Literature summary for 4.2.1.25 extracted from

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 (2017), ACS Chem. Biol., 12, 1919-1927 .

Crystallization (Commentary)

Crystallization (Comment)	Organism
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	Rhizobium leguminosarum bv. trifolii

Crystallization (Comment)

Organism

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

Rhizobium leguminosarum bv. trifolii

Protein Variants

Protein Variants	Comment	Organism
S480A	completely inactive. Upon cocrystallization with calcium arabinonate, a partially bound substrate is observed in the pocket	Rhizobium leguminosarum bv. trifolii

Organism

Organism	UniProt	Comment	Textmining
Rhizobium leguminosarum bv. trifolii	I9XDU6	-	-
Rhizobium leguminosarum bv. trifolii WSM597	I9XDU6	-	-

Synonyms

Synonyms	Comment	Organism
Rleg9DRAFT_6269	-	Rhizobium leguminosarum bv. trifolii

Cofactor

Cofactor	Comment	Organism	Structure
[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)	Rhizobium leguminosarum bv. trifolii

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Release 2023.1 (January 2023)