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Information on EC 4.2.1.25 - L-Arabinonate dehydratase

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EC Tree
     4 Lyases
         4.2 Carbon-oxygen lyases
             4.2.1 Hydro-lyases
                4.2.1.25 L-Arabinonate dehydratase
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UNIPROT: I9XDU6 not found.
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Word Map
The expected taxonomic range for this enzyme is: Bacteria, Archaea
Synonyms
l-arabinonate dehydratase, l-arabonate dehydratase, rlardht, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Dehydratase, L-arabinonate
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L-Arabonate dehydrase
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L-Arabonate dehydratase
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
elimination
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PATHWAY SOURCE
PATHWAYS
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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 hide
9024-30-0
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
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)
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 63738, calculated fro msequence, x * 64000, SDS-PAGE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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°
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
S480A
completely inactive. Upon cocrystallization with calcium arabinonate, a partially bound substrate is observed in the pocket
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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)
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team