2GVK

Crystal structure of a dye-decolorizing peroxidase (DyP) from Bacteroides thetaiotaomicron VPI-5482 at 1.6 A resolution

2GVK の概要

• エントリーDOI: 10.2210/pdb2gvk/pdb
• 分子名称: Heme peroxidase, CHLORIDE ION, SODIUM ION, ... (7 entities in total)
• 機能のキーワード: pc04261d, structural genomics, joint center for structural genomics, jcsg, protein structure initiative, psi, heme peroxidase, oxidoreductase
• 由来する生物種: Bacteroides thetaiotaomicron
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 36196.01

構造登録者

Joint Center for Structural Genomics (JCSG) (登録日: 2006-05-02, 公開日: 2006-05-16, 最終更新日: 2024-11-13)

主引用文献

Zubieta, C.,Krishna, S.S.,Kapoor, M.,Kozbial, P.,McMullan, D.,Axelrod, H.L.,Miller, M.D.,Abdubek, P.,Ambing, E.,Astakhova, T.,Carlton, D.,Chiu, H.J.,Clayton, T.,Deller, M.C.,Duan, L.,Elsliger, M.A.,Feuerhelm, J.,Grzechnik, S.K.,Hale, J.,Hampton, E.,Han, G.W.,Jaroszewski, L.,Jin, K.K.,Klock, H.E.,Knuth, M.W.,Kumar, A.,Marciano, D.,Morse, A.T.,Nigoghossian, E.,Okach, L.,Oommachen, S.,Reyes, R.,Rife, C.L.,Schimmel, P.,van den Bedem, H.,Weekes, D.,White, A.,Xu, Q.,Hodgson, K.O.,Wooley, J.,Deacon, A.M.,Godzik, A.,Lesley, S.A.,Wilson, I.A.
Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif.
Proteins, 69:223-233, 2007

PubMed Abstract: BtDyP from Bacteroides thetaiotaomicron (strain VPI-5482) and TyrA from Shewanella oneidensis are dye-decolorizing peroxidases (DyPs), members of a new family of heme-dependent peroxidases recently identified in fungi and bacteria. Here, we report the crystal structures of BtDyP and TyrA at 1.6 and 2.7 A, respectively. BtDyP assembles into a hexamer, while TyrA assembles into a dimer; the dimerization interface is conserved between the two proteins. Each monomer exhibits a two-domain, alpha+beta ferredoxin-like fold. A site for heme binding was identified computationally, and modeling of a heme into the proposed active site allowed for identification of residues likely to be functionally important. Structural and sequence comparisons with other DyPs demonstrate a conservation of putative heme-binding residues, including an absolutely conserved histidine. Isothermal titration calorimetry experiments confirm heme binding, but with a stoichiometry of 0.3:1 (heme:protein).

PubMed: 17654545
DOI: 10.1002/prot.21550

実験手法

X-RAY DIFFRACTION (1.6 Å)