2IIZ

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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1002/prot.21673

  • 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. Ty ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Melanin biosynthesis protein TyrA, putative
A
312Shewanella oneidensis (strain MR-1)Mutation(s): 0 
Find proteins for Q8EIU4 (Shewanella oneidensis (strain MR-1))
Go to UniProtKB:  Q8EIU4
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA

Download SDF File 
Download CCD File 
A
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 94.837α = 90.00
b = 94.837β = 90.00
c = 116.666γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
MolProbitymodel building
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-14
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description