Genomic analysis reveals widespread occurrence of new classes of copper nitrite reductases
Genomic analysis reveals widespread occurrence of new classes of copper nitrite reductases
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DOI：
10.1007/s00775-007-0282-2
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发表时间：
2007-11-01
影响因子：
3
通讯作者：
Hasnain, S. Samar
中科院分区：
文献类型：
--
作者：
Ellis, Mark J.;Grossmann, J. Guenter;Hasnain, S. Samar
最近，来自脱氮菌丝微生物 (HdNiR) 的含 Cu 亚硝酸还原酶 (NiR) 的结构已被报道，证实了 Cu-NiR 新家族的存在，其中含有铜氧还蛋白结构域的附加 1 型 Cu (T1Cu) 位于 N 末端（Nojiri 等人在 Proc. Natl. Acad. Sci. USA 104:4315-4320 中， 2007）。 HdNiR 保留了特征良好的偶联 T1Cu-2 型 Cu (T2Cu) 核心，其中 T2Cu 催化位点也是利用相邻单体的配体构建的。我们进行了基因组分析，发现这些 NiR 广泛存在，成员分为两组，一组与 HdNiR 的氨基酸序列相似性约为 80%，第二组包括来自极端微生物解纤维酸菌的 NiR，与 HdNiR 的氨基酸序列相似性约为 50%。这让人想起蓝色（木糖氧化产碱菌）和绿色（环碎无色杆菌和粪产碱菌）NiR 之间观察到的差异，这些 NiR 已被广泛研究，并且可能表明它们也形成了新家族的两个不同亚类。基因组分析还显示存在具有 160-190 个残基的 C 端延伸的 Cu-NiR，其中包含具有特征性 β 折叠延伸的 I 类细胞色素 c 结构域。目前不存在该家族任何成员的结构信息。基因组分析表明，这些新型 NiR 广泛存在，在变形菌门的 α、β 和 γ 亚类以及曲霉菌的两种真菌中具有代表性。我们选择来自 Ralstonia pickettii 的酶进行比较建模，并产生了一个合理的结构，突出了电子转移模式，其中 C 末端的细胞色素 c 铁姆可以到达 T1Cu-T2Cu 核心的 T1Cu 中心 16 埃范围内。
Recently, the structure of a Cu-containing nitrite reductase (NiR) from Hyphomicrobium denitrificans (HdNiR) has been reported, establishing the existence of a new family of Cu-NiR where an additional type 1 Cu (T1Cu) containing cupredoxin domain is located at the N-terminus (Nojiri et al. in Proc. Natl. Acad. Sci. USA 104:4315-4320, 2007). HdNiR retains the well-characterised coupled T1Cu-type 2 Cu (T2Cu) core, where the T2Cu catalytic site is also built utilising ligands from neighbouring monomers. We have undertaken a genome analysis and found the wide occurrence of these NiRs, with members clustering in two groups, one showing an amino acid sequence similarity of around 80% with HdNiR, and a second group, including the NiR from the extremophile Acidothermus cellulolyticus, clustering around 50% similarity to HdNiR. This is reminiscent of the difference observed between the blue (Alcaligenes xylosoxidans) and green (Achromobacter cycloclastes and Alcaligenes faecalis) NiRs which have been extensively studied and may indicate that these also form two distinct subclasses of the new family. Genome analysis also showed the presence of Cu-NiRs with a C-terminal extension of 160-190 residues containing a class I cytochrome c domain with a characteristic beta-sheet extension. Currently no structural information exists for any member of this family. Genome analysis suggests the widespread occurrence of these novel NiRs with representatives in the alpha, beta and gamma subclasses of the Proteobacteria and in two species of the fungus Aspergillus. We selected the enzyme from Ralstonia pickettii for comparative modelling and produced a plausible structure highlighting an electron transfer mode in which the cytochrome c haem at the C-terminus can come within 16-angstrom reach of the T1Cu centre of the T1Cu-T2Cu core.