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

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.6 of the entry. See complete history


Identification and structural characterization of heme binding in a novel dye-decolorizing peroxidase, TyrA.

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.

(2007) Proteins 69: 234-243

  • DOI: https://doi.org/10.1002/prot.21673
  • Primary Citation of Related Structures:  

  • 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.

  • Organizational Affiliation

    Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, California, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Melanin biosynthesis protein TyrA, putative312Shewanella oneidensisMutation(s): 13 
Gene Names: NP_716371.1
Find proteins for Q8EIU4 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1))
Explore Q8EIU4 
Go to UniProtKB:  Q8EIU4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8EIU4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.837α = 90
b = 94.837β = 90
c = 116.666γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
MolProbitymodel building
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-11-14
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-01-25
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-09-20
    Changes: Data collection, Refinement description
  • Version 1.6: 2023-11-15
    Changes: Data collection