Methionine synthase encoded by the MTR gene is one of the key enzymes involved in the SAM (S- Adenosyl Methionine) cycle catalyzing the conversion of homocysteine to methionine. Methionine plays an important role in the DNA, RNA, protein, phospholipids, and neurotransmitters methylation. It also maintains serum homocysteine level and indirectly regulates de novo nucleotide synthesis and repair. The current study predicted the functional consequences of nsSNPs in human MTR gene using SIFT, PolyPhen2, PROVEAN, SNAP2, PMut, nsSNPAnalyzer, PhD-SNP, SNPs&GO, I-Mutant, MuPro, and iPTREE-STAB. The PTM sites within the protein were predicted using ModPred and the phylogenetic conservations of amino acids & conserved domains of protein were predicted using ConSurf and NCBI conserved domain search tool respectively. The protein 3D structure was generated using SPARKS-X and analyzed using RAMPAGE. Structural deviation was analyzed using TM-Score. STRING analysis was preformed to predict protein-protein interactions. D621G, G682D, V744L, V766E, and R1027W were predicted to be the most deleterious nsSNPs in MTR. R1027 was predicted to having the three PTM sites and G682 & V744 were predicted as highly conserved residues. D621G, G682D, V744L, V776E, and R1027W were predicted to be within conserved domains of methionine synthase. The G682D, V744L, V776E, and R1027W were predicted to alter protein 3D structure. STRING predicted that methionine synthase interacting with 10 different proteins. The present study predicted D621G, G682D, V744L, V766E, and R1027W as functionally and structurally significant nsSNPs in human MTR gene. The present study can provide the significant information for further experimental analysis.

Abbreviations: cblG: methylcobalamin deficiency G; MTR: 5-methyl tetrahydrofolate-homocysteine methyl transferase; MS: methionine synthase; SAM: S-adenosyl methionine; nsSNPs: non-synonymous single nucleotide polymorphisms; OMIM: online mendelian inheritance in man; NCBI: national center for biological information; SIFT: sorting intolerant from tolerant; PolyPhen2: polymorphism phenotyping 2; PROVEAN: protein variation effect analyzer; SNPs&GO: single nucleotide polymorphisms and gene ontology; PhD-SNP: predictor of human deleterious single nucleotide polymorphisms; RI: reliability index; PTM: post translational modification; SPDBV: Swiss PDB viewer; PDB: protein data bank; RMSD: root mean square deviation; STRING: search tool for the retrieval of interacting proteins

MTR基因编码的蛋氨酸合酶是参与SAM（S-腺苷蛋氨酸）循环的关键酶之一，催化高半胱氨酸向蛋氨酸的转化。蛋氨酸在DNA，RNA，蛋白质，磷脂和神经递质的甲基化中起重要作用。它还保持血清高半胱氨酸水平，并间接调节从头核苷酸的合成和修复。当前的研究预测了nsSNPs在人类MTR中的功能后果使用SIFT，PolyPhen2，PROVEAN，SNAP2，PMut，nsSNPAnalyzer，PhD-SNP，SNPs＆GO，I-Mutant，MuPro和iPTREE-STAB的基因。使用ModPred预测蛋白质中的PTM位点，并分别使用ConSurf和NCBI保守域搜索工具预测氨基酸和蛋白质保守域的系统发育保守性。蛋白质3D结构使用SPARKS-X生成，并使用RAMPAGE分析。使用TM-Score分析结构偏差。进行STRING分析以预测蛋白质-蛋白质相互作用。预计D621G，G682D，V744L，V766E和R1027W是MTR中最有害的nsSNP。R1027被预测具有三个PTM位点，而G682和V744被预测为高度保守的残基。D621G，G682D，V744L，V776E和R1027W预计位于蛋氨酸合酶的保守域内。预计G682D，V744L，V776E和R1027W会改变蛋白质3D结构。STRING预测蛋氨酸合酶与10种不同的蛋白质相互作用。本研究预测D621G，G682D，V744L，V766E和R1027W在人MTR基因中具有功能上和结构上的重要nsSNPs 。本研究可以为进一步的实验分析提供重要的信息。

缩写： cblG：甲基钴胺素缺乏症G；MTR：5-甲基四氢叶酸-高半胱氨酸甲基转移酶；MS：蛋氨酸合酶；SAM：S-腺苷甲硫氨酸；nsSNP：非同义的单核苷酸多态性；OMIM：人类在线孟德尔遗传；NCBI：国家生物信息中心；SIFT：将不宽容分类为宽容；PolyPhen2：多态性表型2；PROVEAN：蛋白质变异效应分析仪；SNPs＆GO：单核苷酸多态性和基因本体；PhD-SNP：人类有害单核苷酸多态性的预测因子；RI：可靠性指标；PTM：翻译后修改；SPDBV：瑞士PDB查看器；PDB：蛋白质数据库；RMSD：均方根偏差；STRING：用于检索相互作用蛋白的搜索工具