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Information on EC 4.2.1.117 - 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) and Organism(s) Shewanella oneidensis and UniProt Accession Q8EJW3

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EC Tree
     4 Lyases
         4.2 Carbon-oxygen lyases
             4.2.1 Hydro-lyases
                4.2.1.117 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
IUBMB Comments
Catalyses the dehydration of (2S,3S)-2-methylcitrate, forming the trans isomer of 2-methyl-aconitate (unlike EC 4.2.1.79, which forms only the cis isomer). Part of a propionate degradation pathway. The enzyme from Shewanella oneidensis can also accept citrate and cis-aconitate, but activity with (2S,3S)-2-methylcitrate was approximately 2.5-fold higher. 2-methylisocitrate and isocitrate were not substrates . An iron-sulfur protein.
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Shewanella oneidensis
UNIPROT: Q8EJW3
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The taxonomic range for the selected organisms is: Shewanella oneidensis
The expected taxonomic range for this enzyme is: Shewanella oneidensis
Synonyms
AcnD, SO_0343, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
PATHWAY SOURCE
PATHWAYS
-
-
SYSTEMATIC NAME
IUBMB Comments
(2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate hydro-lyase (2-methyl-trans-aconitate forming)
Catalyses the dehydration of (2S,3S)-2-methylcitrate, forming the trans isomer of 2-methyl-aconitate (unlike EC 4.2.1.79, which forms only the cis isomer). Part of a propionate degradation pathway. The enzyme from Shewanella oneidensis can also accept citrate and cis-aconitate, but activity with (2S,3S)-2-methylcitrate was approximately 2.5-fold higher. 2-methylisocitrate and isocitrate were not substrates [1]. An iron-sulfur protein.
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(2S,3S)-2-methylcitrate
2-methyl-trans-aconitate + H2O
show the reaction diagram
-
-
-
?
2-methylcitrate
2-methyl-cis-aconitate + H2O
show the reaction diagram
-
-
-
-
?
cis-aconitate + H2O
citrate
show the reaction diagram
-
-
-
-
?
citrate
cis-aconitate + H2O
show the reaction diagram
-
-
-
-
r
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
(2S,3S)-2-methylcitrate
2-methyl-trans-aconitate + H2O
show the reaction diagram
-
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
4Fe-4S-center
-
enzyme requires an intact Fe/S cluster for activity
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Iron
-
enzyme requires an intact Fe/S cluster for activity
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
EDTA
-
complete loss of activity
ferricyanide
-
complete loss of activity
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
2.9
-
pH 8.0, 37°C, substrate citrate
5
-
pH 8.0, 37°C, substrate cis-aconitate
7.8
-
pH 8.0, 37°C, substrate 2-methylcitrate
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
SwissProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
physiological function
the two genes acnD and prpF, encoding 2-methylcitrate dehydratase (AcnD, EC 4.2.1.117) and 2-methyl-aconitate isomerase (SoPrpF, EC 5.3.3.-) from Shewanella oneidensis together can replace gene prpD from Salmonella enterica, which encodes 2-methylcitrate dehydratase, PrpD /EC 4.2.1.79. SoAcnD and SePrpD synthesize different methylaconitate isomers. The SoPrpF protein isomerizes the product of the AcnD reaction into the PrpD product (2-MCA), known substrate of the housekeeping aconitase. It is likely that 4-methylaconitate is the product of the AcnD enzyme. PrpF (SoPrpF) protein isomerizes the product of the SoAcnD dehydratase (putatively 4-methyl-cis-aconitate (4-MCA)) to 2-methyl-cis-aconitate (2-MCA). Thus,the role of SoPrpF in the 2-methylcitrate cycle (2-MCC) is to change the stereochemistry of the SoAcnD reaction product. AcnD and PrpF activities are necessary and sufficient to compensate for the lack of PrpD during growth with propionate of the strain of Salmonella enterica. 2-Methylcitrate is dehydrated by AcnD to 4-methyl-cis-aconitate, which is then isomerized to 2-methyl-cis-aconitate by PrpF, and rehydrated to 2-methylisocitrate by aconitases A and B
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
94000
-
x * 94000, SDS-PAGE and calculated
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
-
x * 94000, SDS-PAGE and calculated
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
in presence of air, activity is lost over time
-
651735
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene acnD, the sequence of prp genes is prpR-prpB-prpC-acnD-prpF, functional recombinant coexpression of the genes acnD and prpF from Shewanella oneidensis in Salmonella enterica strain DELTAprpD, recombinant expression of His-tagged enzyme from gene acnD in Escherichia coli strain BL21(DE3)
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Grimek, T.L.; Escalante-Semerena, J.C.
The acnD genes of Shewenella oneidensis and Vibrio cholerae encode a new Fe/S-dependent 2-methylcitrate dehydratase enzyme that requires prpF function in vivo
J. Bacteriol.
186
454-462
2004
Shewanella oneidensis
Manually annotated by BRENDA team
Rocco, C.J.; Wetterhorn, K.M.; Garvey, G.S.; Rayment, I.; Escalante-Semerena, J.C.
The PrpF protein of Shewanella oneidensis MR-1 catalyzes the isomerization of 2-methyl-cis-aconitate during the catabolism of propionate via the AcnD-dependent 2-methylcitric acid cycle
PLoS ONE
12
e0188130
2017
Shewanella oneidensis (Q8EJW3)
Manually annotated by BRENDA team