3Q08

Crystal Structure of Chlorite Dismutase from D. Aromatica at pH 6.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural features promoting dioxygen production by Dechloromonas aromatica chlorite dismutase.

Goblirsch, B.R.Streit, B.R.DuBois, J.L.Wilmot, C.M.

(2010) J Biol Inorg Chem 15: 879-888

  • DOI: https://doi.org/10.1007/s00775-010-0651-0
  • Primary Citation of Related Structures:  
    3Q08, 3Q09

  • PubMed Abstract: 

    Chlorite dismutase (Cld) is a heme enzyme capable of rapidly and selectively decomposing chlorite (ClO(2) (-)) to Cl(-) and O(2). The ability of Cld to promote O(2) formation from ClO(2) (-) is unusual. Heme enzymes generally utilize ClO(2) (-) as an oxidant for reactions such as oxygen atom transfer to, or halogenation of, a second substrate. The X-ray crystal structure of Dechloromonas aromatica Cld co-crystallized with the substrate analogue nitrite (NO(2) (-)) was determined to investigate features responsible for this novel reactivity. The enzyme active site contains a single b-type heme coordinated by a proximal histidine residue. Structural analysis identified a glutamate residue hydrogen-bonded to the heme proximal histidine that may stabilize reactive heme species. A solvent-exposed arginine residue likely gates substrate entry to a tightly confined distal pocket. On the basis of the proposed mechanism of Cld, initial reaction of ClO(2) (-) within the distal pocket generates hypochlorite (ClO(-)) and a compound I intermediate. The sterically restrictive distal pocket probably facilitates the rapid rebound of ClO(-) with compound I forming the Cl(-) and O(2) products. Common to other heme enzymes, Cld is inactivated after a finite number of turnovers, potentially via the observed formation of an off-pathway tryptophanyl radical species through electron migration to compound I. Three tryptophan residues of Cld have been identified as candidates for this off-pathway radical. Finally, a juxtaposition of hydrophobic residues between the distal pocket and the enzyme surface suggests O(2) may have a preferential direction for exiting the active site.


  • Organizational Affiliation

    Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorite dismutase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
248Dechloromonas aromatica RCBMutation(s): 0 
Gene Names: Daro_2580
EC: 1.13.11.49
UniProt
Find proteins for Q47CX0 (Dechloromonas aromatica (strain RCB))
Explore Q47CX0 
Go to UniProtKB:  Q47CX0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47CX0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
AB [auth I]
CA [auth C]
CC [auth P]
FB [auth J]
GC [auth Q]
AB [auth I],
CA [auth C],
CC [auth P],
FB [auth J],
GC [auth Q],
HA [auth D],
IB [auth K],
KC [auth R],
LA [auth E],
MB [auth L],
OA [auth F],
PC [auth S],
QB [auth M],
SA [auth G],
TC [auth T],
U [auth A],
UB [auth N],
WA [auth H],
Y [auth B],
ZB [auth O]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
MES
Query on MES

Download Ideal Coordinates CCD File 
AA [auth B]
BC [auth O]
CB [auth I]
EA [auth C]
EC [auth P]
AA [auth B],
BC [auth O],
CB [auth I],
EA [auth C],
EC [auth P],
HB [auth J],
IC [auth Q],
JA [auth D],
KB [auth K],
MC [auth R],
NA [auth E],
OB [auth L],
QA [auth F],
RC [auth S],
SB [auth M],
UA [auth G],
VC [auth T],
W [auth A],
WB [auth N],
YA [auth H]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
NO2
Query on NO2

Download Ideal Coordinates CCD File 
AC [auth O]
BB [auth I]
DA [auth C]
DC [auth P]
GB [auth J]
AC [auth O],
BB [auth I],
DA [auth C],
DC [auth P],
GB [auth J],
HC [auth Q],
IA [auth D],
JB [auth K],
LC [auth R],
MA [auth E],
NB [auth L],
PA [auth F],
QC [auth S],
RB [auth M],
TA [auth G],
UC [auth T],
V [auth A],
VB [auth N],
XA [auth H],
Z [auth B]
NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M
CA
Query on CA

Download Ideal Coordinates CCD File 
BA [auth B]
DB [auth I]
EB [auth J]
FA [auth C]
FC [auth P]
BA [auth B],
DB [auth I],
EB [auth J],
FA [auth C],
FC [auth P],
GA [auth D],
JC [auth Q],
KA [auth E],
LB [auth K],
NC [auth R],
OC [auth S],
PB [auth L],
RA [auth F],
SC [auth T],
TB [auth M],
VA [auth G],
X [auth A],
XB [auth N],
YB [auth O],
ZA [auth H]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.704α = 90
b = 202.85β = 90
c = 247.103γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations