氧化DNA/RNA修复酶AlkB的催化复合物的晶体结构
Bomina Yu1, William C Edstrom, Jordi Benach
1Department of Biological Sciences and Northeast Structural Genomics Consortium, 702A Fairchild Center, MC2434, Columbia University, New York, New York 10027, USA.
Nature
|February 17, 2006
概括
大肠杆菌AlkB可以修复基化核酸. 晶体结构揭示了结合基质的柔性盖子,使得DNA和RNA的修复效率高. 蛋白质动态影响其催化活性.
科学领域:
- 生物化学 生物化学
- 分子生物学分子生物学
- 结构生物学 结构生物学
背景情况:
- 环境和内源性化试剂会导致DNA和RNA损伤,导致突变和细胞毒性.
- 这种损伤与癌症化疗相关,因为它具有细胞毒性作用.
- 大肠杆菌AlkB和人类ABH2/ABH3蛋白质修复DNA和RNA中的基.
研究的目的:
- 阐明大肠杆菌AlkB修复功能的生化活性和结构基础.
- 为了确定AlkB与基质和产品复合的晶体结构.
- 研究蛋白质动态在AlkB的催化机制中的作用.
主要方法:
- 用X射线晶体学来确定1.82.3 Å分辨率的结构.
- 胺交换研究,以评估蛋白质的灵活性.
- 生物化学试验用于研究酶活性和基质氧化.
主要成果:
- 晶体结构揭示了一个独特的子域,作为一个灵活的盖子,通过骨干接触将甲基化三核酸基质放置在活性部位.
- 盖子的灵活性允许各种基核酸基质的最佳对接.
- 结构显示了O2扩散道的开放和关闭状态,并且观察到蛋白质动态调节氧化还原化学.
结论:
- 大肠杆菌AlkB使用灵活的盖子机制来结合和修复基质.
- 蛋白质动力学在调节酶的氧化还原化学和催化效率方面发挥着至关重要的作用.
- 结构洞察力为了解基化核酸的修复提供了基础.
相关概念视频
Nucleotide Excision Repair
Overview
Base Excision Repair
One of the common DNA damages is the chemical alteration of single bases by alkylation, oxidation, or deamination. The altered bases cause mispairing and strand breakage during replication. This type of damage causes minimal change to the DNA double helix structure and can be repaired by the base excision repair (BER) pathways. BER corrects damaged DNA sequences by removing the damaged base and restoring the original base sequence using the complementary strand as a template.
The first step of...
The first step of...
Long-patch Base Excision Repair
Since the discovery of the two BER pathways, there has been a debate about how a cell chooses one pathway over the other and the factors determining this selection. Numerous in vitro experiments have pointed out multiple determinants for the sub-pathway selection. These are:
Fixing Double-strand Breaks
The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...
Homologous Recombination
The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
Nucleic Acid Structure
The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...
DNA Structure
DNA has a double-helix structure. The...


