Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37293.50 
• Atom Count: 2502 
• Residue Count: 312 
• Unique protein chains: 1

2IIZ

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

• DOI: 10.2210/pdb2IIZ/pdb

• Classification: Structural Genomics/Unknown function
• Organism(s): Shewanella oneidensis (strain MR-1)
• Expression System: Escherichia coli


• Deposited: 2006-09-28 Released: 2006-11-14 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

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

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

• PubMed: 17654547 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Melanin biosynthesis protein TyrA, putative	A	312	Shewanella 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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
IPA	A	ISOPROPYL ALCOHOL 2-PROPANOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
HEM	A	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.266 
• R-Value Work: 0.205 
• Space Group: P 4₃ 2₁ 2
• Diffraction Data DOI: 
  10.18430/M32IIZ Protein Diffraction

Unit Cell:

Length (Å)	Angle (°)
a = 94.837	α = 90.00
b = 94.837	β = 90.00
c = 116.666	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling
MolProbity	model building
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-09-28 
• Released Date: 2006-11-14 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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