Identification and structural characterization of heme binding in a novel dye-decolorizing peroxidase, TyrA.
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.
Zubieta
Chloe
C
Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, California, USA.
Joseph
Rosanne
R
Krishna
S Sri
SS
McMullan
Daniel
D
Kapoor
Mili
M
Axelrod
Herbert L
HL
Miller
Mitchell D
MD
Abdubek
Polat
P
Acosta
Claire
C
Astakhova
Tamara
T
Carlton
Dennis
D
Chiu
Hsiu-Ju
HJ
Clayton
Thomas
T
Deller
Marc C
MC
Duan
Lian
L
Elias
Ylva
Y
Elsliger
Marc-André
MA
Feuerhelm
Julie
J
Grzechnik
Slawomir K
SK
Hale
Joanna
J
Han
Gye Won
GW
Jaroszewski
Lukasz
L
Jin
Kevin K
KK
Klock
Heath E
HE
Knuth
Mark W
MW
Kozbial
Piotr
P
Kumar
Abhinav
A
Marciano
David
D
Morse
Andrew T
AT
Murphy
Kevin D
KD
Nigoghossian
Edward
E
Okach
Linda
L
Oommachen
Silvya
S
Reyes
Ron
R
Rife
Christopher L
CL
Schimmel
Paul
P
Trout
Christina V
CV
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
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism*; D001665:Binding Sites; D004396:Coloring Agents / Q000378:metabolism*; D018360:Crystallography, X-Ray; D006418:Heme / Q000378:metabolism*; D008969:Molecular Sequence Data; D009097:Multienzyme Complexes / Q000737:chemistry* / Q000378:metabolism*; D010544:Peroxidases / Q000737:chemistry* / Q000378:metabolism*; D011485:Protein Binding; D020592:Shewanella / Q000201:enzymology
D001426:Bacterial Proteins; D004396:Coloring Agents; D009097:Multienzyme Complexes; C076398:TyrA protein, Bacteria; D006418:Heme; D010544:Peroxidases