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Information on EC 4.2.1.141 - 2-dehydro-3-deoxy-D-arabinonate dehydratase
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4.2.1.141 2-dehydro-3-deoxy-D-arabinonate dehydrataseIUBMB Comments
The enzyme participates in pentose oxidation pathways that convert pentose sugars to the tricarboxylic acid cycle intermediate 2-oxoglutarate.
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The expected taxonomic range for this enzyme is: Bacteria, Archaea
Synonyms
2-keto-3-deoxyarabinoate/xylonate dehydratase, D-KDA dehydratase, KdaD, KDXD, KDXD/KDAD, saci_1939, Sso3118, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
2-keto-3-deoxyarabinoate/xylonate dehydratase
D-KDA dehydratase
KdaD
KDXD
KDXD/KDAD
saci_1939
Sso3118
2-keto-3-deoxyarabinoate/xylonate dehydratase
Sulfolobus acidocaldarius ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2-dehydro-3-deoxy-D-arabinonate = 2,5-dioxopentanoate + H2O
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-
-
-
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PATHWAY SOURCE
PATHWAYS
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SYSTEMATIC NAME
IUBMB Comments
2-dehydro-3-deoxy-D-arabinonate hydro-lyase (2,5-dioxopentanoate-forming)
The enzyme participates in pentose oxidation pathways that convert pentose sugars to the tricarboxylic acid cycle intermediate 2-oxoglutarate.
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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-dehydro-3-deoxy-D-arabinonate
2,5-dioxopentanoate + H2O
-
-
-
?
2-dehydro-3-deoxy-D-arabinonate
2,5-dioxopentanoate + H2O
key enzyme in degradation of D-arabinose
-
-
?
2-dehydro-3-deoxy-D-arabinonate
2,5-dioxopentanoate + H2O
the enzyme is involved in the conversion of D-arabinose into the tricarboxylic acid cycle intermediate 2-oxoglutarate via the pentose oxidation pathway
-
-
?
2-dehydro-3-deoxy-D-arabinonate
2,5-dioxopentanoate + H2O
the catalytic activity of the protein is investigated by performing indirect enzyme assays using arabinonate dehydratase with D-arabinonate as a substrate. A 50% decrease in the yield of 2-dehydro-3-deoxy-D-arabinonate is observed when both enzymes are co-incubated in the presence of Mg2+. Given the fact that D-arabinonate is converted to 2-oxoglutarate in D-arabinose cell-free extract, this enzyme is anticipated to be responsible for the dehydration of 2-dehydro-3-deoxy-D-arabinonate to the aldehyde 2,5-dioxopentanoate. Due to the unavailability of 2-dehydro-3-deoxy-D-arabinonate, it is not possible to show this in a direct enzyme assay. 2-Oxoglutarate is produced in an indirect assay using arabinonate dehydratase, the putative 2-dehydro-3-deoxy-D-arabinonate dehydratase and the predicted aldehyde dehydrogenase
-
-
?
2-dehydro-3-deoxy-D-arabinonate
2,5-dioxopentanoate + H2O
-
-
-
?
2-dehydro-3-deoxy-D-arabinonate
2,5-dioxopentanoate + H2O
key enzyme in degradation of D-arabinose
-
-
?
2-dehydro-3-deoxy-D-arabinonate
2,5-dioxopentanoate + H2O
the enzyme is involved in the conversion of D-arabinose into the tricarboxylic acid cycle intermediate 2-oxoglutarate via the pentose oxidation pathway
-
-
?
2-dehydro-3-deoxy-D-arabinonate
2,5-dioxopentanoate + H2O
the catalytic activity of the protein is investigated by performing indirect enzyme assays using arabinonate dehydratase with D-arabinonate as a substrate. A 50% decrease in the yield of 2-dehydro-3-deoxy-D-arabinonate is observed when both enzymes are co-incubated in the presence of Mg2+. Given the fact that D-arabinonate is converted to 2-oxoglutarate in D-arabinose cell-free extract, this enzyme is anticipated to be responsible for the dehydration of 2-dehydro-3-deoxy-D-arabinonate to the aldehyde 2,5-dioxopentanoate. Due to the unavailability of 2-dehydro-3-deoxy-D-arabinonate, it is not possible to show this in a direct enzyme assay. 2-Oxoglutarate is produced in an indirect assay using arabinonate dehydratase, the putative 2-dehydro-3-deoxy-D-arabinonate dehydratase and the predicted aldehyde dehydrogenase
-
-
?
2-dehydro-3-deoxy-D-arabinonate
2,5-dioxopentanoate + H2O
-
-
-
?
2-dehydro-3-deoxy-D-arabinonate
2,5-dioxopentanoate + H2O
Sulfolobus acidocaldarius ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
-
-
-
?
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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
2-dehydro-3-deoxy-D-arabinonate
2,5-dioxopentanoate + H2O
key enzyme in degradation of D-arabinose
-
-
?
2-dehydro-3-deoxy-D-arabinonate
2,5-dioxopentanoate + H2O
the enzyme is involved in the conversion of D-arabinose into the tricarboxylic acid cycle intermediate 2-oxoglutarate via the pentose oxidation pathway
-
-
?
2-dehydro-3-deoxy-D-arabinonate
2,5-dioxopentanoate + H2O
key enzyme in degradation of D-arabinose
-
-
?
2-dehydro-3-deoxy-D-arabinonate
2,5-dioxopentanoate + H2O
the enzyme is involved in the conversion of D-arabinose into the tricarboxylic acid cycle intermediate 2-oxoglutarate via the pentose oxidation pathway
-
-
?
2-dehydro-3-deoxy-D-arabinonate
2,5-dioxopentanoate + H2O
-
-
-
?
2-dehydro-3-deoxy-D-arabinonate
2,5-dioxopentanoate + H2O
Sulfolobus acidocaldarius ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
-
-
-
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
crystal structures of complexes of the enzyme with magnesium or calcium ions and either a substrate analog 2-oxobutyrate, or the aldehyde enzyme product 2,5-dioxopentanoate reveal the divalent metal ion in the active site is coordinated octahedrally by three conserved carboxylate residues, a water molecule, and both the carboxylate and the oxo groups of the substrate molecule
additional information
multiple sequence alignment analysis of the enzyme indicates the presence of a metal binding site consisting of Glu143, Glu145, and Asp164, which may implicate a metal dependent activity
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Sulfolobus acidocaldarius ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
-
UniProt
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
malfunction
the 2-ketoglutarate semialdehyde dehydrogenase (KGSADH, Saci_1938) seems not to be essential for growth on pentoses. The deletion mutant of the 2-keto-3-deoxyarabinoate/xylonate dehydratase (KDXD/KDAD) is no longer able to catabolize D-xylose or L-arabinose, suggesting the absence of the aldolase-dependent branch in Sulfolobus acidocaldarius
malfunction
Sulfolobus acidocaldarius ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
-
the 2-ketoglutarate semialdehyde dehydrogenase (KGSADH, Saci_1938) seems not to be essential for growth on pentoses. The deletion mutant of the 2-keto-3-deoxyarabinoate/xylonate dehydratase (KDXD/KDAD) is no longer able to catabolize D-xylose or L-arabinose, suggesting the absence of the aldolase-dependent branch in Sulfolobus acidocaldarius
-
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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). KDAD_SACS2
Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
298
0
33803
Swiss-Prot
-
KDXD_HALVD
Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2)
289
0
31862
Swiss-Prot
-
A0A7G9ZCN5_9EURY
207
0
22816
TrEMBL
-
Q88J13_PSEPK
Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)
405
0
43371
TrEMBL
-
A0A7R9N0I9_9EURY
256
0
28942
TrEMBL
-
A0A7G9Z870_9EURY
207
0
22743
TrEMBL
-
A0A7R9MY80_9EURY
256
0
28942
TrEMBL
-
A0A6J4KAL9_9CHLR
294
0
31488
TrEMBL
-
A0A7G9ZAC8_9EURY
207
0
22722
TrEMBL
-
Q4J7I6_SULAC
Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)
292
0
32872
TrEMBL
-
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
tetramer
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structures of complexes of the enzyme with magnesium or calcium ions and either a substrate analog 2-oxobutyrate, or the aldehyde enzyme product 2,5-dioxopentanoate, 2.1 A resolution
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
the deletion mutant DELTAKDXD/KDAD of the 2-keto-3-deoxyarabinoate/xylonate dehydratase is no longer able to catabolize D-xylose or L-arabinose, suggesting the absence of the aldolase-dependent branch in Sulfolobus acidocaldarius. In the DELTAKDXD/KDAD mutant, no KDXD/KDAD activity is detected on the four different carbon and energy sources, confirming the absence of an alternative pathway/enzyme for KDX/KDA conversion under these conditions in Sulfolobus acidocaldarius strain MW001
additional information
Sulfolobus acidocaldarius ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
-
the deletion mutant DELTAKDXD/KDAD of the 2-keto-3-deoxyarabinoate/xylonate dehydratase is no longer able to catabolize D-xylose or L-arabinose, suggesting the absence of the aldolase-dependent branch in Sulfolobus acidocaldarius. In the DELTAKDXD/KDAD mutant, no KDXD/KDAD activity is detected on the four different carbon and energy sources, confirming the absence of an alternative pathway/enzyme for KDX/KDA conversion under these conditions in Sulfolobus acidocaldarius strain MW001
-
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
the KDXD/KDAD activity in the wild-type MW001 and DELTAKGSADH mutant strains and the DELTAABC-SBP strain is induced to 35 mU/mg when D-xylose or L-arabinose is used as the growth substrate. In the absence of these sugars, i.e., on N-Z-amine alone and on N-Z-amine plus dextrin as the carbon and energy source, only negligible KDXD/KDAD activity is observed
the KDXD/KDAD activity in the wild-type MW001 and DELTAKGSADH mutant strains and the DELTAABC-SBP strain is induced to 35 mU/mg when D-xylose or L-arabinose is used as the growth substrate. In the absence of these sugars, i.e., on N-Z-amine alone and on N-Z-amine plus dextrin as the carbon and energy source, only negligible KDXD/KDAD activity is observed
the KDXD/KDAD activity in the wild-type MW001 and DELTAKGSADH mutant strains and the DELTAABC-SBP strain is induced to 35 mU/mg when D-xylose or L-arabinose is used as the growth substrate. In the absence of these sugars, i.e., on N-Z-amine alone and on N-Z-amine plus dextrin as the carbon and energy source, only negligible KDXD/KDAD activity is observed
Sulfolobus acidocaldarius ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
-
-
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Brouns, S.J.; Barends, T.R.; Worm, P.; Akerboom, J.; Turnbull, A.P.; Salmon, L.; van der Oost, J.
Structural insight into substrate binding and catalysis of a novel 2-keto-3-deoxy-D-arabinonate dehydratase illustrates common mechanistic features of the FAH superfamily
J. Mol. Biol.
379
357-371
2008
Saccharolobus solfataricus (Q97UA0), Saccharolobus solfataricus P2 (Q97UA0)
brenda
Brouns, S.J.; Walther, J.; Snijders, A.P.; van de Werken, H.J.; Willemen, H.L.; Worm, P.; de Vos, M.G.; Andersson, A.; Lundgren, M.; Mazon, H.F.; van den Heuvel, R.H.; Nilsson, P.; Salmon, L.; de Vos, W.M.; Wright, P.C.; Bernander, R.; van der Oost, J.
Identification of the missing links in prokaryotic pentose oxidation pathways: evidence for enzyme recruitment
J. Biol. Chem.
281
27378-27388
2006
Saccharolobus solfataricus (Q97UA0), Saccharolobus solfataricus P2 (Q97UA0)
brenda
Wagner, M.; Shen, L.; Albersmeier, A.; van der Kolk, N.; Kim, S.; Cha, J.; Bräsen, C.; Kalinowski, J.; Siebers, B.; Albers, S.
Sulfolobus acidocaldarius transports pentoses via a carbohydrate uptake transporter 2 (CUT2)-type ABC transporter and metabolizes them through the aldolase-independent Weimberg pathway
Appl. Environ. Microbiol.
84
pii: e01273-17
2018
Sulfolobus acidocaldarius (Q4J7I6), Sulfolobus acidocaldarius ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770 (Q4J7I6)
brenda
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