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Information on EC 4.1.2.53 - 2-keto-3-deoxy-L-rhamnonate aldolase
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EC Tree
4.1.2.53 2-keto-3-deoxy-L-rhamnonate aldolaseIUBMB 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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Word Map
- 4.1.2.53
-
hyperthermophilic
-
pyrococcus
-
furiosus
-
hyperthermostable
- vinelandii
-
aldolases
-
1-dehydrogenase
-
autoproteolysis
-
azotobacter
- stipitis
- l-lactaldehyde
-
dehydratase
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Synonyms
l-2-keto-3-deoxyrhamnonate aldolase, 2-keto-3-deoxy-l-rhamnonate aldolase, l-kdr aldolase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
AN9425
L-2-keto-3-deoxyrhamnonate aldolase
L-KDR aldolase
LRA4
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2-dehydro-3-deoxy-L-rhamnonate = pyruvate + (S)-lactaldehyde
-
-
-
-
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PATHWAY SOURCE
PATHWAYS
BRENDA
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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].
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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
2-oxobutanoate + benzyl (2R)-2-formylpyrrolidine-1-carboxylate
?
50% conversion
-
-
?
2-oxobutanoate + benzyl (2S)-2-formylpyrrolidine-1-carboxylate
?
71% conversion
-
-
?
2-oxobutanoate + benzyl [(2R)-1-oxopropan-2-yl]carbamate
?
73-88% conversion
-
-
?
2-oxobutanoate + benzyl [(2S)-1-oxopropan-2-yl]carbamate
?
70-94% conversion
-
-
?
2-oxooctanoate + benzyl [(2R)-1-oxopropan-2-yl]carbamate
?
40% conversion
-
-
?
2-oxooctanoate + benzyl [(2S)-1-oxopropan-2-yl]carbamate
?
30% conversion
-
-
?
2-oxopentanoate + benzyl (2R)-2-formylpyrrolidine-1-carboxylate
?
40% conversion
-
-
?
2-oxopentanoate + benzyl (2S)-2-formylpyrrolidine-1-carboxylate
?
45% conversion
-
-
?
2-oxopentanoate + benzyl [(2R)-1-oxopropan-2-yl]carbamate
?
95% conversion
-
-
?
2-oxopentanoate + benzyl [(2S)-1-oxopropan-2-yl]carbamate
?
91% conversion
-
-
?
4-(methylsulfanyl)-2-oxobutanoate + benzyl [(2R)-1-oxopropan-2-yl]carbamate
?
91% conversion
-
-
?
4-(methylsulfanyl)-2-oxobutanoate + benzyl [(2S)-1-oxopropan-2-yl]carbamate
?
75% conversion
-
-
?
4-methyl-2-oxopentanoate + benzyl [(2R)-1-oxopropan-2-yl]carbamate
?
52% conversion
-
-
?
4-methyl-2-oxopentanoate + benzyl [(2S)-1-oxopropan-2-yl]carbamate
?
50% conversion
-
-
?
benzyl (1-oxobutan-2-yl)carbamate + 2-oxopropanoate
(3S)-4-[[(benzyloxy)carbonyl]amino]-3-hydroxyhexanoate + (3R)-4-[[(benzyloxy)carbonyl]amino]-3-hydroxyhexanoate
-
-
-
?
benzyl (1-oxopropan-2-yl)carbamate + 2-oxopropanoate
(3S)-4-[[(benzyloxy)carbonyl]amino]-3-hydroxypentanoate + (3R)-4-[[(benzyloxy)carbonyl]amino]-3-hydroxypentanoate
-
-
-
?
benzyl (2-oxoethyl)carbamate + 2-oxopropanoate
(3S)-4-[[(benzyloxy)carbonyl]amino]-3-hydroxybutanoate + (3R)-4-[[(benzyloxy)carbonyl]amino]-3-hydroxybutanoate
-
-
-
?
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
-
-
-
?
benzyl (3-oxopropyl)carbamate + 2-oxopropanoate
(3R)-5-[[(benzyloxy)carbonyl]amino]-3-hydroxypentanoate + (3S)-5-[[(benzyloxy)carbonyl]amino]-3-hydroxypentanoate
-
-
-
?
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
-
-
-
?
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
-
-
-
?
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
-
-
-
?
pyruvate + (S)-lactaldehyde
2-dehydro-3-deoxy-L-rhamnonate
-
-
-
?
2-dehydro-3-deoxy-L-mannonate
?
-
6.7% activity compared to 2-dehydro-3-deoxy-L-rhamnonate
-
-
?
2-dehydro-3-deoxy-L-mannonate
?
-
13.3% activity compared to 2-dehydro-3-deoxy-L-rhamnonate
-
-
?
2-dehydro-3-deoxy-L-rhamnonate
pyruvate + (L)-lactaldehyde
-
-
-
-
?
2-dehydro-3-deoxy-L-rhamnonate
pyruvate + (R)-lactaldehyde
-
preferred substrate
-
-
?
2-dehydro-3-deoxy-L-rhamnonate
pyruvate + (R)-lactaldehyde
2-dehydro-3-deoxy-L-rhamnonate i.e. 3,6-dideoxy-L-erythro-hex-2-ulosonate
-
-
?
2-dehydro-3-deoxy-L-rhamnonate
pyruvate + (R)-lactaldehyde
-
-
-
-
?
2-dehydro-3-deoxy-L-rhamnonate
pyruvate + (R)-lactaldehyde
-
preferred substrate
-
-
?
2-dehydro-3-deoxy-L-rhamnonate
pyruvate + (R)-lactaldehyde
-
-
-
-
?
2-dehydro-3-deoxy-L-rhamnonate
pyruvate + (R)-lactaldehyde
-
-
-
-
?
2-dehydro-3-deoxy-L-xylonate
?
-
7.6% activity compared to 2-dehydro-3-deoxy-L-rhamnonate
-
-
?
2-dehydro-3-deoxy-L-xylonate
?
-
54.7% activity compared to 2-dehydro-3-deoxy-L-rhamnonate
-
-
?
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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
pyruvate + (S)-lactaldehyde
2-dehydro-3-deoxy-L-rhamnonate
-
-
-
?
2-dehydro-3-deoxy-L-rhamnonate
pyruvate + (L)-lactaldehyde
-
-
-
-
?
2-dehydro-3-deoxy-L-rhamnonate
pyruvate + (R)-lactaldehyde
-
preferred substrate
-
-
?
2-dehydro-3-deoxy-L-rhamnonate
pyruvate + (R)-lactaldehyde
-
-
-
-
?
2-dehydro-3-deoxy-L-rhamnonate
pyruvate + (R)-lactaldehyde
-
preferred substrate
-
-
?
2-dehydro-3-deoxy-L-rhamnonate
pyruvate + (R)-lactaldehyde
-
-
-
-
?
2-dehydro-3-deoxy-L-rhamnonate
pyruvate + (R)-lactaldehyde
-
-
-
-
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Ni2+
additional information
Mg2+
-
more than 250% activity in the presence of Mg2+, 5 mM MgCl2 used in assay conditions
Ni2+
metal-dependent enzyme, Ni2+ activates. Compared to Mg2+ the Ni2+-activated enzyme has a higher turnover, resulting in an elevated substrate specificity constant
additional information
-
not stimulated by Mg2+, Co2+, Ni2+, Zn2+, Fe2+, Cu2+, and Ca2+
additional information
-
not stimulated by Zn2+, Fe2+, Cu2+, and Ca2+
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.915
2-dehydro-3-deoxy-L-rhamnonate
-
in 50 mM sodium phosphate (pH 7.0), 5 mM Mn2+, temperature not specified in the publication
1.37
2-dehydro-3-deoxy-L-rhamnonate
-
in 50 mM sodium phosphate (pH 7.0), 5 mM Mn2+, temperature not specified in the publication
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
49.3
2-dehydro-3-deoxy-L-rhamnonate
-
in 50 mM sodium phosphate (pH 7.0), 5 mM Mn2+, temperature not specified in the publication
54.7
2-dehydro-3-deoxy-L-rhamnonate
-
in 50 mM sodium phosphate (pH 7.0), 5 mM Mn2+, temperature not specified in the publication
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
36.2
2-dehydro-3-deoxy-L-rhamnonate
-
in 50 mM sodium phosphate (pH 7.0), 5 mM Mn2+, temperature not specified in the publication
60.2
2-dehydro-3-deoxy-L-rhamnonate
-
in 50 mM sodium phosphate (pH 7.0), 5 mM Mn2+, temperature not specified in the publication
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
physiological function
an AN9425 deletion mutant shows pseudo-wild type growth on L-rhamnose MM agar plates. Upon growth on 1% L-rhamnose as sole carbon source, the deletion mutant shows a reduced colour intensity of the sporulation zone
physiological function
-
an AN9425 deletion mutant shows pseudo-wild type growth on L-rhamnose MM agar plates. Upon growth on 1% L-rhamnose as sole carbon source, the deletion mutant shows a reduced colour intensity of the sporulation zone
-
Show AA Sequence and Transmembrane Helices (745 entries)
Please use the AA Sequence and Transmembrane Helices Search for a specific query.
Please use the AA Sequence and Transmembrane Helices Search for a specific query.
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
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
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Ni-NTA column chromatography
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in a L-rhamnose-defective mutant of Escherichia coli
expressed in Escherichia coli DH5alpha cells
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
expression is induced on L-rhamnose via the transcriptional activator RhaR
expression is induced on L-rhamnose via the transcriptional activator RhaR
expression is induced on L-rhamnose via the transcriptional activator RhaR
-
-
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Twerdochlib, A.L.; Pedrosa, F.O.; Funayama, S.; Rigo, L.U.
L-Rhamnose metabolism in Pichia stipitis and Debaryomyces polymorphus
Can. J. Microbiol.
40
896-902
1994
Schwanniomyces polymorphus, Scheffersomyces stipitis, Scheffersomyces stipitis NRC 5568, Schwanniomyces polymorphus 1747
-
brenda
Watanabe, S.; Saimura, M.; Makino, K.
Eukaryotic and bacterial gene clusters related to an alternative pathway of non-phosphorylated L-rhamnose metabolism
J. Biol. Chem.
283
20372-20382
2008
Azotobacter vinelandii, Scheffersomyces stipitis
brenda
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)
brenda
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)
brenda
Watanabe, S.; Makino, K.
Novel modified version of nonphosphorylated sugar metabolism-an alternative L-rhamnose pathway of Sphingomonas sp
FEBS J.
276
1554-1567
2009
Azotobacter vinelandii, Scheffersomyces stipitis
brenda
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)
-
brenda
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)
brenda
MacCabe,A.; Sanmartin, G.; Orejas, M.
Identification of the genes encoding the catalytic steps corresponding to LRA4 (l-2-keto-3-deoxyrhamnonate aldolase) and L-lactaldehyde dehydrogenase in Aspergillus nidulans evidence for involvement of the loci AN9425/lraD and AN0544/aldA in the l-rhamnose catabolic pathway
Environ. Microbiol.
2021
2420-2432
2021
Aspergillus nidulans (A0A1U8QYE1), Aspergillus nidulans ATCC 38163 (A0A1U8QYE1)
brenda
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Release 2023.1 (January 2023)
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