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PDBsum entry 2dg1
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* Residue conservation analysis
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PDB id:
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Hydrolase
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Title:
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Crystal structure of drp35, a 35kda drug responsive protein from staphylococcus aureus, complexed with ca2+
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Structure:
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Drp35. Chain: a, b, c, d, e, f. Synonym: lactonase. Engineered: yes
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Source:
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Staphylococcus aureus. Organism_taxid: 1280. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Biol. unit:
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Monomer (from
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Resolution:
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1.72Å
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R-factor:
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0.169
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R-free:
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0.197
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Authors:
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Y.Tanaka,Y.Ohki,K.Morikawa,M.Yao,N.Watanabe,T.Ohta,I.Tanaka
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Key ref:
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Y.Tanaka
et al.
(2007).
Structural and mutational analyses of Drp35 from Staphylococcus aureus: a possible mechanism for its lactonase activity.
J Biol Chem,
282,
5770-5780.
PubMed id:
DOI:
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Date:
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07-Mar-06
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Release date:
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12-Dec-06
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PROCHECK
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Headers
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References
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Q99QV3
(DRP35_STAAM) -
Lactonase drp35 from Staphylococcus aureus (strain Mu50 / ATCC 700699)
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Seq:
Struc:
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324 a.a.
321 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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DOI no:
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J Biol Chem
282:5770-5780
(2007)
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PubMed id:
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Structural and mutational analyses of Drp35 from Staphylococcus aureus: a possible mechanism for its lactonase activity.
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Y.Tanaka,
K.Morikawa,
Y.Ohki,
M.Yao,
K.Tsumoto,
N.Watanabe,
T.Ohta,
I.Tanaka.
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ABSTRACT
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Drp35 is a protein induced by cell wall-affecting antibiotics or detergents; it
possesses calcium-dependent lactonase activity. To determine the molecular basis
of the lactonase activity, we first solved the crystal structures of Drp35 with
and without Ca(2+); these showed that the molecule has a six-bladed
beta-propeller structure with two calcium ions bound at the center of the
beta-propeller and surface region. Mutational analyses of evolutionarily
conserved residues revealed that the central calcium-binding site is essential
for the enzymatic activity of Drp35. Substitution of some other amino acid
residues for the calcium-binding residues demonstrated the critical
contributions of Glu(48), Asp(138), and Asp(236) to the enzymatic activity.
Differential scanning calorimetric analysis revealed that the loss of activity
of E48Q and D236N, but not D138N, was attributed to their inability to hold the
calcium ion. Further structural analysis of the D138N mutant indicates that it
lacks a water molecule bound to the calcium ion rather than the calcium ion
itself. Based on these observations and structural information, a possible
catalytic mechanism in which the calcium ion and its binding residues play
direct roles was proposed for the lactonase activity of Drp35.
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Selected figure(s)
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Figure 5.
FIGURE 5. Differential scanning calorimetry of Drp35, E48Q,
D138N, and D236N. Shown are heat capacity curves in 50 mM
acetate, pH 5.6, and 1 mM EDTA (A) and in 50 mM acetate, pH 5.6,
and 1 mM CaCl[2] (B). Solid lines, wild type; dotted lines,
E48Q; dashed lines, D138N; dashed and dotted lines, D236N.
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Figure 8.
FIGURE 8. Schematic representation of proposed mechanism
for lactonase activity of Drp35. A water molecule bound to Ca1
and Asp^138 is activated by Asp^138 and Ca1 (left). The
generated hydroxyl group attacks the carbon atom in the carbonyl
group of the substrate, and the oxygen atom whose covalent bond
is broken is protonated by Asp^236 (center).
3-(2-Hydroxyphenyl)propionic acid is generated.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2007,
282,
5770-5780)
copyright 2007.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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J.G.Bogner-Strauss,
A.Prokesch,
F.Sanchez-Cabo,
D.Rieder,
H.Hackl,
K.Duszka,
A.Krogsdam,
B.Di Camillo,
E.Walenta,
A.Klatzer,
A.Lass,
M.Pinent,
W.C.Wong,
F.Eisenhaber,
and
Z.Trajanoski
(2010).
Reconstruction of gene association network reveals a transmembrane protein required for adipogenesis and targeted by PPARĪ³.
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Cell Mol Life Sci,
67,
4049-4064.
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S.Chakraborti,
and
B.J.Bahnson
(2010).
Crystal structure of human senescence marker protein 30: insights linking structural, enzymatic, and physiological functions .
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Biochemistry,
49,
3436-3444.
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PDB codes:
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M.M.Blum,
M.Mustyakimov,
H.Rüterjans,
K.Kehe,
B.P.Schoenborn,
P.Langan,
and
J.C.Chen
(2009).
Rapid determination of hydrogen positions and protonation states of diisopropyl fluorophosphatase by joint neutron and X-ray diffraction refinement.
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Proc Natl Acad Sci U S A,
106,
713-718.
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PDB code:
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M.Watanabe,
Y.Tanaka,
A.Suenaga,
M.Kuroda,
M.Yao,
N.Watanabe,
F.Arisaka,
T.Ohta,
I.Tanaka,
and
K.Tsumoto
(2008).
Structural basis for multimeric heme complexation through a specific protein-heme interaction: the case of the third neat domain of IsdH from Staphylococcus aureus.
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J Biol Chem,
283,
28649-28659.
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PDB codes:
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T.Ishikawa,
H.Nishikawa,
Y.Gao,
Y.Sawa,
H.Shibata,
Y.Yabuta,
T.Maruta,
and
S.Shigeoka
(2008).
The pathway via D-galacturonate/L-galactonate is significant for ascorbate biosynthesis in Euglena gracilis: identification and functional characterization of aldonolactonase.
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J Biol Chem,
283,
31133-31141.
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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.
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Links
