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Information on EC 1.13.11.91 - 3-mercaptopropionate dioxygenase
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1.13.11.91 3-mercaptopropionate dioxygenaseIUBMB Comments
This bacterial enzyme contains an iron(2+) atom coordinated by three protein-derived histidines and a Ser-His-Tyr motif. It is similar to EC 1.13.11.20, cysteine dioxygenase, and can act on L-cysteine, but has a much higher activity with its native substrate, 3-sulfanylpropanoate.
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Word Map
- 1.13.11.91
-
non-heme
-
sulfinic
- l-cysteine
- vinelandii
-
paramagnetic
- cysteamine
-
3-sulfinopropionic
-
dioxygenation
-
ferrous
-
denticity
-
bidentate
- paradoxus
-
polythioester
- thioether
-
advenella
-
thiol-containing
-
iron-nitrosyl
- so2
-
biotechnical
-
variovorax
- dtdp
- mercaptosuccinate
- mimigardefordensis
The enzyme appears in viruses and cellular organisms
Synonyms
3-mercaptopropionate dioxygenase, 3-mercaptopropionic acid dioxygenase, 3mp dioxygenase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
3-mercaptopropionic acid dioxygenase
-
-
-
-
3-sulfanylpropanoate dioxygenase
-
-
-
-
3MDO
CdoA
H16_B1863
MDO
NP_251292
PA2602
MDO
-
-
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
3-sulfanylpropanoate + O2 = 3-sulfinopropanoate
-
-
-
-
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PATHWAY SOURCE
PATHWAYS
-
,
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SYSTEMATIC NAME
IUBMB Comments
3-sulfanylpropanoate:oxygen oxidoreductase
This bacterial enzyme contains an iron(2+) atom coordinated by three protein-derived histidines and a Ser-His-Tyr motif. It is similar to EC 1.13.11.20, cysteine dioxygenase, and can act on L-cysteine, but has a much higher activity with its native substrate, 3-sulfanylpropanoate.
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
(2R)-2-sulfanylbutanedioic acid + O2
?
i.e. (R)-mercaptosuccinate, no substrate for wild-type, but mutant Q62R
-
-
?
(2R)-2-sulfanylbutanedioic acid + O2
?
i.e. (R)-mercaptosuccinate, no substrate for wild-type, but mutant Q62R
-
-
?
3-mercaptopropanoate + O2
3-sulfinopropanoate
-
-
-
-
?
3-mercaptopropanoate + O2
3-sulfinopropanoate
-
-
-
?
3-mercaptopropanoate + O2
3-sulfinopropanoate
-
-
-
?
L-cysteine + O2
3-sulfinoalanine
plus some cysteine sulfinic acid, reaction of EC 1.13.11.20
-
-
?
L-cysteine + O2
3-sulfinoalanine
reaction of EC 1.13.11.20
-
-
?
L-cysteine + O2
3-sulfinoalanine
reaction of EC 1.13.11.20
-
-
?
L-cysteine + O2
3-sulfinoalanine
plus some cysteine sulfinic acid, reaction of EC 1.13.11.20
-
-
?
additional information
?
-
-
enzyme exhibits a specificity for 3-mercaptopropanoate nearly 2 orders of magnitude greater than those for cysteine
-
-
-
additional information
?
-
3-mercaptopropanoate is preferred over cysteine. No substrate: cysteamine
-
-
-
additional information
?
-
enzyme shows only minor cysteine dioxygenase activity
-
-
-
additional information
?
-
-
enzyme shows only minor cysteine dioxygenase activity
-
-
-
additional information
?
-
3-mercaptopropanoate is preferred over cysteine. No substrate: cysteamine
-
-
-
additional information
?
-
Cupriavidus necator H16 / ATCC 23440 / NCIB 10442 / S-10-1
-
3-mercaptopropanoate is preferred over cysteine. No substrate: cysteamine
-
-
-
additional information
?
-
enzyme shows only minor cysteine dioxygenase activity
-
-
-
additional information
?
-
recombinant 3MDO is able to oxidize both cysteine and 3-mercaptopropionic acid in vitro, with a marked preference for 3-mercaptopropionic acid. Substrate binding to the ferrous iron is through the thiol but each substrate may adopt different coordination geometries
-
-
-
additional information
?
-
-
recombinant 3MDO is able to oxidize both cysteine and 3-mercaptopropionic acid in vitro, with a marked preference for 3-mercaptopropionic acid. Substrate binding to the ferrous iron is through the thiol but each substrate may adopt different coordination geometries
-
-
-
additional information
?
-
recombinant 3MDO is able to oxidize both cysteine and 3-mercaptopropionic acid in vitro, with a marked preference for 3-mercaptopropionic acid. Substrate binding to the ferrous iron is through the thiol but each substrate may adopt different coordination geometries
-
-
-
additional information
?
-
no substrates: cysteine and cysteamine
-
-
-
additional information
?
-
-
no substrates: cysteine and cysteamine
-
-
-
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Iron
Iron
-
iron content is 0.8 mol of iron per mol of MDO. Addition of NO to 3-mercaptopropanoate-bound enzyme quantitatively yields an iron-nitrosyl species with EPR features consistent with a mononuclear (FeNO)7 site
Iron
active site iron is coordinated by 3 histidines and 3 water molecules
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
EDTA
0.05 mM, 80% of initial activity, 0.1 mM, 61% of initial activity
ethylxanthate
0.002 mM, 110% of initial activity, 0.004 mM, 89% of initial activity
additional information
addition of cysteine results in a minor decrease of activity
-
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
ethylxanthate
0.002 mM, 110% of initial activity, 0.004 mM, 89% of initial activity
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.5
(2R)-2-sulfanylbutanedioic acid
mutant Q62R, pH not specified in the publication, temperature not specified in the publication
0.009
3-Mercaptopropanoate
-
mutant Y159F, 37°C, pH not specified in the publication
0.012
3-Mercaptopropanoate
-
mutant H157N, 37°C, pH not specified in the publication
0.013
3-Mercaptopropanoate
-
wild-type, 20°C, pH not specified in the publication
0.7
3-Mercaptopropanoate
pH not specified in the publication, temperature not specified in the publication
0.8
3-Mercaptopropanoate
wild-type, pH not specified in the publication, temperature not specified in the publication
0.9
3-Mercaptopropanoate
mutant G95C, PIPES buffer pH 6.5, 37°C
0.9
3-Mercaptopropanoate
mutant Q62R, pH not specified in the publication, temperature not specified in the publication
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.02
(2R)-2-sulfanylbutanedioic acid
mutant Q62R, pH not specified in the publication, temperature not specified in the publication
0.007
3-Mercaptopropanoate
mutant G95C, PIPES buffer pH 6.5, 37°C
0.081
3-Mercaptopropanoate
-
mutant Y159F, 37°C, pH not specified in the publication
0.092
3-Mercaptopropanoate
-
mutant H157N, 37°C, pH not specified in the publication
0.11
3-Mercaptopropanoate
wild-type, acetate buffer pH 4.7, 37°C
0.22
3-Mercaptopropanoate
wild-type, acetate buffer pH 5.5, 37°C
0.28
3-Mercaptopropanoate
wild-type, pH not specified in the publication, temperature not specified in the publication
0.35
3-Mercaptopropanoate
pH not specified in the publication, temperature not specified in the publication
0.45
3-Mercaptopropanoate
-
wild-type, 20°C, pH not specified in the publication
0.67
3-Mercaptopropanoate
mutant Q62R, pH not specified in the publication, temperature not specified in the publication
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.04
(2R)-2-sulfanylbutanedioic acid
mutant Q62R, pH not specified in the publication, temperature not specified in the publication
0.03
3-Mercaptopropanoate
wild-type, acetate buffer pH 4.7, 37°C
0.05
3-Mercaptopropanoate
wild-type, acetate buffer pH 5.5, 37°C
0.35
3-Mercaptopropanoate
wild-type, pH not specified in the publication, temperature not specified in the publication
0.5
3-Mercaptopropanoate
pH not specified in the publication, temperature not specified in the publication
0.74
3-Mercaptopropanoate
mutant Q62R, pH not specified in the publication, temperature not specified in the publication
7.8
3-Mercaptopropanoate
-
mutant H157N, 37°C, pH not specified in the publication
9
3-Mercaptopropanoate
-
mutant Y159F, 37°C, pH not specified in the publication
27
3-Mercaptopropanoate
-
wild-type, 20°C, pH not specified in the publication
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
the monoprotonated ES complexes with 3-mercaptopropionic acid and cysteine have different pKs. At higher pH, kcat decreases sigmoidally with a similar pK regardless of substrate. Loss of reactivity at high pH is attributed to deprotonation of tyrosine 159 and its influence on dioxygen binding
additional information
-
the monoprotonated ES complexes with 3-mercaptopropionic acid and cysteine have different pKs. At higher pH, kcat decreases sigmoidally with a similar pK regardless of substrate. Loss of reactivity at high pH is attributed to deprotonation of tyrosine 159 and its influence on dioxygen binding
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
physiological function
metabolism
active-site cluster models and comparison of CDO, EC 1.13.11.20, and 3-mercaptopropionate dioxygenase MDO. The enzymes have different iron(III)-superoxo-bound structures due to differences in ligand coordination. The differences in the second-coordination sphere and particularly the position of a positively charged Arg residue result in changes in substrate positioning, mobility and enzymatic turnover. For both enzymes, the second oxygen atom transfer has the highest barriers with magnitudes of 14.2 and 15.8 kcal/mol, respectively. Both enzymes have an open-shell singlet-spin iron(III)-superoxo reactant with the substrate bound as a bidentate ligand in the equatorial plane, in MDO the quintet spin state is within 1 kcal/mol. MDO binds the substrate through two anionic bonds of the substrate carboxylate and thiolate groups, and a strong hydrogen-bonding interaction of a Tyr residue towards the superoxo group in MDO is found
metabolism
-
active-site cluster models and comparison of CDO, EC 1.13.11.20, and 3-mercaptopropionate dioxygenase MDO. The enzymes have different iron(III)-superoxo-bound structures due to differences in ligand coordination. The differences in the second-coordination sphere and particularly the position of a positively charged Arg residue result in changes in substrate positioning, mobility and enzymatic turnover. For both enzymes, the second oxygen atom transfer has the highest barriers with magnitudes of 14.2 and 15.8 kcal/mol, respectively. Both enzymes have an open-shell singlet-spin iron(III)-superoxo reactant with the substrate bound as a bidentate ligand in the equatorial plane, in MDO the quintet spin state is within 1 kcal/mol. MDO binds the substrate through two anionic bonds of the substrate carboxylate and thiolate groups, and a strong hydrogen-bonding interaction of a Tyr residue towards the superoxo group in MDO is found
-
physiological function
-
a network of hydrogen bonds connects residues H157-Y159 and Fe-bound ligands within the enzymatic Fe site. The hydroxyl group of Y159 hydrogen bonds to Fe-bound NO and, by extension, Fe-bound oxygen during native catalysis. This interaction alters both the NO binding affinity and rhombicity of the 3-mercaptopropanoate-bound iron-nitrosyl site
physiological function
mutants are impaired in growth on 3,3-thiodipropionic acid
physiological function
the monoprotonated ES complexes with 3-mercaptopropionic acid and cysteine have different pKs. At higher pH, kcat decreases sigmoidally with a similar pK regardless of substrate. Loss of reactivity at high pH is attributed to deprotonation of tyrosine 159 and its influence on dioxygen binding. A mechanism model shows deprotonation of tyrosine 159 both blocks oxygen binding and concomitantly promotes cystine formation
physiological function
-
the pL-dependent activity of MDO can be rationalized assuming a diprotic enzyme model in which three ionic forms of the enzyme are present [cationic, E(z+1), neutral, Ez, and anionic, E(z-1)]. The activities observed for substrates 3-mercaptopropanoate and cysteine appear to be dominated by electrostatic interactions within the enzymatic active site
physiological function
-
the monoprotonated ES complexes with 3-mercaptopropionic acid and cysteine have different pKs. At higher pH, kcat decreases sigmoidally with a similar pK regardless of substrate. Loss of reactivity at high pH is attributed to deprotonation of tyrosine 159 and its influence on dioxygen binding. A mechanism model shows deprotonation of tyrosine 159 both blocks oxygen binding and concomitantly promotes cystine formation
-
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). 3MDO_PSEAE
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
201
0
22548
Swiss-Prot
-
Q0K029_CUPNH
Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337)
205
0
22587
TrEMBL
-
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
dimer
Cupriavidus necator H16 / ATCC 23440 / NCIB 10442 / S-10-1
-
2 * 22580, calculated from sequence
-
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POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
no modification
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
comparison with mammalian cysteine dioxygenase. The overall active site geometry is conserved but the different substrate specificity may be related to replacement of an arginine by a glutamine in the active site
structural comparison with cysteine dioxygenase homologs that conserve an active site Gln residue, cf. EC 1.13.11.20
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Y159F
-
3fold reduction in kcat/Km value. Fe coordination of cysteine is switched from thiolate only to bidentate (thiolate/amine) for the variant
G95C
variant is able to form a cysteine-tyrosine crosslink homologous to that found in mammalian cysteine dioxygenases. Activity of this variant is severely impaired
Q62R
variant retains both 3-mercaptopropanoate and cysteine dioxygenase activity
G95C
-
variant is able to form a cysteine-tyrosine crosslink homologous to that found in mammalian cysteine dioxygenases. Activity of this variant is severely impaired
-
Q62R
-
variant retains both 3-mercaptopropanoate and cysteine dioxygenase activity
-
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
low expression under standard growth conditions
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Wenning, L.; Stoeveken, N.; Wuebbeler, J.H.; Steinbuechel, A.
Substrate and cofactor range differences of two cysteine dioxygenases from Ralstonia eutropha H16
Appl. Environ. Microbiol.
82
910-921
2015
Cupriavidus necator (Q0K029), Cupriavidus necator DSM 428 (Q0K029)
brenda
Driggers, C.M.; Hartman, S.J.; Karplus, P.A.
Structures of Arg- and Gln-type bacterial cysteine dioxygenase homologs
Protein Sci.
24
154-161
2015
Variovorax paradoxus (B9U5L8)
brenda
Crowell, J.K.; Sardar, S.; Hossain, M.S.; Foss, F.W.; Pierce, B.S.
Non-chemical proton-dependent steps prior to O2-activation limit Azotobacter vinelandii 3-mercaptopropionic acid dioxygenase (MDO) catalysis
Arch. Biochem. Biophys.
604
86-94
2016
Azotobacter vinelandii
brenda
Pierce, B.S.; Subedi, B.P.; Sardar, S.; Crowell, J.K.
The ''Gln-Type'' thiol dioxygenase from Azotobacter vinelandii is a 3-mercaptopropionic acid dioxygenase
Biochemistry
54
7477-7490
2015
Azotobacter vinelandii
brenda
Fellner, M.; Aloi, S.; Tchesnokov, E.P.; Wilbanks, S.M.; Jameson, G.N.
Substrate and pH-dependent kinetic profile of 3-mercaptopropionate dioxygenase from Pseudomonas aeruginosa
Biochemistry
55
1362-1371
2016
Pseudomonas aeruginosa (Q9I0N5), Pseudomonas aeruginosa, Pseudomonas aeruginosa DSM 22644 (Q9I0N5)
brenda
Aloi, S.; Davies, C.G.; Karplus, P.A.; Wilbanks, S.M.; Jameson, G.N.L.
Substrate specificity in thiol dioxygenases
Biochemistry
58
2398-2407
2019
Cupriavidus necator (Q9I0N5), Cupriavidus necator, Pseudomonas aeruginosa (Q9I0N5), Pseudomonas aeruginosa DSM 22644 (Q9I0N5), Cupriavidus necator JMP 134 (Q9I0N5)
brenda
Sardar, S.; Weitz, A.; Hendrich, M.P.; Pierce, B.S.
Outer-sphere tyrosine 159 within the 3-mercaptopropionic acid dioxygenase S-H-Y motif gates substrate-coordination denticity at the non-heme iron active site
Biochemistry
58
5135-5150
2019
Azotobacter vinelandii
brenda
Bruland, N.; Wuebbeler, J.H.; Steinbuechel, A.
3-Mercaptopropionate dioxygenase, a cysteine dioxygenase homologue, catalyzes the initial step of 3-mercaptopropionate catabolism in the 3,3-thiodipropionic acid-degrading bacterium variovorax paradoxus
J. Biol. Chem.
284
660-672
2009
Variovorax paradoxus (B9U5L8), Variovorax paradoxus
brenda
Tchesnokov, E.P.; Fellner, M.; Siakkou, E.; Kleffmann, T.; Martin, L.W.; Aloi, S.; Lamont, I.L.; Wilbanks, S.M.; Jameson, G.N.
The cysteine dioxygenase homologue from Pseudomonas aeruginosa is a 3-mercaptopropionate dioxygenase
J. Biol. Chem.
290
24424-24437
2015
Pseudomonas aeruginosa (Q9I0N5), Pseudomonas aeruginosa, Pseudomonas aeruginosa DSM 22644 (Q9I0N5)
brenda
Yeh, C.G.; Pierides, C.; Jameson, G.N.L.; de Visser, S.P.
Structure and functional differences of cysteine and 3-mercaptopropionate dioxygenases A computational study
Chemistry
27
13793-13806
2021
Pseudomonas aeruginosa (Q9I0N5), Pseudomonas aeruginosa DSM 22644 (Q9I0N5)
brenda
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Release 2023.1 (January 2023)
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