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Information on EC 4.2.1.25 - L-Arabinonate dehydratase
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4.2.1.25 L-Arabinonate dehydrataseSpecify your search results
Word Map
- 4.2.1.25
- trifolii
- leguminosarum
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rhizobium
- pentose
- d-xylonate
- tetramer
- crescentus
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caulobacter
The enzyme appears in viruses and cellular organisms
Synonyms
Dehydratase, L-arabinonate, L-Arabonate dehydrase, L-Arabonate dehydratase, RlArDHT, Rleg9DRAFT_6269, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
Dehydratase, L-arabinonate
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L-Arabonate dehydrase
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L-Arabonate dehydratase
Rleg9DRAFT_6269
L-Arabonate dehydratase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
L-Arabinonate = 2-dehydro-3-deoxy-L-arabinonate + H2O
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
elimination
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PATHWAY SOURCE
PATHWAYS
BRENDA
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SYSTEMATIC NAME
IUBMB Comments
L-arabinonate hydro-lyase (2-dehydro-3-deoxy-L-arabinonate-forming)
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CAS REGISTRY NUMBER
COMMENTARY
9024-30-0
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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
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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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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
[2Fe-2S]-center
presence of a planar [2Fe-2S] cluster in the N-terminal domain, where Fe1 is tetrahedrally coordinated by two bridging sulfide ions and two cysteines and Fe2 is three-coordinated by two bridging sulfides and one cysteine (Cys200)
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Dehydration
Crystallization and X-ray diffraction analysis of an L-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii and a D-xylonate dehydratase from Caulobacter crescentus.
Gaucher Disease
Immunological cell type characterization and Th1-Th17 cytokine production in a mouse model of Gaucher disease.
Lysosomal Storage Diseases
Immunological cell type characterization and Th1-Th17 cytokine production in a mouse model of Gaucher disease.
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SPECIFIC ACTIVITY [µmol/min/mg]
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
KT260159
the enzyme is involved in a nonphosphorylative oxidation pathway of pentose sugars
Show AA Sequence and Transmembrane Helices (715 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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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
?
x * 63738, calculated fro msequence, x * 64000, SDS-PAGE
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x * 63738, calculated fro msequence, x * 64000, SDS-PAGE
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging-drop vapour-diffusion method at 20°C. Crystals of RlArDHT that diffract to 2.4 A resolution are obtained using sodium formate as a precipitating agent. They belong to space group P21, with unit-cell parameters a = 106.07, b = 208.61, c = 147.09 A, beta = 90.43°
KT260159
the active site contains a catalytically important [2Fe-2S] cluster and Mg2+ ion and is buried between two domains, and at the dimer interface. The active site Lys129 is carbamylated. Ser480 and Thr482 are essential residues for catalysis, and the S480A mutant structure shows an open conformation in which the active site is more accessible for the substrate. The alkoxide ion form of the Ser480 side chain may function as a base and the [2Fe-2S] cluster may function as a Lewis acid in the elimination reaction
to 2.4 A resolution, space group P21, with unit-cell parameters a = 106.07, b = 208.61, c = 147.09 A , beta = 90.43°
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C124A
non-colored inactive mutant enzyme, the UV visible absorption spectrum contained no characteristic element of [4Fe-4S]2+
C197A
non-colored inactive mutant enzyme, the UV visible absorption spectrum contained no characteristic element of [4Fe-4S]2+
C441A
brown-colored mutant is significantly active and UV-visible absorption spectrum is similar to those of the wild-type enzyme
C47A
brown-colored mutant is significantly active and UV-visible absorption spectrum is similar to those of the wild-type enzyme
C56A
inactive mutant partiall shares similar behavior to the wild-type in color and UV-visible absorption spectrum
S480A
S480A
completely inactive. Upon cocrystallization with calcium arabinonate, a partially bound substrate is observed in the pocket
S480A
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completely inactive. Upon cocrystallization with calcium arabinonate, a partially bound substrate is observed in the pocket
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
mutant enzymes C47A, C56A, C124A, C197A, and C441A overexpressed in Escherichia coli cells as a His6-tagged enzymes
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Pedrosa, F.O.; Zancan, G.T.
L-Arabinose metabolism in Rhizobium japonicum
J. Bacteriol.
119
336-338
1974
Bradyrhizobium japonicum
brenda
Novick, N.J.; Tyler, M.E.
L-Arabinose metabolism in Azospirillum brasiliense
J. Bacteriol.
149
364-367
1982
Azospirillum brasilense
brenda
Schimz, K.L.; Kurz, G.
Regulation of L-arabinose metabolism in Pseudomonas fluorescens
Biochem. Soc. Trans.
3
1087-1089
1975
Pseudomonas fluorescens
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Dilworth, M.J.; Arwas, R.; McKay, I.A.; Saroso, S.; Glenn, A.R.
Pentose metabolism in Rhizobium leguminosarum MNF300 and in cowpea Rhizobium NGR234
J. Gen. Microbiol.
132
2733-2742
1986
Rhizobium leguminosarum, Rhizobium sp., Rhizobium leguminosarum MNF300, Rhizobium sp. NGR234
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brenda
Watanabe, S.; Shimada, N.; Tajima, K.; Kodaki, T.; Makino, K.
Identification and Characterization of L-Arabonate Dehydratase, L-2-Keto-3-deoxyarabonate Dehydratase, and L-Arabinolactonase Involved in an Alternative Pathway of L-Arabinose Metabolism: Novel Evolution ary Insight into Sugar Metabolism
J. Biol. Chem.
281
33521-33536
2006
Azospirillum brasilense (Q1JUQ1), Azospirillum brasilense
brenda
Rahman, M.M.; Andberg, M.; Thangaraj, S.K.; Parkkinen, T.; Penttilae, M.; Jaenis, J.; Koivula, A.; Rouvinen, J.; Hakulinen, N.
The crystal structure of a bacterial L-arabinonate dehydratase contains a [2Fe-2S] cluster
ACS Chem. Biol.
12
1919-1927
2017
Rhizobium leguminosarum bv. trifolii (I9XDU6), Rhizobium leguminosarum bv. trifolii, Rhizobium leguminosarum bv. trifolii WSM597 (I9XDU6)
brenda
Rahman, M.M.; Andberg, M.; Koivula, A.; Rouvinen, J.; Hakulinen, N.
Crystallization and X-ray diffraction analysis of an L-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii and a D-xylonate dehydratase from Caulobacter crescentus
Acta Crystallogr. Sect. F
72
604-608
2016
Rhizobium leguminosarum bv. trifolii (KT260159), Rhizobium leguminosarum bv. trifolii
brenda
Rahman, M.; Andberg, M.; Koivula, A.; Rouvinen, J.; Hakulinen, N.
Crystallization and X-ray diffraction analysis of an L-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii and a D-xylonate dehydratase from Caulobacter crescentus
Acta Crystallogr. Sect.F
72
604-608
2016
Rhizobium leguminosarum bv. trifolii (I9XDU6), Rhizobium leguminosarum bv. trifolii, Rhizobium leguminosarum bv. trifolii WSM597 (I9XDU6)
brenda
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