کد مقاله | کد نشریه | سال انتشار | مقاله انگلیسی | نسخه تمام متن |
---|---|---|---|---|
5913727 | 1162699 | 2016 | 39 صفحه PDF | دانلود رایگان |
عنوان انگلیسی مقاله ISI
Structural and biochemical characterization of bacterial YpgQ protein reveals a metal-dependent nucleotide pyrophosphohydrolase
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کلمات کلیدی
NTPdNMPdNTPRMSDPDBTLCPPISubstrate specificity - خصوصیات زیربناییSeMet - خودشانdeoxyribonucleoside triphosphate - دز اکسید ریبونوکلئوزید تری فسفاتribonucleoside triphosphate - ریبونوکلئوزید تری فسفاتCrystal structure - ساختار کریستالیSelenomethionine - سلنمتینیونSAD - غمگینManganese - منگنز root mean square deviation - میانگین انحراف مربع ریشهsingle-wavelength anomalous dispersion - پراکندگی غیر طبیعی در طول موج تکProtein Data Bank - پروتئین بانک اطلاعاتیPyrophosphate - پیرو فسفاتinorganic pyrophosphate - پیرو فسفات معدنیthin-layer chromatography - کروماتوگرافی نازک لایه
موضوعات مرتبط
علوم زیستی و بیوفناوری
بیوشیمی، ژنتیک و زیست شناسی مولکولی
زیست شناسی مولکولی
پیش نمایش صفحه اول مقاله

چکیده انگلیسی
The optimal balance of cellular nucleotides and the efficient elimination of non-canonical nucleotides are critical to avoiding erroneous mutation during DNA replication. One such mechanism involves the degradation of excessive or abnormal nucleotides by nucleotide-hydrolyzing enzymes. YpgQ contains the histidine-aspartate (HD) domain that is involved in the hydrolysis of nucleotides or nucleic acids, but the enzymatic activity and substrate specificity of YpgQ have never been characterized. Here, we unravel the catalytic activity and structural features of YpgQ to report the first Mn2+-dependent pyrophosphohydrolase that hydrolyzes (deoxy)ribonucleoside triphosphate [(d)NTP] to (deoxy)ribonucleoside monophosphate and pyrophosphate using the HD domain. YpgQ from Bacillus subtilis (bsYpgQ) displays a helical structure and assembles into a unique dimeric architecture that has not been observed in other HD domain-containing proteins. Each bsYpgQ monomer accommodates a metal ion and a nucleotide substrate in a cavity located between the N- and C-terminal lobes. The metal cofactor is coordinated by the canonical residues of the HD domain, namely, two histidine residues and two aspartate residues, and is positioned in close proximity to the β-phosphate group of the nucleotide, allowing us to propose a nucleophilic attack mechanism for the nucleotide hydrolysis reaction. YpgQ enzymes from other bacterial species also catalyze pyrophosphohydrolysis but exhibit different substrate specificity. Comparative structural and mutational studies demonstrated that residues outside the major substrate-binding site of bsYpgQ are responsible for the species-specific substrate preference. Taken together, our structural and biochemical analyses highlight the substrate-recognition mode and catalysis mechanism of YpgQ in pyrophosphohydrolysis.
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Journal of Structural Biology - Volume 195, Issue 1, July 2016, Pages 113-122
Journal: Journal of Structural Biology - Volume 195, Issue 1, July 2016, Pages 113-122
نویسندگان
Ye Ji Jeon, Sun Cheol Park, Wan Seok Song, Ok-Hee Kim, Byung-Chul Oh, Sung-il Yoon,