1dlq: Difference between revisions

Revision as of 13:17, 21 February 2008

STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER SP. ADP1 INHIBITED BY BOUND MERCURY

OverviewOverview

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-heme ferric ion per monomer, that is (alphaFe(3+))(2). This is in contrast to the archetypical intradiol dioxygenase protocatechuate 3,4-dioxygenase (3,4-PCD), which forms more diverse oligomers, such as (alphabetaFe(3+))(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 A resolution. The structures of the enzyme complexed with catechol and 4-methylcatechol were also determined at resolutions of 1.9 A and 1.8 A, 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 A 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.

About this StructureAbout this Structure

1DLQ is a Single protein structure of sequence from Acinetobacter sp. with , and as ligands. Active as Catechol 1,2-dioxygenase, with EC number 1.13.11.1 Full crystallographic information is available from OCA.

ReferenceReference

The 1.8 A crystal structure of catechol 1,2-dioxygenase reveals a novel hydrophobic helical zipper as a subunit linker., Vetting MW, Ohlendorf DH, Structure. 2000 Apr 15;8(4):429-40. PMID:10801478

Page seeded by OCA on Thu Feb 21 12:17:52 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1dlq.gif|left|200px]]<br /><applet load="1dlq" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1dlq.gif|left|200px]]<br /><applet load="1dlq" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1dlq, resolution 2.3&Aring;" />
 '''STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER SP. ADP1 INHIBITED BY BOUND MERCURY'''<br />
 ==Overview==
-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-heme ferric ion per, monomer, that is (alphaFe(3+))(2). This is in contrast to the archetypical, intradiol dioxygenase protocatechuate 3,4-dioxygenase (3,4-PCD), which, forms more diverse oligomers, such as (alphabetaFe(3+))(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 A, resolution. The structures of the enzyme complexed with catechol and, 4-methylcatechol were also determined at resolutions of 1.9 A and 1.8 A, 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 A 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.
+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-heme ferric ion per monomer, that is (alphaFe(3+))(2). This is in contrast to the archetypical intradiol dioxygenase protocatechuate 3,4-dioxygenase (3,4-PCD), which forms more diverse oligomers, such as (alphabetaFe(3+))(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 A resolution. The structures of the enzyme complexed with catechol and 4-methylcatechol were also determined at resolutions of 1.9 A and 1.8 A, 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 A 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.
 ==About this Structure==
-DLQ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Acinetobacter_sp. Acinetobacter sp.] with FE, HG and LIO as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Catechol_1,2-dioxygenase Catechol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.1 1.13.11.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DLQ OCA].
+DLQ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Acinetobacter_sp. Acinetobacter sp.] with <scene name='pdbligand=FE:'>FE</scene>, <scene name='pdbligand=HG:'>HG</scene> and <scene name='pdbligand=LIO:'>LIO</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Catechol_1,2-dioxygenase Catechol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.1 1.13.11.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DLQ OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Catechol 1,2-dioxygenase]]
 [[Category: Single protein]]
-[[Category: Ohlendorf, D.H.]]
+[[Category: Ohlendorf, D H.]]
-[[Category: Vetting, M.W.]]
+[[Category: Vetting, M W.]]
 [[Category: FE]]
 [[Category: HG]]
@@ Line 25: / Line 25: @@
 [[Category: mixed alpha/beta structure]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:23:29 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:17:52 2008''