Structures of apo- and ssDNA-bound YdbC from Lactococcus lactis uncover the function of protein domain family DUF2128 and expand the single-stranded DNA-binding domain proteome.
Structures of apo- and ssDNA-bound YdbC from Lactococcus lactis uncover the function of protein domain family DUF2128 and expand the single-stranded DNA-binding domain proteome.
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DOI：
10.1093/nar/gks1348
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发表时间：
2013-02-01
影响因子：
14.9
通讯作者：
Montelione GT
中科院分区：
文献类型：
--
作者：
Rossi P;Barbieri CM;Aramini JM;Bini E;Lee HW;Janjua H;Xiao R;Acton TB;Montelione GT
单链DNA结合蛋白在基因转录、重组、DNA修复和复制的基础代谢途径中发挥着重要作用。它们在细胞中的主要作用是稳定融化的双链DNA，保护基因组DNA不被降解。我们已经发现了未知功能的蛋白结构域家族结构域DUF2128(PF09901)的分子功能，它是一个新的单链DNA结合域。这个细菌结构域强烈结合成一个二聚体，并呈现一个高度正电的表面，这与它在非特异性单链DNA结合中的功能是一致的。乳酸乳球菌YDBC是DUF2128的代表菌株。测定了20 kDa apo-YdbC二聚体和YdbC：dT19G1配合物的溶液核磁共振结构。用等温滴定量热法表征了YDBC与单链DNA的结合能。YDBC对嘧啶和混合寡核苷酸显示出类似的纳摩尔亲和力，并且亲和力足够强，足以破坏双链DNA。此外，YDBC与单链RNA的亲和力较低，使其成为一个多功能的核酸结合域。DUF2128家族在折叠相似性和分子功能上都与真核细胞核蛋白阳性辅因子4(PC4)家族和PUR家族相关。
Single-stranded DNA (ssDNA) binding proteins are important in basal metabolic pathways for gene transcription, recombination, DNA repair and replication in all domains of life. Their main cellular role is to stabilize melted duplex DNA and protect genomic DNA from degradation. We have uncovered the molecular function of protein domain family domain of unknown function DUF2128 (PF09901) as a novel ssDNA binding domain. This bacterial domain strongly associates into a dimer and presents a highly positively charged surface that is consistent with its function in non-specific ssDNA binding. Lactococcus lactis YdbC is a representative of DUF2128. The solution NMR structures of the 20 kDa apo-YdbC dimer and YdbC:dT19G1 complex were determined. The ssDNA-binding energetics to YdbC were characterized by isothermal titration calorimetry. YdbC shows comparable nanomolar affinities for pyrimidine and mixed oligonucleotides, and the affinity is sufficiently strong to disrupt duplex DNA. In addition, YdbC binds with lower affinity to ssRNA, making it a versatile nucleic acid-binding domain. The DUF2128 family is related to the eukaryotic nuclear protein positive cofactor 4 (PC4) family and to the PUR family both by fold similarity and molecular function.
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影响因子：
5.8
作者：
Glaser, F;Pupko, T;Ben-Tal, N
通讯作者：
Ben-Tal, N
影响因子：
5.8
作者：
Gouet, P;Courcelle, E;Métoz, F
通讯作者：
Métoz, F
影响因子：
14.9
作者：
Geer LY;Marchler-Bauer A;Geer RC;Han L;He J;He S;Liu C;Shi W;Bryant SH
通讯作者：
Bryant SH
影响因子：
3.7
作者：
Graebsch, Almut;Roche, Stephane;Niessing, Dierk
通讯作者：
Niessing, Dierk
影响因子：
2.9
作者：
FERRARI, ME;LOHMAN, TM
通讯作者：
LOHMAN, TM