Structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae BI
Structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae BI
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DOI：
10.1186/1472-6807-7-10
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发表时间：
2007-03-09
影响因子：
--
通讯作者：
Ramaswamy, S.
中科院分区：
文献类型：
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作者：
Ferraro, Daniel J.;Brown, Eric N.;Ramaswamy, S.
背景资料：涉及微生物Sphingobium yanoikuyae菌株BI（BI）（先前称为Sphingomonas yanoikuyae菌株BI和Beijerinckia sp.菌株BI）的单芳族和多芳族化合物的氧化羟基化的初始步骤由一组多末端Rieske非血红素铁加氧酶进行。这些酶共享由还原酶和铁氧还蛋白（BPDO-FBI）组成的单一电子供体系统。联苯2，3-双加氧酶（biphenyl 2，3-dioxygenase，BPDO-OBI）是Rieske加氧酶的末端酶之一，它能使苯并[a]芘和芘等大分子芳香族化合物发生二羟基化反应。与其他Rieske加氧酶的序列和结构比较表明，该酶与来自假单胞菌菌株NCIB 9816-4的萘双加氧酶最相似，具有43.5%的序列同一性。虽然在结构上类似于萘1，2-双加氧酶，但活性位点入口明显大于萘1，2-双加氧酶的入口。活性位点残基的差异也允许大的芳香族底物的结合。结合底物后未观察到重大结构变化。BPDO-F-BI具有很大的序列同一性，其他细菌的Rieske铁氧化还原蛋白的结构是已知的，并表现出较高的结构同源性，但是，侧链组成和构象的差异周围的Rieske集群binding sites are noted.Conclusion：这是第一个结构的Rieske加氧酶，氧化底物与五个芳香环的报告。这种催化较大底物氧化的能力是活性位点的较大入口以及活性位点容纳较大底物的能力的结果。虽然联苯铁氧还蛋白在结构上与其他Rieske铁氧还蛋白相似，但在铁-硫簇附近的氨基酸中存在明显的变化。因为这种铁氧还蛋白被BI生物体中存在的多种加氧酶使用，所以这种铁氧还蛋白-加氧酶系统提供了结构平台来剖析蛋白质-蛋白质电子传递系统中混杂性和选择性之间的平衡。
Background: The initial step involved in oxidative hydroxylation of monoaromatic and polyaromatic compounds by the microorganism Sphingobium yanoikuyae strain BI ( BI), previously known as Sphingomonas yanoikuyae strain BI and Beijerinckia sp. strain BI, is performed by a set of multiple terminal Rieske non-heme iron oxygenases. These enzymes share a single electron donor system consisting of a reductase and a ferredoxin ( BPDO-FBI). One of the terminal Rieske oxygenases, biphenyl 2,3-dioxygenase (BPDO-OBI), is responsible for BI' s ability to dihydroxylate large aromatic compounds, such as chrysene and benzo[a] pyrene.Results: In this study, crystal structures of BPDO-O-BI in both native and biphenyl bound forms are described. Sequence and structural comparisons to other Rieske oxygenases show this enzyme to be most similar, with 43.5% sequence identity, to naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4. While structurally similar to naphthalene 1,2- dioxygenase, the active site entrance is significantly larger than the entrance for naphthalene 1,2- dioxygenase. Differences in active site residues also allow the binding of large aromatic substrates. There are no major structural changes observed upon binding of the substrate. BPDO-F-BI has large sequence identity to other bacterial Rieske ferredoxins whose structures are known and demonstrates a high structural homology; however, differences in side chain composition and conformation around the Rieske cluster binding site are noted.Conclusion: This is the first structure of a Rieske oxygenase that oxidizes substrates with five aromatic rings to be reported. This ability to catalyze the oxidation of larger substrates is a result of both a larger entrance to the active site as well as the ability of the active site to accommodate larger substrates. While the biphenyl ferredoxin is structurally similar to other Rieske ferredoxins, there are distinct changes in the amino acids near the iron- sulfur cluster. Because this ferredoxin is used by multiple oxygenases present in the BI organism, this ferredoxin- oxygenase system provides the structural platform to dissect the balance between promiscuity and selectivity in protein- protein electron transport systems.