TY - JOUR
T1 - The 1.8 Å crystal structure of catechol 1,2-dioxygenase reveals a novel hydrophobic helical zipper as a subunit linker
AU - Vetting, Matthew W.
AU - Ohlendorf, Douglas H.
N1 - Funding Information:
The authors acknowledge the Minnesota Supercomputer Institute for providing computational resources. We thank L Nicholas Ornston of Yale University for providing the Ac 1,2-CTD E. coli clone pIB1343. This work was supported by GM 46436 (to DHO). MWV was partially supported by a NIH biophysics training grant (GM07323).
PY - 2000/4/1
Y1 - 2000/4/1
N2 - Background: Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. Catechol 1,2-dioxygenases (1,2-CTDs) have a rudimentary design structure - a homodimer with one catalytic non-berne ferric ion per monomer, that is (αFe3+)2. This is in contrast to the archetypical intradiol dioxygenase protocatechuate 3,4-dioxygenase (3,4-PCD), which forms more diverse oligomers, such as (αFe3+)2-12. Results: The crystal structure of 1,2-CTD from Acinetobacter sp. ADP1 (Ac 1,2-CTD) was solved by single isomorphous replacement and refined to 2.0 Å resolution. The structures of the enzyme complexed with catechol and 4-methylcatechol were also determined at resolutions of 1.9 Å and 1.8 Å, respectively. While the characteristics of the iron ligands are similar, Ac 1,2-CTD differs from 3,4-PCDs in that only one subunit is used to fashion each active-site cavity. In addition, a novel 'helical zipper', consisting of five N-terminal helices from each subunit, forms the molecular dimer axis. Two phospholipids were unexpectedly found to bind within an 8 x 35 Å hydrophobic tunnel along this axis. Conclusions: The helical zipper domain of Ac 1,2-CTD has no equivalent in other proteins of known structure. Sequence analysis suggests the domain is a common motif in all members of the 1,2-CTD family. Complexes with catechol and 4-methylcatechol are the highest resolution complex structures to date of an intradiol dioxygenase. Furthermore, they confirm several observations seen in 3,4-PCDs, including ligand displacement upon binding exogenous ligands. The structures presented here are the first of a new family of intradiol dioxygenases.
AB - Background: Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. Catechol 1,2-dioxygenases (1,2-CTDs) have a rudimentary design structure - a homodimer with one catalytic non-berne ferric ion per monomer, that is (αFe3+)2. This is in contrast to the archetypical intradiol dioxygenase protocatechuate 3,4-dioxygenase (3,4-PCD), which forms more diverse oligomers, such as (αFe3+)2-12. Results: The crystal structure of 1,2-CTD from Acinetobacter sp. ADP1 (Ac 1,2-CTD) was solved by single isomorphous replacement and refined to 2.0 Å resolution. The structures of the enzyme complexed with catechol and 4-methylcatechol were also determined at resolutions of 1.9 Å and 1.8 Å, respectively. While the characteristics of the iron ligands are similar, Ac 1,2-CTD differs from 3,4-PCDs in that only one subunit is used to fashion each active-site cavity. In addition, a novel 'helical zipper', consisting of five N-terminal helices from each subunit, forms the molecular dimer axis. Two phospholipids were unexpectedly found to bind within an 8 x 35 Å hydrophobic tunnel along this axis. Conclusions: The helical zipper domain of Ac 1,2-CTD has no equivalent in other proteins of known structure. Sequence analysis suggests the domain is a common motif in all members of the 1,2-CTD family. Complexes with catechol and 4-methylcatechol are the highest resolution complex structures to date of an intradiol dioxygenase. Furthermore, they confirm several observations seen in 3,4-PCDs, including ligand displacement upon binding exogenous ligands. The structures presented here are the first of a new family of intradiol dioxygenases.
KW - Aromatic catabolism
KW - Intradiol dioxygenase
KW - Ligand dissociation
KW - Metalloenzyme
KW - Phospholipid
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U2 - 10.1016/S0969-2126(00)00122-2
DO - 10.1016/S0969-2126(00)00122-2
M3 - Article
C2 - 10801478
AN - SCOPUS:0034654852
SN - 0969-2126
VL - 8
SP - 429
EP - 440
JO - Structure
JF - Structure
IS - 4
ER -