Crystal structure of the YffB protein from Pseudomonas aeruginosa

suggests a glutathione-dependent thiol reductase function

Alexey Teplyakiv, Sadhana Pullalarevu, Galina Obmolova, Victoria Doseeva, Andrey Galkin, Osnat Herzberg, Miroslawa Daueter, Zbigniew Dauter, and Gary L Gilliland

Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute and the National Institute of Standards and Technology

BMC Structural Biology 2004, 4:5

PDB ID ： 1RW1

前言

The yffB ( PA 3664 ) gene of Pseudomonas aeruginosa encodes an uncharacterized protein of 13 kD molecular weight with a marginal sequence similarity to arsenate reductase from E. coli 。

The crystal structure determination of YffB was undertaken as part of a structural genomics effort in order to assist with the functional assignment of the protein 。

結果

The structure was determined at 1.0 Å resolution by single-wavelength anormalous diffraction 。

The fold is very similar to that arsenate reductase, which is an extension of the thioredoxin 。

所探討的生物問題

Yffb 蛋白和 arsenate reductase 在序列上的相似性，但最後結果發現在功能上被認為是 glutathione-dependent thiol reductase

到期末要做的事

試著了解 yffb protein 、 arsenate reductase、 glutathione-dependent thiol reductase 的差異處和相似處

是否也有相似的其他案例 從現在到期末所學任何方法

可能得到的知識

對蛋白質進行基本的了解和解析 知道從何處找到關於蛋白質結構相關之網站

我嘗試做的一些分析

在 ExPASy Molecular Biology Server 進行序列比對

在 NCBI 進行序列比對 在 EBI 比較之間的 conservation 最後利用 pdb 看他們的親源關傒

>gi|32038782|ref|ZP_00137054.1| COG1393: Arsenate reductase and related proteins, glutaredoxin family [Pseudomonas aeruginosa UCBPP-PA14] Length = 115

Score = 226 bits (577), Expect = 1e-58 Identities = 109/114 (95%), Positives = 110/114 (96%)

Query: 1 TYVLYGIKACDTXKKARTWLDEHKVAYDFHDYKAVGIDREHLRRWCAEHGWQTVLNRAGT 60 TYVLYGIKACDT KKARTWLDEHKVAYDFHDYKAVGIDREHL+RWCAEHGWQTVLNRAGT Sbjct: 2 TYVLYGIKACDTMKKARTWLDEHKVAYDFHDYKAVGIDREHLQRWCAEHGWQTVLNRAGT 61

Query: 61 TFRKLDEAQKADLDEAKAIELXLAQPSXIKRPVLELGGRTLVGFKPDAYAAALA 114 TFRKLDEAQKADLDEAKAIEL LAQPS IKRPVLELG RTLVGFKPDAYAAALA Sbjct: 62 TFRKLDEAQKADLDEAKAIELMLAQPSMIKRPVLELGSRTLVGFKPDAYAAALA 115

>gi|56460562|ref|YP_155843.1| Glutaredoxin family protein [Idiomarina loihiensis L2TR] gi|56179572|gb|AAV82294.1| Glutaredoxin family protein [Idiomarina loihiensis L2TR] Length = 114

Score = 79.0 bits (193), Expect = 3e-14 Identities = 38/101 (37%), Positives = 61/101 (60%)

Query: 4 LYGIKACDTXKKARTWLDEHKVAYDFHDYKAVGIDREHLRRWCAEHGWQTVLNRAGTTFR 63

+YGIK CDT KK+ WLD+++VAY+F D + + +E + W + +++LN+ T++R Sbjct: 4

VYGIKNCDTVKKSLKWLDKNEVAYEFIDVRQQPLQKETVSGWLQKLPAESLLNKRSTSWR 63

Query: 64 KLDEAQKADLDEAKAIELXLAQPSXIKRPVLELGGRTLVGF 104 L + QK+ +D EL QP+ KRP++E G GF Sbjct: 64 NLSDEQKSVVDANAIAELVAEQPTLFKRPLVESGQAVHCGF 104

此篇報告利用的分析

X-ray diffration Protein data bank MALDI

經過分析得到的結果

至少知道蛋白質基本結構組成 知道有哪些蛋白質結構的網站 未來也許會有可能做蛋白質分析