7DCM

Crystal structure of CITX

7DCM の概要

• エントリーDOI: 10.2210/pdb7dcm/pdb
• 分子名称: Probable apo-citrate lyase phosphoribosyl-dephospho-CoA transferase, ZINC ION (3 entities in total)
• 機能のキーワード: zinc finger, transferase
• 由来する生物種: Escherichia coli
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 20787.74

構造登録者

Xu, H.,Wang, B.,Su, X.D. (登録日: 2020-10-26, 公開日: 2021-11-03, 最終更新日: 2024-10-09)

主引用文献

Cheng, Y.,Wang, H.,Xu, H.,Liu, Y.,Ma, B.,Chen, X.,Zeng, X.,Wang, X.,Wang, B.,Shiau, C.,Ovchinnikov, S.,Su, X.D.,Wang, C.
Co-evolution-based prediction of metal-binding sites in proteomes by machine learning.
Nat.Chem.Biol., 19:548-555, 2023

PubMed Abstract: Metal ions have various important biological roles in proteins, including structural maintenance, molecular recognition and catalysis. Previous methods of predicting metal-binding sites in proteomes were based on either sequence or structural motifs. Here we developed a co-evolution-based pipeline named 'MetalNet' to systematically predict metal-binding sites in proteomes. We applied MetalNet to proteomes of four representative prokaryotic species and predicted 4,849 potential metalloproteins, which substantially expands the currently annotated metalloproteomes. We biochemically and structurally validated previously unannotated metal-binding sites in several proteins, including apo-citrate lyase phosphoribosyl-dephospho-CoA transferase citX, an Escherichia coli enzyme lacking structural or sequence homology to any known metalloprotein (Protein Data Bank (PDB) codes: 7DCM and 7DCN ). MetalNet also successfully recapitulated all known zinc-binding sites from the human spliceosome complex. The pipeline of MetalNet provides a unique and enabling tool for interrogating the hidden metalloproteome and studying metal biology.

PubMed: 36593274
DOI: 10.1038/s41589-022-01223-z

実験手法

X-RAY DIFFRACTION (2.495 Å)