PDBsum entry 2hag

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protein links
Hydrolase PDB id
Protein chain
307 a.a. *
Waters ×48
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of a putative dyp-type peroxidase protein from shewanella oneidensis at 2.75 a resolution
Structure: Melanin biosynthesis protein tyra, putative. Chain: a. Engineered: yes
Source: Shewanella oneidensis. Organism_taxid: 70863. Gene: np_716371.1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
2.75Å     R-factor:   0.193     R-free:   0.229
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref:
C.Zubieta et al. (2007). Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif. Proteins, 69, 223-233. PubMed id: 17654545 DOI: 10.1002/prot.21550
12-Jun-06     Release date:   08-Aug-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q8EIU4  (Q8EIU4_SHEON) -  Dyp-type heme-dependent peroxidase
311 a.a.
307 a.a.
Key:    PfamA domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     molecular_function     4 terms  


DOI no: 10.1002/prot.21550 Proteins 69:223-233 (2007)
PubMed id: 17654545  
Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif.
C.Zubieta, S.S.Krishna, M.Kapoor, P.Kozbial, D.McMullan, H.L.Axelrod, M.D.Miller, P.Abdubek, E.Ambing, T.Astakhova, D.Carlton, H.J.Chiu, T.Clayton, M.C.Deller, L.Duan, M.A.Elsliger, J.Feuerhelm, S.K.Grzechnik, J.Hale, E.Hampton, G.W.Han, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, A.Kumar, D.Marciano, A.T.Morse, E.Nigoghossian, L.Okach, S.Oommachen, R.Reyes, C.L.Rife, P.Schimmel, H.van den Bedem, D.Weekes, A.White, Q.Xu, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, I.A.Wilson.
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).
  Selected figure(s)  
Figure 2.
Figure 2. Structural comparisons of BtDyP and related proteins: (A) Stereo ribbon diagram of a structural superposition of BtDyP (grey), TyrA (yellow), TT1485 (green), and chlorite dismutase (blue) monomers. All of these proteins contain duplicated ferredoxin-like folds arranged as a -barrel. (B) Stereo diagram of the BtDyP hexamer, with dimers shown in different shades of the same color. (C) Stereo diagram of the TyrA dimer (grey) overlaid on the BtDyP dimer (green). In BtDyP, three dimers pack around the central threefold axis to form the hexamer.
Figure 4.
Figure 4. Heme binding model for BtDyP: (A) BtDyP dimer showing two independent heme-binding sites. (B) Stereo view of putative heme-binding residues. The heme is colored by atom, with carbons (cyan), nitrogens (blue), oxygens (red), and iron (orange). Residues from BtDyP are labeled and colored by atom as for the heme, with carbons in green. Side chain conformations were not optimized for heme binding.
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2007, 69, 223-233) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21358756 K.C.Yam, S.Okamoto, J.N.Roberts, and L.D.Eltis (2011).
Adventures in Rhodococcus - from steroids to explosives.
  Can J Microbiol, 57, 155-168.  
  20944226 A.E.Speers, and B.F.Cravatt (2010).
Ligands in crystal structures that aid in functional characterization.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1306-1308.  
19756587 C.Liers, C.Bobeth, M.Pecyna, R.Ullrich, and M.Hofrichter (2010).
DyP-like peroxidases of the jelly fungus Auricularia auricula-judae oxidize nonphenolic lignin model compounds and high-redox potential dyes.
  Appl Microbiol Biotechnol, 85, 1869-1879.  
19967355 E.van Bloois, D.E.Torres Pazmiño, R.T.Winter, and M.W.Fraaije (2010).
A robust and extracellular heme-containing peroxidase from Thermobifida fusca as prototype of a bacterial peroxidase superfamily.
  Appl Microbiol Biotechnol, 86, 1419-1430.  
20422179 H.J.Ogola, N.Hashimoto, S.Miyabe, H.Ashida, T.Ishikawa, H.Shibata, and Y.Sawa (2010).
Enhancement of hydrogen peroxide stability of a novel Anabaena sp. DyP-type peroxidase by site-directed mutagenesis of methionine residues.
  Appl Microbiol Biotechnol, 87, 1727-1736.  
20495915 M.Hofrichter, R.Ullrich, M.J.Pecyna, C.Liers, and T.Lundell (2010).
New and classic families of secreted fungal heme peroxidases.
  Appl Microbiol Biotechnol, 87, 871-897.  
19801472 H.J.Ogola, T.Kamiike, N.Hashimoto, H.Ashida, T.Ishikawa, H.Shibata, and Y.Sawa (2009).
Molecular characterization of a novel peroxidase from the cyanobacterium Anabaena sp. strain PCC 7120.
  Appl Environ Microbiol, 75, 7509-7518.  
19172747 M.Sutter, D.Boehringer, S.Gutmann, S.Günther, D.Prangishvili, M.J.Loessner, K.O.Stetter, E.Weber-Ban, and N.Ban (2008).
Structural basis of enzyme encapsulation into a bacterial nanocompartment.
  Nat Struct Mol Biol, 15, 939-947.
PDB code: 3dkt
17654547 C.Zubieta, R.Joseph, S.S.Krishna, D.McMullan, M.Kapoor, H.L.Axelrod, M.D.Miller, P.Abdubek, C.Acosta, T.Astakhova, D.Carlton, H.J.Chiu, T.Clayton, M.C.Deller, L.Duan, Y.Elias, M.A.Elsliger, J.Feuerhelm, S.K.Grzechnik, J.Hale, G.W.Han, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, P.Kozbial, A.Kumar, D.Marciano, A.T.Morse, K.D.Murphy, E.Nigoghossian, L.Okach, S.Oommachen, R.Reyes, C.L.Rife, P.Schimmel, C.V.Trout, H.van den Bedem, D.Weekes, A.White, Q.Xu, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2007).
Identification and structural characterization of heme binding in a novel dye-decolorizing peroxidase, TyrA.
  Proteins, 69, 234-243.
PDB code: 2iiz
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.