Genome-based identification and analysis of collagen-related structural motifs in bacterial and viral proteins
Genome-based identification and analysis of collagen-related structural motifs in bacterial and viral proteins
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DOI：
10.1074/jbc.m304709200
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发表时间：
2003-08-22
影响因子：
4.8
通讯作者：
Björck, L
中科院分区：
文献类型：
--
作者：
Rasmussen, M;Jacobsson, M;Björck, L
胶原蛋白是由重复序列甘氨酸-X-Y组成的延伸的三聚体蛋白质。含有甘氨酸-X-Y重复序列的bar胶原相关（S）bar结构（m）bar otiff（CSM）下的A（c）也存在于通常称为胶原样蛋白的许多蛋白质中。对细菌和病毒中的CSM知之甚少，但最近已经证明了这种基序的存在。此外，细菌CSM形成胶原样三聚体，即使这些生物体不能合成羟脯氨酸，羟脯氨酸是胶原三螺旋稳定性的关键残基。在这里，我们提出了100种新的蛋白质的细菌和病毒（包括噬菌体）含有CSM的基因组序列的计算机分析确定。这些CSM在氨基酸含量和分布方面与人类胶原蛋白显著不同;细菌和病毒CSM具有较低的脯氨酸含量，并且在GXY三联体的X位置上偏好脯氨酸。此外，确定的CSM含有更多的苏氨酸比胶原蛋白，并在17的53个细菌CSM苏氨酸是占主导地位的氨基酸在Y位置。分子模拟表明，苏氨酸在Y位置的直接氢键相邻的骨架羰基，从而取代羟脯氨酸的稳定的胶原样三螺旋的细菌CSM。大多数剩余的CSM富含脯氨酸或富含带电残基。含有CSM的细菌蛋白可以被功能性注释为表面结构或孢子组分，而病毒蛋白通常可以被注释为病毒颗粒的结构组分。真细菌和低等真核生物中CSM的有限发生以及古细菌中CSM的缺乏表明编码CSM的DNA已经水平转移，可能从多细胞生物转移到细菌。
Collagens are extended trimeric proteins composed of the repetitive sequence glycine-X-Y. A (c) under bar ollagen- related (S) under bar tructural (m) under bar otif (CSM) containing glycine-X-Y repeats is also found in numerous proteins often referred to as collagen-like proteins. Little is known about CSMs in bacteria and viruses, but the occurrence of such motifs has recently been demonstrated. Moreover, bacterial CSMs form collagen-like trimers, even though these organisms cannot synthesize hydroxyproline, a critical residue for the stability of the collagen triple helix. Here we present 100 novel proteins of bacteria and viruses (including bacteriophages) containing CSMs identified by in silico analyses of genomic sequences. These CSMs differ significantly from human collagens in amino acid content and distribution; bacterial and viral CSMs have a lower proline content and a preference for proline in the X position of GXY triplets. Moreover, the CSMs identified contained more threonine than collagens, and in 17 of 53 bacterial CSMs threonine was the dominating amino acid in the Y position. Molecular modeling suggests that threonines in the Y position make direct hydrogen bonds to neighboring backbone carbonyls and thus substitute for hydroxyproline in the stabilization of the collagen-like triple-helix of bacterial CSMs. The majority of the remaining CSMs were either rich in proline or rich in charged residues. The bacterial proteins containing a CSM that could be functionally annotated were either surface structures or spore components, whereas the viral proteins generally could be annotated as structural components of the viral particle. The limited occurrence of CSMs in eubacteria and lower eukaryotes and the absence of CSMs in archaebacteria suggests that DNA encoding CSMs has been transferred horizontally, possibly from multicellular organisms to bacteria.