2GVK

Crystal structure of a dye-decolorizing peroxidase (DyP) from Bacteroides thetaiotaomicron VPI-5482 at 1.6 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif.

Zubieta, C., Krishna, S.S., Kapoor, M., Kozbial, P., McMullan, D., Axelrod, H.L., Miller, M.D., Abdubek, P., Ambing, E., Astakhova, T., Carlton, D., Chiu, H.J., Clayton, T., Deller, M.C., Duan, L., Elsliger, M.A., Feuerhelm, J., Grzechnik, S.K., Hale, J., Hampton, E., Han, G.W., Jaroszewski, L., Jin, K.K., Klock, H.E., Knuth, M.W., Kumar, A., Marciano, D., Morse, A.T., Nigoghossian, E., Okach, L., Oommachen, S., Reyes, R., Rife, C.L., Schimmel, P., 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: 223-233

  • DOI: 10.1002/prot.21550
  • Primary Citation of Related Structures:  
    2GVK, 2HAG

  • PubMed Abstract: 

    • 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 ...

    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).

    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Heme peroxidaseA317Bacteroides thetaiotaomicron VPI-5482Mutation(s): 11 
Gene Names: BT_1219
UniProt
Find proteins for Q8A8E8 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A8E8 
Go to UniProtKB:  Q8A8E8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A8E8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
ACY
Query on ACY
Download Ideal Coordinates CCD File 
L [auth A],
M [auth A]		ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
E [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
UNL
Query on UNL
Download Ideal Coordinates CCD File 
F [auth A]Unknown ligand
FKNQFGJONOIPTF-UHFFFAOYSA-N		 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 = 109.09α = 90
b = 109.09β = 90
c = 122.1γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SOLVEphasing

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-16
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2023-01-25
    Changes: Database references, Derived calculations