Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA.
Amino Acids. 2011 Jun;41(1):91-102. doi: 10.1007/s00726-010-0518-2. Epub 2010 Mar 1.
Proteins in the cupin superfamily have a wide range of biological functions in archaea, bacteria and eukaryotes. Although proteins in the cupin superfamily show very low overall sequence similarity, they all contain two short but partially conserved cupin sequence motifs separated by a less conserved intermotif region that varies both in length and amino acid sequence. Furthermore, these proteins all share a common architecture described as a six-stranded β-barrel core, and this canonical cupin or "jelly roll" β-barrel is formed with cupin motif 1, the intermotif region, and cupin motif 2 each forming two of the core six β-strands in the folded protein structure. The recently obtained crystal structures of cysteine dioxygenase (CDO), with contains conserved cupin motifs, show that it has the predicted canonical cupin β-barrel fold. Although there had been no reports of CDO activity in prokaryotes, we identified a number of bacterial cupin proteins of unknown function that share low similarity with mammalian CDO and that conserve many residues in the active-site pocket of CDO. Putative bacterial CDOs predicted to have CDO activity were shown to have similar substrate specificity and kinetic parameters as eukaryotic CDOs. Information gleaned from crystal structures of mammalian CDO along with sequence information for homologs shown to have CDO activity facilitated the identification of a CDO family fingerprint motif. One key feature of the CDO fingerprint motif is that the canonical metal-binding glutamate residue in cupin motif 1 is replaced by a cysteine (in mammalian CDOs) or by a glycine (bacterial CDOs). The recent report that some putative bacterial CDO homologs are actually 3-mercaptopropionate dioxygenases suggests that the CDO family may include proteins with specificities for other thiol substrates. A paralog of CDO in mammals was also identified and shown to be the other mammalian thiol dioxygenase, cysteamine dioxygenase (ADO). A tentative fingerprint motif for ADOs, or DUF1637 family members, is proposed. In ADOs, the conserved glutamate residue in cupin motif 1 is replaced by either glycine or valine. Both ADOs and CDOs appear to represent unique clades within the cupin superfamily.
杯蛋白超家族中的蛋白质在古菌、细菌和真核生物中具有广泛的生物学功能。尽管杯蛋白超家族中的蛋白质整体序列相似性很低，但它们都含有两个短但部分保守的杯蛋白序列基序，中间由一个保守性较弱的基序间隔区隔开，该间隔区在长度和氨基酸序列上均存在差异。此外，这些蛋白质都具有一个共同的结构，被描述为一个六链β-桶核心，这个典型的杯蛋白或“果冻卷”β-桶由杯蛋白基序 1、基序间隔区和杯蛋白基序 2 形成，每个基序都形成折叠蛋白质结构中六个核心β-链中的两个。最近获得的含保守杯蛋白基序的半胱氨酸双加氧酶（CDO）晶体结构表明，它具有预测的典型杯蛋白β-桶折叠。尽管以前没有报道过原核生物中的 CDO 活性，但我们鉴定出许多具有未知功能的细菌杯蛋白，它们与哺乳动物 CDO 相似度较低，但在 CDO 的活性口袋中保留了许多残基。预测具有 CDO 活性的假定细菌 CDO 具有与真核 CDO 相似的底物特异性和动力学参数。从哺乳动物 CDO 的晶体结构中获取的信息以及具有 CDO 活性的同源物的序列信息有助于确定 CDO 家族指纹基序。CDO 指纹基序的一个关键特征是杯蛋白基序 1 中的典型金属结合谷氨酸残基被半胱氨酸（在哺乳动物 CDO 中）或甘氨酸（在细菌 CDO 中）取代。最近的报道表明，一些假定的细菌 CDO 同源物实际上是 3-巯基丙酸双加氧酶，这表明 CDO 家族可能包括对其他硫醇底物具有特异性的蛋白质。哺乳动物中 CDO 的一个旁系同源物也被鉴定出来，并被证明是另一种哺乳动物硫醇双加氧酶，半胱氨酸胺双加氧酶（ADO）。提出了 ADO 或 DUF1637 家族成员的暂定指纹基序。在 ADO 中，杯蛋白基序 1 中的保守谷氨酸残基被甘氨酸或缬氨酸取代。ADO 和 CDO 似乎都代表了杯蛋白超家族中的独特分支。
