Ilyina T V, Koonin E V
Institute of Microbiology, Academy of Sciences, Moscow, Russia.
Nucleic Acids Res. 1992 Jul 11;20(13):3279-85. doi: 10.1093/nar/20.13.3279.
An amino acid motif was identified that consists of the sequence HisHydrHisHydrHydrHydr (Hydr--bulky hydrophobic residue) and is conserved in two vast classes of proteins, one of which is involved in initiation and termination of rolling circle DNA replication, or RCR (Rep proteins), and the other in mobilization (conjugal transfer) of plasmid DNA (Mob proteins). Based on analogies with metalloenzymes, it is hypothesized that the two conserved His residues in this motif may be involved in metal ion coordination required for the activity of the Rep and Mob proteins. Rep proteins contained two additional conserved motifs, one of which was located upstream, and the other downstream from the 'two His' motif. The C-terminal motif encompassed the Tyr residue(s) forming the covalent link with nicked DNA. Mob proteins were characterized by the opposite orientation of the conserved motifs, with the (putative) DNA-linking Tyr being located near their N-termini. Both Rep and Mob protein classes further split into several distinct families. Although it was not possible to find a motif or pattern that would be unique for the entire Rep or Mob class, unique patterns were derived for large subsets of the proteins of each class. These observations allowed the prediction of the amino acid residues involved in DNA nicking, which is required for the initiation of RCR or conjugal transfer of single-stranded (ss) DNA, in Rep and Mob proteins encoded by a number of replicons of highly diverse size, structure and origin. It is conjectured that recombination has played a major part in the dissemination of genes encoding related Rep or Mob proteins among the replicons exploiting RCR. It is speculated that the eucaryotic small ssDNA replicons encoding proteins with the conserved RCR motifs and replicating via RCR-related mechanisms, such as geminiviruses and parvoviruses, may have evolved from eubacterial replicons.
已鉴定出一种氨基酸基序，其序列为HisHydrHisHydrHydrHydr（Hydr为大的疏水残基），在两大类蛋白质中保守，其中一类参与滚环DNA复制的起始和终止，即RCR（Rep蛋白），另一类参与质粒DNA的转移（接合转移）（Mob蛋白）。基于与金属酶的类比，推测该基序中的两个保守His残基可能参与Rep和Mob蛋白活性所需的金属离子配位。Rep蛋白包含另外两个保守基序，其中一个位于“两个His”基序的上游，另一个位于下游。C端基序包含与带切口DNA形成共价连接的Tyr残基。Mob蛋白的特征是保守基序的方向相反，（假定的）与DNA连接的Tyr位于其N端附近。Rep和Mob蛋白类又进一步分为几个不同的家族。虽然无法找到整个Rep或Mob类特有的基序或模式，但为每个类别的大量蛋白质子集推导了独特的模式。这些观察结果使得能够预测参与DNA切口的氨基酸残基，这是多种大小、结构和来源的许多复制子编码的Rep和Mob蛋白中RCR起始或单链（ss）DNA接合转移所必需的。据推测，重组在利用RCR的复制子之间编码相关Rep或Mob蛋白的基因传播中起了主要作用。据推测，编码具有保守RCR基序并通过RCR相关机制复制的真核小ssDNA复制子，如双生病毒和细小病毒，可能从真细菌复制子进化而来。
