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Information on EC 4.1.2.53 - 2-keto-3-deoxy-L-rhamnonate aldolase and Organism(s) Escherichia coli and UniProt Accession P76469

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EC Tree
     4 Lyases
         4.1 Carbon-carbon lyases
             4.1.2 Aldehyde-lyases
                4.1.2.53 2-keto-3-deoxy-L-rhamnonate aldolase
IUBMB Comments
Requires Mg2+ for activity. The enzyme can also use 2-oxo-3-deoxy-L-mannonate, 2-oxo-3-deoxy-L-lyxonate and 4-hydroxy-2-ketoheptane-1,7-dioate (HKHD) as substrates .
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This record set is specific for:
Escherichia coli
UNIPROT: P76469
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The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Synonyms
l-2-keto-3-deoxyrhamnonate aldolase, l-kdr aldolase, 2-keto-3-deoxy-l-rhamnonate aldolase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
2-dehydro-3-deoxyrhamnonate aldolase
-
2-keto-3-deoxy acid sugar aldolase
-
KDR aldolase
-
SYSTEMATIC NAME
IUBMB Comments
2-dehydro-3-deoxy-L-rhamnonate (R)-lactaldehyde lyase (pyruvate-forming)
Requires Mg2+ for activity. The enzyme can also use 2-oxo-3-deoxy-L-mannonate, 2-oxo-3-deoxy-L-lyxonate and 4-hydroxy-2-ketoheptane-1,7-dioate (HKHD) as substrates [2].
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2-dehydro-3-deoxy-L-lyxonate
?
show the reaction diagram
-
-
-
?
2-dehydro-3-deoxy-L-mannonate
?
show the reaction diagram
-
-
-
?
2-dehydro-3-deoxy-L-rhamnonate
pyruvate + (R)-lactaldehyde
show the reaction diagram
2-dehydro-3-deoxy-L-rhamnonate i.e. 3,6-dideoxy-L-erythro-hex-2-ulosonate
-
-
?
2-oxobutanoate + benzyl (2R)-2-formylpyrrolidine-1-carboxylate
?
show the reaction diagram
50% conversion
-
-
?
2-oxobutanoate + benzyl (2S)-2-formylpyrrolidine-1-carboxylate
?
show the reaction diagram
71% conversion
-
-
?
2-oxobutanoate + benzyl [(2R)-1-oxopropan-2-yl]carbamate
?
show the reaction diagram
73-88% conversion
-
-
?
2-oxobutanoate + benzyl [(2S)-1-oxopropan-2-yl]carbamate
?
show the reaction diagram
70-94% conversion
-
-
?
2-oxooctanoate + benzyl [(2R)-1-oxopropan-2-yl]carbamate
?
show the reaction diagram
40% conversion
-
-
?
2-oxooctanoate + benzyl [(2S)-1-oxopropan-2-yl]carbamate
?
show the reaction diagram
30% conversion
-
-
?
2-oxopentanoate + benzyl (2R)-2-formylpyrrolidine-1-carboxylate
?
show the reaction diagram
40% conversion
-
-
?
2-oxopentanoate + benzyl (2S)-2-formylpyrrolidine-1-carboxylate
?
show the reaction diagram
45% conversion
-
-
?
2-oxopentanoate + benzyl [(2R)-1-oxopropan-2-yl]carbamate
?
show the reaction diagram
95% conversion
-
-
?
2-oxopentanoate + benzyl [(2S)-1-oxopropan-2-yl]carbamate
?
show the reaction diagram
91% conversion
-
-
?
4-(methylsulfanyl)-2-oxobutanoate + benzyl [(2R)-1-oxopropan-2-yl]carbamate
?
show the reaction diagram
91% conversion
-
-
?
4-(methylsulfanyl)-2-oxobutanoate + benzyl [(2S)-1-oxopropan-2-yl]carbamate
?
show the reaction diagram
75% conversion
-
-
?
4-hydroxy-2-oxoheptane-1,7-dioate
?
show the reaction diagram
-
-
-
?
4-hydroxy-2-oxohexanoate
?
show the reaction diagram
-
-
-
?
4-hydroxy-2-oxopentanoate
?
show the reaction diagram
-
-
-
?
4-methyl-2-oxopentanoate + benzyl [(2R)-1-oxopropan-2-yl]carbamate
?
show the reaction diagram
52% conversion
-
-
?
4-methyl-2-oxopentanoate + benzyl [(2S)-1-oxopropan-2-yl]carbamate
?
show the reaction diagram
50% conversion
-
-
?
benzyl (1-oxobutan-2-yl)carbamate + 2-oxopropanoate
(3S)-4-[[(benzyloxy)carbonyl]amino]-3-hydroxyhexanoate + (3R)-4-[[(benzyloxy)carbonyl]amino]-3-hydroxyhexanoate
show the reaction diagram
-
-
-
?
benzyl (1-oxopropan-2-yl)carbamate + 2-oxopropanoate
(3S)-4-[[(benzyloxy)carbonyl]amino]-3-hydroxypentanoate + (3R)-4-[[(benzyloxy)carbonyl]amino]-3-hydroxypentanoate
show the reaction diagram
-
-
-
?
benzyl (2-oxoethyl)carbamate + 2-oxopropanoate
(3S)-4-[[(benzyloxy)carbonyl]amino]-3-hydroxybutanoate + (3R)-4-[[(benzyloxy)carbonyl]amino]-3-hydroxybutanoate
show the reaction diagram
-
-
-
?
benzyl (3-methyl-1-oxobutan-2-yl)carbamate + 2-oxopropanoate
(3S)-4-[[(benzyloxy)carbonyl]amino]-3-hydroxy-5-methylhexanoate + (3R)-4-[[(benzyloxy)carbonyl]amino]-3-hydroxy-5-methylhexanoate
show the reaction diagram
-
-
-
?
benzyl (3-oxopropyl)carbamate + 2-oxopropanoate
(3R)-5-[[(benzyloxy)carbonyl]amino]-3-hydroxypentanoate + (3S)-5-[[(benzyloxy)carbonyl]amino]-3-hydroxypentanoate
show the reaction diagram
-
-
-
?
benzyl (4-methyl-1-oxopentan-2-yl)carbamate + 2-oxopropanoate
(3S)-4-[[(benzyloxy)carbonyl]amino]-3-hydroxy-6-methylheptanoate + (3R)-4-[[(benzyloxy)carbonyl]amino]-3-hydroxy-6-methylheptanoate
show the reaction diagram
-
-
-
?
benzyl 2-formylpyrrolidine-1-carboxylate + 2-oxopropanoate
(4S)-4-[1-[(benzyloxy)carbonyl]pyrrolidin-2-yl]-4-hydroxy-2-oxobutanoate + (4R)-4-[1-[(benzyloxy)carbonyl]pyrrolidin-2-yl]-4-hydroxy-2-oxobutanoate
show the reaction diagram
-
-
-
?
benzyl [(3S)-3-methyl-1-oxopentan-2-yl]carbamate + 2-oxopropanoate
(3S,5R)-4-[[(benzyloxy)carbonyl]amino]-3-hydroxy-5-methylheptanoate + (3R,5R)-4-[[(benzyloxy)carbonyl]amino]-3-hydroxy-5-methylheptanoate
show the reaction diagram
-
-
-
?
pyruvate + (S)-lactaldehyde
2-dehydro-3-deoxy-L-rhamnonate
show the reaction diagram
-
-
-
?
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
pyruvate + (S)-lactaldehyde
2-dehydro-3-deoxy-L-rhamnonate
show the reaction diagram
-
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.8
2-dehydro-3-deoxy-L-lyxonate
0.14
2-dehydro-3-deoxy-L-mannonate
0.078
2-dehydro-3-deoxy-L-rhamnonate
0.1 - 0.15
4-hydroxy-2-oxoheptane-1,7-dioate
0.05
4-hydroxy-2-oxohexanoate
pH 8.0, 25°C, 25°C, Ni2+-activated
0.1
4-hydroxy-2-oxopentanoate
pH 8.0, 25°C, 25°C, Ni2+-activated
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.3
2-dehydro-3-deoxy-L-lyxonate
0.3 - 0.4
2-dehydro-3-deoxy-L-rhamnonate
0.54 - 299
4-hydroxy-2-oxoheptane-1,7-dioate
447
4-hydroxy-2-oxohexanoate
pH 8.0, 25°C, 25°C, Ni2+-activated
396
4-hydroxy-2-oxopentanoate
pH 8.0, 25°C, 25°C, Ni2+-activated
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3.8
2-dehydro-3-deoxy-L-lyxonate
2.1
2-dehydro-3-deoxy-L-mannonate
5.1
2-dehydro-3-deoxy-L-rhamnonate
3.6 - 2700
4-hydroxy-2-oxoheptane-1,7-dioate
9900
4-hydroxy-2-oxohexanoate
pH 8.0, 25°C, 25°C, Ni2+-activated
3900
4-hydroxy-2-oxopentanoate
pH 8.0, 25°C, 25°C, Ni2+-activated
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
L216A
the mutant shows a high efficiency in the aldol additions of pyruvate
W23A/L216A
the mutant shows a high efficiency in the aldol additions of pyruvate
W23V
the mutant shows a high efficiency in the aldol additions of pyruvate
W23V/F174V/L216A
the mutant shows a high efficiency in the aldol additions of pyruvate
W23V/L216A
the mutant shows a high efficiency in the aldol additions of pyruvate
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
HiTrap column chromatography, and Superdex 200 gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli M-15[pREP-4] cells
expression in Escherichia coli BL21(DE3)
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Rea, D.; Hovington, R.; Rakus, J.F.; Gerlt, J.A.; Fueloep, V.; Bugg, T.D.; Roper, D.I.
Crystal structure and functional assignment of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12
Biochemistry
47
9955-9965
2008
Escherichia coli (P76469)
Manually annotated by BRENDA team
Rakus, J.F.; Fedorov, A.A.; Fedorov, E.V.; Glasner, M.E.; Hubbard, B.K.; Delli, J.D.; Babbitt, P.C.; Almo, S.C.; Gerlt, J.A.
Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase
Biochemistry
47
9944-9954
2008
Escherichia coli (P76469)
Manually annotated by BRENDA team
Hernandez, K.; Gomez, A.; Joglar, J.; Bujons, J.; Parella, T.; Clapes, P.
2-Keto-3-deoxy-L-rhamnonate aldolase (YfaU) as catalyst in aldol additions of pyruvate to amino aldehyde derivatives
Adv. Synth. Catal.
359
2090-2100
2017
Escherichia coli (P76469)
-
Manually annotated by BRENDA team
Hernandez, K.; Joglar, J.; Bujons, J.; Parella, T.; Clapes, P.
Nucleophile promiscuity of engineered class II pyruvate aldolase YfaU from E. coli
Angew. Chem. Int. Ed. Engl.
57
3583-3587
2018
Escherichia coli (P76469)
Manually annotated by BRENDA team