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Information on EC 4.2.1.25 - L-Arabinonate dehydratase for references in articles please use BRENDA:EC4.2.1.25
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EC Tree
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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Dehydratase, L-arabinonate
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L-Arabonate dehydrase
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L-Arabonate dehydratase
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L-Arabonate dehydratase
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Rleg9DRAFT_6269
gene name
Rleg9DRAFT_6269
gene name; gene name
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L-Arabinonate = 2-dehydro-3-deoxy-L-arabinonate + H2O
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L-arabinonate hydro-lyase (2-dehydro-3-deoxy-L-arabinonate-forming)
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L-Arabinonate
2-Dehydro-3-deoxy-L-arabinonate
L-Arabinonate
2-Dehydro-3-deoxy-L-arabinonate
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L-Arabinonate
2-Dehydro-3-deoxy-L-arabinonate
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L-Arabinonate
2-Dehydro-3-deoxy-L-arabinonate
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L-Arabinonate
2-Dehydro-3-deoxy-L-arabinonate
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L-Arabinonate
2-Dehydro-3-deoxy-L-arabinonate
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L-Arabinonate
2-Dehydro-3-deoxy-L-arabinonate
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L-Arabinonate
2-Dehydro-3-deoxy-L-arabinonate
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L-Arabinonate
2-Dehydro-3-deoxy-L-arabinonate
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L-Arabinonate
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L-Arabinonate
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metabolism of L-arabinose
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L-Arabinonate
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metabolism of L-arabinose
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L-Arabinonate
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induction with arabinose
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L-Arabinonate
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L-Arabinonate
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L-Arabinonate
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L-Arabinonate
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L-Arabinonate
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L-Arabinonate
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metabolism of L-arabinose
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L-Arabinonate
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metabolism of L-arabinose
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L-Arabinonate
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induction with arabinose
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L-Arabinonate
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L-Arabinonate
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L-Arabinonate
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L-Arabinonate
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[2Fe-2S]-center
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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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Iron
the enzyme contains a [4Fe-4S]2+ cluster
Mg2+
optimal concentration: 1-10 mM
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brenda
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MNF300
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UniProt
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MNF300
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NGR234
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NGR234
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ATCC 29145
UniProt
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UniProt
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KT260159
GenBank
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metabolism
KT260159
the enzyme is involved in a nonphosphorylative oxidation pathway of pentose sugars
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62000
2 * 62000, SDS-PAGE
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dimer
2 * 62000, SDS-PAGE
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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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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
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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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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
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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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expression in Escherichia coli
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heterologously expressed in Escherichia coli
KT260159
mutant enzymes C47A, C56A, C124A, C197A, and C441A overexpressed in Escherichia coli cells as a His6-tagged enzymes
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Pedrosa, F.O.; Zancan, G.T.
L-Arabinose metabolism in Rhizobium japonicum
J. Bacteriol.
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336-338
1974
Bradyrhizobium japonicum
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Novick, N.J.; Tyler, M.E.
L-Arabinose metabolism in Azospirillum brasiliense
J. Bacteriol.
149
364-367
1982
Azospirillum brasilense
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Schimz, K.L.; Kurz, G.
Regulation of L-arabinose metabolism in Pseudomonas fluorescens
Biochem. Soc. Trans.
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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.
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2733-2742
1986
Rhizobium leguminosarum, Rhizobium leguminosarum MNF300, Rhizobium sp., Rhizobium sp. NGR234
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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, Azospirillum brasilense (Q1JUQ1)
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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.
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1919-1927
2017
Rhizobium leguminosarum bv. trifolii (I9XDU6), Rhizobium leguminosarum bv. trifolii, Rhizobium leguminosarum bv. trifolii WSM597 (I9XDU6)
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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
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604-608
2016
Rhizobium leguminosarum bv. trifolii (KT260159), Rhizobium leguminosarum bv. trifolii
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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)
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4.2.1.25 L-Arabinonate dehydratase
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