Structural features of the minimal DNA binding domain (M98-F219) of human nucleotide excision repair protein XPA
Structural features of the minimal DNA binding domain (M98-F219) of human nucleotide excision repair protein XPA
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DOI：
10.1093/nar/26.11.2779
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发表时间：
1998-06-01
影响因子：
14.9
通讯作者：
Kennedy, MA
中科院分区：
文献类型：
--
作者：
Buchko, GW;Ni, SS;Kennedy, MA
XPA是核苷酸切除修复（NER）中的一种必需蛋白，与受损DNA和其他蛋白（RPA，ERCC 1和TFIIH）相互作用，以从真核基因组中去除各种化学和结构上不同的DNA损伤。为了理解XPA在修复过程中的作用的结构基础，通过NMR光谱研究了人XPA的最小DNA结合结构域[XPA-MBD（M98-F219）]的结构。使用距离几何和模拟退火方法从基于NOB的距离约束、氢键和Zn-S距离约束以及二面角约束生成XPA-MBD的三维结构。结构计算表明，XPA-MBD含有明确定义的二级结构的元素，这些二级结构与组织成两个非相互作用的亚结构域的无序环间隔开：锌结合核心（D101-K137）和富含环的结构域（L138-F219）。锌相关的核心包含一个反平行的β-折叠（Y102-C105和K110-M113）和一个α-螺旋（C126-K137），它们之间由一个不明确的转角分开，这让人想起鸡红细胞转录因子加塔-1与其同源DNA序列结合时的锌结合结构域的结构。富含环的结构域含有三链反平行P-折叠（L138-T140、L182-M178和K163-K167）、三个环（K151-L162、N169-D177和Q208-F219）和三个α-螺旋（K141-L150、K183-W194和Q197-R207）。XPA-MBD结构在已知功能方面进行了讨论：结合单链和双链DNA和结合RPA。
XPA, an essential protein in nucleotide excision repair (NER), interacts with damaged DNA and other proteins (RPA, ERCC1 and TFIIH) to remove a wide variety of chemically and structurally distinct DNA lesions from the eukaryotic genome. To understand the structural basis for the role of XPA in the repair process, the structure of the minimal DNA binding domain of human XPA [XPA-MBD (M98-F219)] was studied by NMR spectroscopy, A three-dimensional structure for XPA-MBD was generated using distance geometry and simulated annealing methods from NOB-based distance restraints, hydrogen bond and Zn-S distance restraints, and dihedral restraints. The structure calculations indicate that XPA-MBD contains elements of well-defined secondary structure interspaced with disordered loops organized into two non-interactive sub-domains: a zinc-binding core (D101-K137) and a loop-rich domain (L138-F219). The zinc-associated core contains an antiparallel beta-sheet (Y102-C105 and K110-M113) and an alpha-helix (C126-K137) separated by a poorly defined turn, reminiscent of the structure of the zinc-binding domain of the chicken erythroid transcription factor GATA-1 when bound to its cognate DNA sequence. The loop rich domain contains a triple-strand antiparallel P-sheet (L138-T140, L182-M178 and K163-K167), three loops (K151-L162, N169-D177 and Q208-F219) and three alpha-helices (K141-L150, K183-W194 and Q197-R207). The XPA-MBD structure is discussed in terms of known functions: binding single- and double-stranded DNA and binding RPA.