4PF6

CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM ROSEOBACTER DENITRIFICANS (RD1_0742, TARGET EFI-510239) WITH BOUND 3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID (KDO)

4PF6 の概要

• エントリーDOI: 10.2210/pdb4pf6/pdb
• 関連するPDBエントリー: 4PF8
• 分子名称: C4-dicarboxylate-binding protein, 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid, TRIETHYLENE GLYCOL, ... (5 entities in total)
• 機能のキーワード: trap periplasmic solute binding family, enzyme function initiative, efi, structural genomics, transport protein
• 由来する生物種: Roseobacter denitrificans (Erythrobacter sp. (strain OCh 114))
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 37251.82

構造登録者

Vetting, M.W.,Al Obaidi, N.F.,Morisco, L.L.,Wasserman, S.R.,Stead, M.,Attonito, J.D.,Scott Glenn, A.,Chowdhury, S.,Evans, B.,Hillerich, B.,Love, J.,Seidel, R.D.,Whalen, K.L.,Gerlt, J.A.,Almo, S.C.,Enzyme Function Initiative (EFI) (登録日: 2014-04-28, 公開日: 2014-05-14, 最終更新日: 2024-10-16)

主引用文献

Vetting, M.W.,Al-Obaidi, N.,Zhao, S.,San Francisco, B.,Kim, J.,Wichelecki, D.J.,Bouvier, J.T.,Solbiati, J.O.,Vu, H.,Zhang, X.,Rodionov, D.A.,Love, J.D.,Hillerich, B.S.,Seidel, R.D.,Quinn, R.J.,Osterman, A.L.,Cronan, J.E.,Jacobson, M.P.,Gerlt, J.A.,Almo, S.C.
Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.
Biochemistry, 54:909-931, 2015

PubMed Abstract: The rate at which genome sequencing data is accruing demands enhanced methods for functional annotation and metabolism discovery. Solute binding proteins (SBPs) facilitate the transport of the first reactant in a metabolic pathway, thereby constraining the regions of chemical space and the chemistries that must be considered for pathway reconstruction. We describe high-throughput protein production and differential scanning fluorimetry platforms, which enabled the screening of 158 SBPs against a 189 component library specifically tailored for this class of proteins. Like all screening efforts, this approach is limited by the practical constraints imposed by construction of the library, i.e., we can study only those metabolites that are known to exist and which can be made in sufficient quantities for experimentation. To move beyond these inherent limitations, we illustrate the promise of crystallographic- and mass spectrometric-based approaches for the unbiased use of entire metabolomes as screening libraries. Together, our approaches identified 40 new SBP ligands, generated experiment-based annotations for 2084 SBPs in 71 isofunctional clusters, and defined numerous metabolic pathways, including novel catabolic pathways for the utilization of ethanolamine as sole nitrogen source and the use of d-Ala-d-Ala as sole carbon source. These efforts begin to define an integrated strategy for realizing the full value of amassing genome sequence data.

PubMed: 25540822
DOI: 10.1021/bi501388y

実験手法

X-RAY DIFFRACTION (1.75 Å)