Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif.
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).
Zubieta
Chloe
C
Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, California, USA.
Krishna
S Sri
SS
Kapoor
Mili
M
Kozbial
Piotr
P
McMullan
Daniel
D
Axelrod
Herbert L
HL
Miller
Mitchell D
MD
Abdubek
Polat
P
Ambing
Eileen
E
Astakhova
Tamara
T
Carlton
Dennis
D
Chiu
Hsiu-Ju
HJ
Clayton
Thomas
T
Deller
Marc C
MC
Duan
Lian
L
Elsliger
Marc-André
MA
Feuerhelm
Julie
J
Grzechnik
Slawomir K
SK
Hale
Joanna
J
Hampton
Eric
E
Han
Gye Won
GW
Jaroszewski
Lukasz
L
Jin
Kevin K
KK
Klock
Heath E
HE
Knuth
Mark W
MW
Kumar
Abhinav
A
Marciano
David
D
Morse
Andrew T
AT
Nigoghossian
Edward
E
Okach
Linda
L
Oommachen
Silvya
S
Reyes
Ron
R
Rife
Christopher L
CL
Schimmel
Paul
P
van den Bedem
Henry
H
Weekes
Dana
D
White
Aprilfawn
A
Xu
Qingping
Q
Hodgson
Keith O
KO
Wooley
John
J
Deacon
Ashley M
AM
Godzik
Adam
A
Lesley
Scott A
SA
Wilson
Ian A
IA
D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000502:physiology; D001439:Bacteroides / Q000201:enzymology; D020134:Catalytic Domain; D004396:Coloring Agents / Q000378:metabolism*; D017124:Conserved Sequence; D018360:Crystallography, X-Ray; D006418:Heme / Q000378:metabolism*; D008969:Molecular Sequence Data; D009097:Multienzyme Complexes / Q000737:chemistry* / Q000502:physiology; D010544:Peroxidases / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D017510:Protein Folding; D017433:Protein Structure, Secondary; D020592:Shewanella / Q000201:enzymology
D001426:Bacterial Proteins; D004396:Coloring Agents; D009097:Multienzyme Complexes; C076398:TyrA protein, Bacteria; D006418:Heme; D010544:Peroxidases