2IIZ

Crystal structure of putative melanin biosynthesis protein TyrA with bound heme (NP_716371.1) from Shewanella Oneidensis at 2.30 A resolution

Summary for 2IIZ

• Entry DOI: 10.2210/pdb2iiz/pdb
• Descriptor: Melanin biosynthesis protein TyrA, putative, SODIUM ION, PROTOPORPHYRIN IX CONTAINING FE, ... (6 entities in total)
• Functional Keywords: np_716371.1, putative melanin biosynthesis protein tyra, structural genomics, psi-2, protein structure initiative, joint center for structural genomics, jcsg, structural genomics-unknown function complex, structural genomics/unknown function
• Biological source: Shewanella oneidensis
• Total number of polymer chains: 1
• Total formula weight: 37293.50

Authors

Joint Center for Structural Genomics (JCSG) (deposition date: 2006-09-28, release date: 2006-11-14, Last modification date: 2024-11-13)

Primary citation

Zubieta, C.,Joseph, R.,Krishna, S.S.,McMullan, D.,Kapoor, M.,Axelrod, H.L.,Miller, M.D.,Abdubek, P.,Acosta, C.,Astakhova, T.,Carlton, D.,Chiu, H.J.,Clayton, T.,Deller, M.C.,Duan, L.,Elias, Y.,Elsliger, M.A.,Feuerhelm, J.,Grzechnik, S.K.,Hale, J.,Han, G.W.,Jaroszewski, L.,Jin, K.K.,Klock, H.E.,Knuth, M.W.,Kozbial, P.,Kumar, A.,Marciano, D.,Morse, A.T.,Murphy, K.D.,Nigoghossian, E.,Okach, L.,Oommachen, S.,Reyes, R.,Rife, C.L.,Schimmel, P.,Trout, C.V.,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.
Identification and structural characterization of heme binding in a novel dye-decolorizing peroxidase, TyrA.
Proteins, 69:234-243, 2007

PubMed Abstract: TyrA is a member of the dye-decolorizing peroxidase (DyP) family, a new family of heme-dependent peroxidase recently identified in fungi and bacteria. Here, we report the crystal structure of TyrA in complex with iron protoporphyrin (IX) at 2.3 A. TyrA is a dimer, with each monomer exhibiting a two-domain, alpha/beta ferredoxin-like fold. Both domains contribute to the heme-binding site. Co-crystallization in the presence of an excess of iron protoporphyrin (IX) chloride allowed for the unambiguous location of the active site and the specific residues involved in heme binding. The structure reveals a Fe-His-Asp triad essential for heme positioning, as well as a novel conformation of one of the heme propionate moieties compared to plant peroxidases. Structural comparison to the canonical DyP family member, DyP from Thanatephorus cucumeris (Dec 1), demonstrates conservation of this novel heme conformation, as well as residues important for heme binding. Structural comparisons with representative members from all classes of the plant, bacterial, and fungal peroxidase superfamily demonstrate that TyrA, and by extension the DyP family, adopts a fold different from all other structurally characterized heme peroxidases. We propose that a new superfamily be added to the peroxidase classification scheme to encompass the DyP family of heme peroxidases.

PubMed: 17654547
DOI: 10.1002/prot.21673

Experimental method

X-RAY DIFFRACTION (2.3 Å)