• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利：CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法，用中文像聊天一样搜索，搜遍4000万医学文献。AI智能推荐，让科研检索更轻松。

立即免费搜索

文件翻译

保留排版，准确专业，支持PDF/Word/PPT等文件格式，支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述，25分钟生成高质量综述，智能提取关键信息，辅助科研写作。

立即免费体验

细菌和真菌来源的2-卤代链烷酸脱卤酶的计算机系统发育分析和分子建模研究

In Silico Phylogenetic Analysis and Molecular Modelling Study of 2-Haloalkanoic Acid Dehalogenase Enzymes from Bacterial and Fungal Origin.

作者信息

Satpathy Raghunath, Konkimalla V B, Ratha Jagnyeswar

机构信息

School of Life Science, Sambalpur University, Jyoti Vihar, Burla, Odisha 768019, India.

School of Biological Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar, Odisha 751005, India.

出版信息

Adv Bioinformatics. 2016;2016:8701201. doi: 10.1155/2016/8701201. Epub 2016 Jan 6.

DOI:10.1155/2016/8701201
PMID:26880911
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4736600/
Abstract

2-Haloalkanoic acid dehalogenase enzymes have broad range of applications, starting from bioremediation to chemical synthesis of useful compounds that are widely distributed in fungi and bacteria. In the present study, a total of 81 full-length protein sequences of 2-haloalkanoic acid dehalogenase from bacteria and fungi were retrieved from NCBI database. Sequence analysis such as multiple sequence alignment (MSA), conserved motif identification, computation of amino acid composition, and phylogenetic tree construction were performed on these primary sequences. From MSA analysis, it was observed that the sequences share conserved lysine (K) and aspartate (D) residues in them. Also, phylogenetic tree indicated a subcluster comprised of both fungal and bacterial species. Due to nonavailability of experimental 3D structure for fungal 2-haloalkanoic acid dehalogenase in the PDB, molecular modelling study was performed for both fungal and bacterial sources of enzymes present in the subcluster. Further structural analysis revealed a common evolutionary topology shared between both fungal and bacterial enzymes. Studies on the buried amino acids showed highly conserved Leu and Ser in the core, despite variation in their amino acid percentage. Additionally, a surface exposed tryptophan was conserved in all of these selected models.

摘要

2-卤代链烷酸脱卤酶具有广泛的应用，从生物修复到有用化合物的化学合成，这些酶广泛分布于真菌和细菌中。在本研究中，从NCBI数据库检索到了来自细菌和真菌的总共81条2-卤代链烷酸脱卤酶的全长蛋白质序列。对这些原始序列进行了诸如多序列比对（MSA）、保守基序鉴定、氨基酸组成计算和系统发育树构建等序列分析。从MSA分析中可以观察到，这些序列中存在保守的赖氨酸（K）和天冬氨酸（D）残基。此外，系统发育树显示了一个由真菌和细菌物种组成的亚群。由于PDB中没有真菌2-卤代链烷酸脱卤酶的实验性三维结构，因此对该亚群中存在的真菌和细菌来源的酶进行了分子建模研究。进一步的结构分析揭示了真菌和细菌酶之间共有的进化拓扑结构。对埋藏氨基酸的研究表明，尽管它们的氨基酸百分比存在差异，但核心区域的亮氨酸和丝氨酸高度保守。此外，在所有这些选定的模型中，一个表面暴露的色氨酸是保守的。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/289b/4736600/2d1766c35abf/ABI2016-8701201.007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/289b/4736600/028f6e34074b/ABI2016-8701201.001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/289b/4736600/e575e22536c0/ABI2016-8701201.002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/289b/4736600/81b6907c6ccc/ABI2016-8701201.003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/289b/4736600/0830fc6cc4f5/ABI2016-8701201.004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/289b/4736600/4e0bc7d11205/ABI2016-8701201.005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/289b/4736600/01147b8bc9a6/ABI2016-8701201.006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/289b/4736600/2d1766c35abf/ABI2016-8701201.007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/289b/4736600/028f6e34074b/ABI2016-8701201.001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/289b/4736600/e575e22536c0/ABI2016-8701201.002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/289b/4736600/81b6907c6ccc/ABI2016-8701201.003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/289b/4736600/0830fc6cc4f5/ABI2016-8701201.004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/289b/4736600/4e0bc7d11205/ABI2016-8701201.005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/289b/4736600/01147b8bc9a6/ABI2016-8701201.006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/289b/4736600/2d1766c35abf/ABI2016-8701201.007.jpg

相似文献

1
In Silico Phylogenetic Analysis and Molecular Modelling Study of 2-Haloalkanoic Acid Dehalogenase Enzymes from Bacterial and Fungal Origin.细菌和真菌来源的2-卤代链烷酸脱卤酶的计算机系统发育分析和分子建模研究
Adv Bioinformatics. 2016;2016:8701201. doi: 10.1155/2016/8701201. Epub 2016 Jan 6.
2
Characterization of tannase protein sequences of bacteria and fungi: an in silico study.细菌和真菌单宁酶蛋白序列的特性：一项计算机研究。
Protein J. 2012 Apr;31(4):306-27. doi: 10.1007/s10930-012-9405-x.
3
In silico analysis of L-asparaginase from different source organisms.不同来源生物体中L-天冬酰胺酶的计算机模拟分析
Interdiscip Sci. 2014 Jun;6(2):93-9. doi: 10.1007/s12539-012-0041-0. Epub 2014 Jun 17.
4
Insights to sequence information of polyphenol oxidase enzyme from different source organisms.不同来源生物体中多酚氧化酶酶的序列信息研究进展。
Appl Biochem Biotechnol. 2011 Sep;165(2):397-405. doi: 10.1007/s12010-011-9259-2. Epub 2011 Apr 27.
5
Bacterial DL-2-haloacid dehalogenase from Pseudomonas sp. strain 113: gene cloning and structural comparison with D- and L-2-haloacid dehalogenases.来自假单胞菌属菌株113的细菌DL-2-卤代酸脱卤酶：基因克隆及与D-和L-2-卤代酸脱卤酶的结构比较
J Bacteriol. 1997 Jul;179(13):4232-8. doi: 10.1128/jb.179.13.4232-4238.1997.
6
In Silico Evaluation, Phylogenetic Analysis, and Structural Modeling of the Class II Hydrophobin Family from Different Fungal Phytopathogens.不同真菌植物病原体中II类疏水蛋白家族的计算机模拟评估、系统发育分析和结构建模
Microorganisms. 2023 Oct 26;11(11):2632. doi: 10.3390/microorganisms11112632.
7
Identification of functional residues essential for dehalogenation by the non-stereospecific α-haloalkanoic acid dehalogenase from Rhizobium sp. RC1.根瘤菌属RC1中对非立体特异性α-卤代链烷酸脱卤酶脱卤作用至关重要的功能残基的鉴定。
J Basic Microbiol. 2015 Mar;55(3):324-30. doi: 10.1002/jobm.201300526.
8
In silico characterization of histidine Acid phytase sequences.组氨酸酸性植酸酶序列的计算机模拟表征
Enzyme Res. 2012;2012:845465. doi: 10.1155/2012/845465. Epub 2012 Dec 5.
9
Phylogenetic analyses reveal molecular signatures associated with functional divergence among Subtilisin like Serine Proteases are linked to lifestyle transitions in Hypocreales.系统发育分析表明，枯草杆菌蛋白酶样丝氨酸蛋白酶之间与功能分化相关的分子特征与肉座菌目的生活方式转变有关。
BMC Evol Biol. 2016 Oct 19;16(1):220. doi: 10.1186/s12862-016-0793-y.
10
Nucleotide sequence of the structural gene encoding a 2-haloalkanoic acid dehalogenase of Pseudomonas putida strain AJ1 and purification of the encoded protein.恶臭假单胞菌AJ1菌株2-卤代链烷酸脱卤酶结构基因的核苷酸序列及编码蛋白的纯化
J Gen Microbiol. 1992 Apr;138(4):675-83. doi: 10.1099/00221287-138-4-675.

引用本文的文献

1
Mini Review: Advances in 2-Haloacid Dehalogenases.迷你综述：2-卤代酸脱卤酶的研究进展
Front Microbiol. 2021 Oct 15;12:758886. doi: 10.3389/fmicb.2021.758886. eCollection 2021.

本文引用的文献

1
The I-TASSER Suite: protein structure and function prediction.I-TASSER套件：蛋白质结构与功能预测
Nat Methods. 2015 Jan;12(1):7-8. doi: 10.1038/nmeth.3213.
2
Aromatic amino acid mutagenesis at the substrate binding pocket of Yarrowia lipolytica lipase Lip2 affects its activity and thermostability.解脂耶氏酵母脂肪酶Lip2底物结合口袋处的芳香族氨基酸诱变影响其活性和热稳定性。
ScientificWorldJournal. 2014;2014:382581. doi: 10.1155/2014/382581. Epub 2014 Aug 13.
3
MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.MEGA6：分子进化遗传学分析版本 6.0。
Mol Biol Evol. 2013 Dec;30(12):2725-9. doi: 10.1093/molbev/mst197. Epub 2013 Oct 16.
4
Microorganisms and their roles in fundamental biogeochemical cycles.微生物及其在基本生物地球化学循环中的作用。
Curr Opin Biotechnol. 2011 Jun;22(3):456-64. doi: 10.1016/j.copbio.2011.01.008. Epub 2011 Feb 16.
5
Crystal structure of the probable haloacid dehalogenase PH0459 from Pyrococcus horikoshii OT3.来自嗜热栖热菌OT3的可能的卤代酸脱卤酶PH0459的晶体结构。
Protein Sci. 2006 Feb;15(2):373-7. doi: 10.1110/ps.051922406. Epub 2005 Dec 29.
6
Conservation and relative importance of residues across protein-protein interfaces.蛋白质-蛋白质界面上残基的保守性及相对重要性。
Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15447-52. doi: 10.1073/pnas.0505425102. Epub 2005 Oct 12.
7
Variation in structural location and amino acid conservation of functional sites in protein domain families.蛋白质结构域家族中功能位点的结构位置和氨基酸保守性的变异
BMC Bioinformatics. 2005 Aug 25;6:210. doi: 10.1186/1471-2105-6-210.
8
The Neurospora crassa gene responsible for the cut and ovc phenotypes encodes a protein of the haloacid dehalogenase family.粗糙脉孢菌中负责切割和ovc表型的基因编码一种卤代酸脱卤酶家族的蛋白质。
Mol Microbiol. 2005 Feb;55(3):828-38. doi: 10.1111/j.1365-2958.2004.04424.x.
9
Microorganisms degrading chlorobenzene via a meta-cleavage pathway harbor highly similar chlorocatechol 2,3-dioxygenase-encoding gene clusters.通过间位裂解途径降解氯苯的微生物含有高度相似的编码氯儿茶酚2,3-双加氧酶的基因簇。
Arch Microbiol. 2004 Oct;182(2-3):147-56. doi: 10.1007/s00203-004-0681-5. Epub 2004 Aug 31.
10
Quantifying the effect of burial of amino acid residues on protein stability.量化氨基酸残基埋藏对蛋白质稳定性的影响。
Proteins. 2004 Feb 1;54(2):315-22. doi: 10.1002/prot.10584.