate
?
show the reaction diagram
5-aminolevulinate
porphobilinogen + H2O
show the reaction diagram
5-aminolevulinate + 5-aminolevulinate
porphobilinogen + 2 H2O
show the reaction diagram
additional information
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ca2+
Acutodesmus obliquus
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about 80% reactivation of the demetalled protein
Cu2+
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inhibits enzymatic activity. High molecular weight fraction as well as metallothionein are involved in the detoxification of harmful heavy metals
Ni(2+)
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(4E)-6-oxodec-4-enedioic acid
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1,1',1''-[(3-ethoxyprop-1-ene-1,1,2-triyl)triselanyl]tribenzene ethyl 2,3,3-tris(phenylselanyl)prop-2-en-1-yl ether
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0.6 mM, 65% inhibition
1,1',1''-[(3-ethoxyprop-1-ene-1,1,2-triyl)triselanyl]tris(2,4,6-trimethylbenzene) ethyl 2,3,3-tris[(2,4,6-trimethylphenyl)selanyl]prop-2-en-1-yl ether
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0.6 mM, 44% inhibition
1,1',1''-[(3-ethoxyprop-1-ene-1,1,2-triyl)triselanyl]tris(4-chlorobenzene) ethyl 2,3,3-tris[(4-chlorophenyl)selanyl]prop-2-en-1-yl ether
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modest inhibition
1,10-phenanthroline
1-amino-4-hydroxy-2-butanone
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1-amino-4-methoxy-2-butanone
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1-amino-5-hydroxy-2-pentanone
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2,2'-dipyridine
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2,2-difluorosuccinic acid
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competitive
2,3-dimercaptopropane-1-sulfonic acid
2,3-Dimercaptopropanol
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cysteine and ZnCl2 protects. Dithiothreitol protects inhibition by 1 mM 2,3-dimercaptopropanol in a concentration dependent manner
2-bromo-3-(imidazol-5-yl)propionic acid
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3-acetyl-4-oxoheptane-1,7-dioic acid
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formation of a Schiff base complex between the inhibitors and the active site Lys
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4,7-dioxosebacic acid
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hanging-drop method, irreversible inhibitor binds by forming Schiff-base linkages with lysines 200 and 253 at the active site. 4,7-dioxosebacic acid is a better inhibitor of the zinc-dependent 5-aminolaevulinic acid dehydratases than of the zinc-independent 5-aminolaevulinic acid dehydratases
4,7-dioxosebaic acid
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4-amino-3-oxobutanoate
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4-nitro-2-butanone
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4-oxo-pentanenitrile
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4-oxo-sebacic acid
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4-oxosebaic acid
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active site-directed irreversible inhibitor, less potent than 4,7-dioxosebaic acid
5,5'-dithio(bis-2-nitrobenzoic acid)
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5,5'-dithiobis(2-nitrobenzoic acid)
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5,5'-iminobis(4-oxopentanoic acid)
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5,5'-oxybis(4-oxopentanoic acid)
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5,5'-sulfinylbis(4-oxopentanoic acid)
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5,5'-sulfonylbis(4-oxopentanoic acid)
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5,5'-thiobis(4-oxopentanoic acid)
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5-amino-4-oxopentanenitrile
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5-bromo-levulinic acid
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5-bromolevulinic acid
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5-chlorolevulinic acid
5-fluorolevulinic acid
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both inhibitor molecules are covalently bound to two conserved, active-site lysine residues, Lys205 and lys260, through Schiff bases
5-hydroxy-4-oxo-L-norvaline
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competitive
5-hydroxy-4-oxopentanoic acid
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5-hydroxylaevulinic acid
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the competitive inhibitor is bound by a Schiff-base link to one of the invariant active-site lysine residues (Lys263). The inhibitor appears to bind in two well defined conformations
5-hydroxylevulinate
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competitive
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5-hydroxylevulinic acid
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5-iodolevulinic acid
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5-nitrilo-4-oxopentanoic acid
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5-oxo-hexanoic acid
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6-amino-5-oxohexanoic acid
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7-(3-aminopentan-3-yl)-5-chloroquinolin-8-ol
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using in silico screening two hexamer-stabilizing inhibitors of PBGS are identified: N-(3-methoxyphenyl)-1-methyl-6-oxo-2-[(pyridin-2-ylmethyl)sulfanyl]-1,6-dihydropyrimidine-5-carboxamide and 7-(3-aminopentan-3-yl)-5-chloroquinolin-8-ol
8-hydroxyquinoline
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8-Hydroxyquinoline-5-sulfonic acid
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Al2(SO4)3
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ALA-D inhibition may be due to the fact that aluminum present in the growth medium can compete with Mg2+ or reduce the expression of ALA-D
Al3+
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IC50: 0.319 mM, GSH has no protective effect
alaremycin
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porphobilinogen synthase is cocrystallized with the alaremycin. At 1.75 A resolution, the crystal structure reveals that the antibiotic efficiently blocks the active site of porphobilinogen synthase. The antibiotic binds as a reduced derivative of 5-acetamido-4-oxo-5-hexenoic acid. The corresponding methyl group is not coordinated by any amino acid residues of the active site, excluding its functional relevance for alaremycin inhibition. Alaremycin is covalently bound by the catalytically important active-site lysine residue 260 and is tightly coordinated by several active-site amino acids
AlCl3
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0.001-0.01 mM AlCl3
alloxan
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i.e. 2,4,5,6-tetraoxypyrimidine 5,6-dioxyuracil , 0.00125-0.02 mM alloxan causes a concentration-dependent uncompetitive inhibition. Dithiothreitol (0.7and 1 mM) completely prevents the inhibition induced by 0.01 and 0.02 mM alloxan. Similar protection is obtained in the presence of 2 mMglutathione
alpha-lipoic acid
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significant inhibition
arsenic acid
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inhibition of 5-aminolevulinic acid dehydratase activity by arsenic in excised etiolated maize leaf segments during greening. KNO3, chloramphenical, cycloheximide, DTNB and levulinic aciddecrease inhibition. GSH increase inhibition
ascorbic acid
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0.4 mM, 23% inhibition
bathocuproine disulfonic acid
bis(4-chlorophenyl)diselenide
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bis(4-methoxyphenyl)diselenide
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bis[3-(trifluoromethy)phenyl]diselenide
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Butanedione
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protection by 5-aminolevulinate
Carbonate
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using a carbonate buffer rather than phosphate causes nearly a 90% drop in activity in the developed assay method
Coproporphyrinogen III
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Cuprizone
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bis-cyclohexanoneoxaldihydrazone
D-fructose
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formation of a Schiff base with the critical lysine residue of the enzyme is involved in inhibition of the enzyme by hexoses and pentoses
D-glucose
D-ribose
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formation of a Schiff base with the critical lysine residue of the enzyme is involved in inhibition of the enzyme by hexoses and pentoses
diammine(dichloro)platinum
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mechanism of inhibition is a direct interaction of the inhibitor with sulfhydryl groups, whereas zinc site appears to be involved with the higher doses only
dibutyl diselenide
dicholesteroyl diselenide
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significant at 0.1 mM
diethyl dicarbonate
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diethyldithiocarbamate
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diphenyl diselenide
diphenyl ditelluride
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dithiothreitol protects
DTNB
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reversible loss of activity
ebselen
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dithiothreitol protects
Fe2+
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noncompetitive
Ga3+
-
inhibits by competing with Zn2+, IC50: 0.442 mM, GSH has no protective effect, Zn2+ completely recovers inhibition
GSH
-
a weak inhibitor
HgCl2
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pretreatment with a nontoxic dose of Na2SeO3 partially or totally prevents in vivo mercury effects in kidney, including prevention of inhibition of delta-aminolevulinate dehydratase
In3+
-
inhibits by competing with Zn2+, IC50: 0.298 mM, GSH reduces inhibition, DL-dithiothreitol has modest effect on inhibition, Zn2+ completely recovers inhibition
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iodoacetamide
iodoacetate
levulinic acid
Mercury ions
-
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meso-2,3-dimercaptosuccinic acid
methyl methanethiosulfonate
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N-(3-methoxyphenyl)-1-methyl-6-oxo-2-[(pyridin-2-ylmethyl)sulfanyl]-1,6-dihydropyrimidine-5-carboxamide
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using in silico screening two hexamer-stabilizing inhibitors of PBGS are identified: N-(3-methoxyphenyl)-1-methyl-6-oxo-2-[(pyridin-2-ylmethyl)sulfanyl]-1,6-dihydropyrimidine-5-carboxamide and 7-(3-aminopentan-3-yl)-5-chloroquinolin-8-ol
Na2SeO3
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inhibits renal and hepatic enzyme
Neocuproine
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2,9-dimethyl-1,10-phenanthroline
Ni2+
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0.5 mM, 8% inhibition
p-hydroxymercuribenzoate
-
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phenyl selenoacetylene
phenyl selenoxideacetylene
phosphate
-
competitive against Mg2+
protoporphyrin IX
-
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pyridoxal 5'-phosphate
pyridoxal phosphate
-
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pyridoxamine phosphate
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rac-2-hydroxy-4-oxopentanoic acid
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rac-3-hydroxy-4-oxopentanoic acid
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sodium selenide
succinic acid
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noncompetitive
succinic acid monomethyl ester
-
competitive
succinylacetone
Tl3+
-
inhibits by direct oxidation of essential sulfhydryl groups, IC50: 0.0085 mM, DL-dithiothreitol restores completely enzyme activity inhibited by Tl3+, Zn2+ is unable to change inhibition
additional information
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-mercaptoethanol
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required at very low concentrations of substrate
glucose
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incubations of erythrocytes for 24 h with glucose result in an increase of delta-ALA-D activity. Incubations of erythrocytes with 100 to 200 mM glucose for 48 h inhibit delta-ALA-D activity
NH4+
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stimulates
thiol
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.043 - 2
5-aminolevulinate
0.00032 - 18
5-aminolevulinic acid
additional information
additional information
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the kinetic data do not follow a simple Michaelis-Menten relationship, but can be attributed to catalysis by two different forms of the enzyme that have different Km-values
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