2GVK

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

Summary for 2GVK

• Entry DOI: 10.2210/pdb2gvk/pdb
• Descriptor: Heme peroxidase, CHLORIDE ION, SODIUM ION, ... (7 entities in total)
• Functional Keywords: pc04261d, structural genomics, joint center for structural genomics, jcsg, protein structure initiative, psi, heme peroxidase, oxidoreductase
• Biological source: Bacteroides thetaiotaomicron
• Total number of polymer chains: 1
• Total formula weight: 36196.01

Authors

Joint Center for Structural Genomics (JCSG) (deposition date: 2006-05-02, release date: 2006-05-16, Last modification date: 2024-11-13)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.6 Å)