BRENDA - Enzyme Database
show all sequences of 4.2.1.25

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)
Crystallization
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
Engineering
Amino acid exchange
Commentary
Organism
S480A
completely inactive. Upon cocrystallization with calcium arabinonate, a partially bound substrate is observed in the pocket
Rhizobium leguminosarum bv. trifolii
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Rhizobium leguminosarum bv. trifolii
I9XDU6
-
-
Rhizobium leguminosarum bv. trifolii WSM597
I9XDU6
-
-
Cofactor
Cofactor
Commentary
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
Cofactor (protein specific)
Cofactor
Commentary
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
Crystallization (Commentary) (protein specific)
Crystallization
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
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
S480A
completely inactive. Upon cocrystallization with calcium arabinonate, a partially bound substrate is observed in the pocket
Rhizobium leguminosarum bv. trifolii
Other publictions for EC 4.2.1.25
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [C]
Temperature Range [C]
Temperature Stability [C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [C] (protein specific)
Temperature Range [C] (protein specific)
Temperature Stability [C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
746594
Rahman
The crystal structure of a ba ...
Rhizobium leguminosarum bv. trifolii, Rhizobium leguminosarum bv. trifolii WSM597
ACS Chem. Biol.
12
1919-1927
2017
-
-
-
1
1
-
-
-
-
-
-
-
-
4
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
1
1
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
746662
Rahman
Crystallization and X-ray dif ...
Rhizobium leguminosarum bv. trifolii
Acta Crystallogr. Sect. F
72
604-608
2016
-
-
1
1
-
-
-
-
-
-
-
-
-
4
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
1
-
-
-
746676
Rahman
Crystallization and X-ray dif ...
Rhizobium leguminosarum bv. trifolii, Rhizobium leguminosarum bv. trifolii WSM597
Acta Crystallogr. Sect.F
72
604-608
2016
-
-
1
1
-
-
-
-
-
-
-
-
-
6
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
674689
Watanabe
Identification and Characteriz ...
Azospirillum brasilense
J. Biol. Chem.
281
33521-33536
2006
-
-
1
-
5
-
-
-
-
2
2
-
-
4
-
-
1
-
-
-
1
-
1
1
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
5
-
-
-
-
-
-
2
2
-
-
-
-
1
-
-
1
-
1
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
33852
Dilworth
-
Pentose metabolism in Rhizobiu ...
Rhizobium leguminosarum, Rhizobium leguminosarum MNF300, Rhizobium sp., Rhizobium sp. NGR234
J. Gen. Microbiol.
132
2733-2742
1986
-
-
-
-
-
-
-
-
-
-
-
4
-
5
-
-
-
-
-
-
-
-
8
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
4
-
-
-
-
-
-
-
-
8
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
5062
Novick
L-Arabinose metabolism in Azos ...
Azospirillum brasilense
J. Bacteriol.
149
364-367
1982
-
-
-
-
-
-
-
-
-
-
-
1
-
1
-
-
-
-
-
-
1
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
1
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
5607
Schimz
-
Regulation of L-arabinose meta ...
Pseudomonas fluorescens
Biochem. Soc. Trans.
3
1087-1089
1975
-
-
-
-
-
-
-
-
-
-
-
2
-
1
-
-
-
-
-
-
-
-
3
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
3
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
5059
Pedrosa
L-Arabinose metabolism in Rhiz ...
Bradyrhizobium japonicum
J. Bacteriol.
119
336-338
1974
-
-
-
-
-
-
-
-
-
-
-
1
-
1
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-