BRENDA - Enzyme Database

The crystal structure of a bacterial L-arabinonate dehydratase contains a [2Fe-2S] cluster

Rahman, M.M.; Andberg, M.; Thangaraj, S.K.; Parkkinen, T.; Penttilae, M.; Jaenis, J.; Koivula, A.; Rouvinen, J.; Hakulinen, N.; ACS Chem. Biol. 12, 1919-1927 (2017)

Data extracted from this reference:

Crystallization (Commentary)
EC Number
Crystallization
Organism
4.2.1.25
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
Engineering
EC Number
Amino acid exchange
Commentary
Organism
4.2.1.25
S480A
completely inactive. Upon cocrystallization with calcium arabinonate, a partially bound substrate is observed in the pocket
Rhizobium leguminosarum bv. trifolii
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
4.2.1.25
Rhizobium leguminosarum bv. trifolii
I9XDU6
-
-
4.2.1.25
Rhizobium leguminosarum bv. trifolii WSM597
I9XDU6
-
-
Cofactor
EC Number
Cofactor
Commentary
Organism
Structure
4.2.1.25
[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
Cofactor (protein specific)
EC Number
Cofactor
Commentary
Organism
Structure
4.2.1.25
[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
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
4.2.1.25
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
Engineering (protein specific)
EC Number
Amino acid exchange
Commentary
Organism
4.2.1.25
S480A
completely inactive. Upon cocrystallization with calcium arabinonate, a partially bound substrate is observed in the pocket
Rhizobium leguminosarum bv. trifolii