Fomenko Dmitri E, Gladyshev Vadim N
Department of Biochemistry, University of Nebraska-Lincoln, 68588-0664, USA.
Protein Sci. 2002 Oct;11(10):2285-96. doi: 10.1110/ps.0218302.
Redox reactions involving thiol groups in proteins are major participants in cellular redox regulation and antioxidant defense. Although mechanistically similar, thiol-dependent redox processes are catalyzed by structurally distinct families of enzymes, which are difficult to identify by available protein function prediction programs. Herein, we identified a functional motif, CxxS (cysteine separated from serine by two other residues), that was often conserved in redox enzymes, but rarely in other proteins. Analyses of complete Escherichia coli, Campylobacter jejuni, Methanococcus jannaschii, and Saccharomyces cerevisiae genomes revealed a high proportion of proteins known to use the CxxS motif for redox function. This allowed us to make predictions in regard to redox function and identity of redox groups for several proteins whose function previously was not known. Many proteins containing the CxxS motif had a thioredoxin fold, but other structural folds were also present, and CxxS was often located in these proteins upstream of an alpha-helix. Thus, a conserved CxxS sequence followed by an alpha-helix is typically indicative of a redox function and corresponds to thiol-dependent redox sites in proteins. The data also indicate a general approach of genome-wide identification of redox proteins by searching for simple conserved motifs within secondary structure patterns.
涉及蛋白质中巯基的氧化还原反应是细胞氧化还原调节和抗氧化防御的主要参与者。尽管在机制上相似，但巯基依赖性氧化还原过程由结构不同的酶家族催化，而现有蛋白质功能预测程序难以识别这些酶家族。在此，我们鉴定出一个功能性基序CxxS（半胱氨酸与丝氨酸被另外两个残基隔开），它在氧化还原酶中常常保守，但在其他蛋白质中很少见。对完整的大肠杆菌、空肠弯曲菌、詹氏甲烷球菌和酿酒酵母基因组的分析表明，已知使用CxxS基序进行氧化还原功能的蛋白质比例很高。这使我们能够对几种功能此前未知的蛋白质的氧化还原功能和氧化还原基团的身份进行预测。许多含有CxxS基序的蛋白质具有硫氧还蛋白折叠，但也存在其他结构折叠，并且CxxS常常位于这些蛋白质中α螺旋的上游。因此，一个保守的CxxS序列后接一个α螺旋通常表明具有氧化还原功能，并且对应于蛋白质中巯基依赖性氧化还原位点。数据还表明了一种通过在二级结构模式中搜索简单保守基序来进行全基因组范围氧化还原蛋白质鉴定的通用方法。
