 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Oxidoreductase
|
PDB id
|
|
|
|
1uuv
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
PDB id:
|
|
|
|
| Name: |
|
Oxidoreductase
|
|
|
Title:
|
|
Naphthalene 1,2-dioxygenase with nitric oxide and indole bound in the active site.
|
|
Structure:
|
|
Naphthalene 1,2-dioxygenase alpha subunit. Chain: a. Synonym: naphthalene 1,2-dioxygenase isp alpha. Engineered: yes. Naphthalene 1,2-dioxygenase beta subunit. Chain: b. Synonym: naphthalene 1,2-dioxygenase isp beta. Engineered: yes
|
|
Source:
|
|
Pseudomonas putida. Organism_taxid: 303. Strain: ncib9816-4. Expressed in: escherichia coli. Expression_system_taxid: 562.
|
|
Biol. unit:
|
|
Hexamer (from PDB file)
|
|
Resolution:
|
|
|
1.65Å
|
R-factor:
|
0.184
|
R-free:
|
0.204
|
|
|
Authors:
|
|
A.Karlsson,J.V.Parales,R.E.Parales,D.T.Gibson,H.Eklund, S.Ramaswamy
|
|
Key ref:
|
|
A.Karlsson
et al.
(2005).
NO binding to naphthalene dioxygenase.
J Biol Inorg Chem,
10,
483-489.
PubMed id:
DOI:
|
|
|
Date:
|
|
|
11-Jan-04
|
Release date:
|
09-Feb-05
|
|
|
|
|
|
|
PROCHECK
|
|
|
|
|
|
Headers
|
|
|
|
References
|
|
|
|
|
|
|
|
|
|
|
|
Enzyme class:
|
|
Chains A, B:
E.C.1.14.12.12
- Naphthalene 1,2-dioxygenase.
|
|
|
|
|
|
|
Pathway:
|
|
Aromatic 1,2-Dioxygenases
|
|
|
|
|
|
Reaction:
|
|
Naphthalene + NADH + O2 = (1R,2S)-1,2-dihydronaphthalene-1,2-diol + NAD+
|
|
|
|
|
|
Naphthalene
Bound ligand (Het Group name = )
matches with 72.00% similarity
|
+
|
NADH
|
+
|
O(2)
|
=
|
(1R,2S)-1,2-dihydronaphthalene-1,2-diol
|
+
|
NAD(+)
|
|
|
|
|
|
|
|
|
|
Cofactor:
|
|
Iron
|
|
|
|
|
|
|
|
|
Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
|
|
|
|
|
|
|
|
|
|
|
Gene Ontology (GO) functional annotation
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Biological process
|
oxidation reduction
|
3 terms
|
|
|
Biochemical function
|
catalytic activity
|
11 terms
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
|
| |
|
DOI no:
|
J Biol Inorg Chem
10:483-489
(2005)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
NO binding to naphthalene dioxygenase.
|
|
A.Karlsson,
J.V.Parales,
R.E.Parales,
D.T.Gibson,
H.Eklund,
S.Ramaswamy.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
Nitric oxide (NO) is commonly used as an analogue for dioxygen in structural and
spectroscopic studies of oxygen binding and oxygen activation. In this study,
crystallographic structures of naphthalene dioxygenase (NDO) in complex with
nitric oxide are reported. In the presence of the aromatic substrate indole, NO
is bound end-on to the active-site mononuclear iron of NDO. The structural
observations correlate well with spectroscopic measurements of NO binding to NDO
in solution. However, the end-on binding of NO is in contrast to the recently
reported structure of oxygen to the active-site iron of NDO that binds side-on.
While NO is a good oxygen analogue with many similarities to O(2), the different
binding mode of NO to the active-site iron atom leads to different mechanistic
implications. Hence, caution needs to be used in extrapolating NO as an analogue
to O(2) binding.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
P.C.Bruijnincx,
G.van Koten,
and
R.J.Klein Gebbink
(2008).
Mononuclear non-heme iron enzymes with the 2-His-1-carboxylate facial triad: recent developments in enzymology and modeling studies.
|
| |
Chem Soc Rev, 37,
2716-2744.
|
|
|
|
|
|
|
T.Ohta,
S.Chakrabarty,
J.D.Lipscomb,
and
E.I.Solomon
(2008).
Near-IR MCD of the nonheme ferrous active site in naphthalene 1,2-dioxygenase: correlation to crystallography and structural insight into the mechanism of Rieske dioxygenases.
|
| |
J Am Chem Soc, 130,
1601-1610.
|
|
|
|
|
|
|
D.J.Ferraro,
E.N.Brown,
C.L.Yu,
R.E.Parales,
D.T.Gibson,
and
S.Ramaswamy
(2007).
Structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1.
|
| |
BMC Struct Biol, 7,
10.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.B.Neibergall,
A.Stubna,
Y.Mekmouche,
E.Münck,
and
J.D.Lipscomb
(2007).
Hydrogen peroxide dependent cis-dihydroxylation of benzoate by fully oxidized benzoate 1,2-dioxygenase.
|
| |
Biochemistry, 46,
8004-8016.
|
|
|
|
|
|
|
M.Tarasev,
A.Pinto,
D.Kim,
S.J.Elliott,
and
D.P.Ballou
(2006).
The "bridging" aspartate 178 in phthalate dioxygenase facilitates interactions between the Rieske center and the iron(II)--mononuclear center.
|
| |
Biochemistry, 45,
10208-10216.
|
|
|
|
|
|
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
codes are
shown on the right.
|
| |
Links
