The Metal-binding Protein Atlas (MbPA): An Integrated Database for Curating Metalloproteins in All Aspects

• Published in: Journal of molecular biology 2023-07, Vol.435 (14), p.168117-168117, Article 168117
• Main Authors: Li, Jinzhao, He, Xiang, Gao, Shuang, Liang, Yuchao, Qi, Zhi, Xi, Qilemuge, Zuo, Yongchun, Xing, Yongqiang
• Format: Article
• Language: English
• Subjects: Amino Acids - chemistry; Binding Sites; Cations - chemistry; diversity measure; metal-binding proteins; Metalloproteins - chemistry; Metalloproteins - genetics; Metals - chemistry; mutation information; protein structures
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2023.168117

[Display omitted] •MbPA is the most comprehensive resource of metal type, binding sites, sequences, structures and proteomics of metal-binding protein across multiple species.•MbPA embraces potential pathogenic mutations related to metalloprotein.•The Diversity Measure is firstly employed to describe the specificity of metal-binding in different area of periodic table. Metal-binding proteins are essential for the vital activities and engage in their roles by acting in concert with metal cations. MbPA (The Metal-binding Protein Atlas) is the most comprehensive resource up to now dedicated to curating metal-binding proteins. Currently, it contains 106,373 entries and 440,187 sites related to 54 metals and 8169 species. Users can view all metal-binding proteins and species-specific proteins in MbPA. There are also metal-proteomics data that quantitatively describes protein expression in different tissues and organs. By analyzing the data of the amino acid residues at the metal-binding site, it is found that about 80% of the metal ions tend to bind to cysteine, aspartic acid, glutamic acid, and histidine. Moreover, we use Diversity Measure to confirm that the diversity of metal-binding is specific in different area of periodic table, and further elucidate the binding modes of 19 transition metals on 20 amino acids. In addition, MbPA also embraces 6855 potential pathogenic mutations related to metalloprotein. The resource is freely available at http://bioinfor.imu.edu.cn/mbpa.