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PDBsum entry 1md9
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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.6.2.1.71
- 2,3-dihydroxybenzoate--[aryl-carrier protein] ligase.
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Reaction:
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2,3-dihydroxybenzoate + holo-[ACP] + ATP = 2,3-dihydroxybenzoyl-[ACP] + AMP + diphosphate
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2,3-dihydroxybenzoate
Bound ligand (Het Group name = )
corresponds exactly
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+
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holo-[ACP]
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+
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ATP
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=
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2,3-dihydroxybenzoyl-[ACP]
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+
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AMP
Bound ligand (Het Group name = )
corresponds exactly
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+
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diphosphate
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Proc Natl Acad Sci U S A
99:12120-12125
(2002)
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PubMed id:
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Crystal structure of DhbE, an archetype for aryl acid activating domains of modular nonribosomal peptide synthetases.
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J.J.May,
N.Kessler,
M.A.Marahiel,
M.T.Stubbs.
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ABSTRACT
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The synthesis of the catecholic siderophore bacillibactin is accomplished by the
nonribosomal peptide synthetase (NRPS) encoded by the dhb operon. DhbE is
responsible for the initial step in bacillibactin synthesis, the activation of
the aryl acid 2,3-dihydroxybenzoate (DHB). The stand-alone adenylation (A)
domain DhbE, the structure of which is presented here, exhibits greatest
homology to other NRPS A-domains, acyl-CoA ligases and luciferases. It's
structure is solved in three different states, without the ligands ATP and DHB
(native state), with the product DHB-AMP (adenylate state) and with the
hydrolyzed product AMP and DHB (hydrolyzed state). The 59.9-kDa protein folds
into two domains, with the active site at the interface between them. In
contrast to previous proposals of a major reorientation of the large and small
domains on substrate binding, we observe only local structural rearrangements.
The structure of the phosphate binding loop could be determined, a motif common
to many adenylate-forming enzymes, as well as with bound DHB-adenylate and the
hydrolyzed product DHB*AMP. Based on the structure and amino acid sequence
alignments, an adapted specificity conferring code for aryl acid activating
domains is proposed, allowing assignment of substrate specificity to gene
products of previously unknown function.
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Selected figure(s)
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Figure 1.
Fig 1. (A) Bacillibactin NRPS cluster from B. subtilis with
the corresponding domain organization of synthetase modules.
ICL, isochorismatase; C, condensation domain; T, thiolation
domain. (B) Structure of the trilactone Bacillibactin, with one
of the catecholic moiety activated by DhbE shaded in gray. (C)
The DhbE-dependent aryl acid adenylation in peptide synthesis is
an ATP-consuming process leading to a protein-bound adenylate.
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Figure 5.
Fig 5. Determination of the specificity conferring code of
ca-activating domains. The primary sequence between core A4 and
A5 (see Fig. 3) of nine ca activating domains are aligned by
using the Clustal method. Based on the structural data of DhbE,
extraction of the 10 residues conferring the substrate
specificity leads to the identification of the signature
sequence of ca activating A domain. The asterisks define the
residues that allow discrimination between DHB and SAL.
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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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N.R.Tawari,
and
M.S.Degani
(2011).
Predictive models for nucleoside bisubstrate analogs as inhibitors of siderophore biosynthesis in Mycobacterium tuberculosis: pharmacophore mapping and chemometric QSAR study.
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Mol Divers,
15,
435-444.
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A.K.Bera,
V.Atanasova,
S.Gamage,
H.Robinson,
and
J.F.Parsons
(2010).
Structure of the D-alanylgriseoluteic acid biosynthetic protein EhpF, an atypical member of the ANL superfamily of adenylating enzymes.
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Acta Crystallogr D Biol Crystallogr,
66,
664-672.
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PDB code:
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A.L.Sikora,
D.J.Wilson,
C.C.Aldrich,
and
J.S.Blanchard
(2010).
Kinetic and inhibition studies of dihydroxybenzoate-AMP ligase from Escherichia coli.
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Biochemistry,
49,
3648-3657.
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B.D.Ames,
and
C.T.Walsh
(2010).
Anthranilate-activating modules from fungal nonribosomal peptide assembly lines.
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Biochemistry,
49,
3351-3365.
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H.A.Crosby,
E.K.Heiniger,
C.S.Harwood,
and
J.C.Escalante-Semerena
(2010).
Reversible N epsilon-lysine acetylation regulates the activity of acyl-CoA synthetases involved in anaerobic benzoate catabolism in Rhodopseudomonas palustris.
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Mol Microbiol,
76,
874-888.
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K.Fujiwara,
N.Maita,
H.Hosaka,
K.Okamura-Ikeda,
A.Nakagawa,
and
H.Taniguchi
(2010).
Global conformational change associated with the two-step reaction catalyzed by Escherichia coli lipoate-protein ligase A.
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J Biol Chem,
285,
9971-9980.
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PDB codes:
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M.Moon,
and
S.G.Van Lanen
(2010).
Characterization of a dual specificity aryl acid adenylation enzyme with dual function in nikkomycin biosynthesis.
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Biopolymers,
93,
791-801.
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R.Teta,
M.Gurgui,
E.J.Helfrich,
S.Künne,
A.Schneider,
G.Van Echten-Deckert,
A.Mangoni,
and
J.Piel
(2010).
Genome mining reveals trans-AT polyketide synthase directed antibiotic biosynthesis in the bacterial phylum bacteroidetes.
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Chembiochem,
11,
2506-2512.
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T.V.Lee,
L.J.Johnson,
R.D.Johnson,
A.Koulman,
G.A.Lane,
J.S.Lott,
and
V.L.Arcus
(2010).
Structure of a eukaryotic nonribosomal peptide synthetase adenylation domain that activates a large hydroxamate amino acid in siderophore biosynthesis.
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J Biol Chem,
285,
2415-2427.
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PDB code:
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A.Koglin,
and
C.T.Walsh
(2009).
Structural insights into nonribosomal peptide enzymatic assembly lines.
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Nat Prod Rep,
26,
987.
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A.M.Gulick
(2009).
Conformational dynamics in the Acyl-CoA synthetases, adenylation domains of non-ribosomal peptide synthetases, and firefly luciferase.
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ACS Chem Biol,
4,
811-827.
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J.Zaitseva,
K.M.Meneely,
and
A.L.Lamb
(2009).
Structure of Escherichia coli malate dehydrogenase at 1.45 A resolution.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
65,
866-869.
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PDB code:
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K.Ishida,
M.Welker,
G.Christiansen,
S.Cadel-Six,
C.Bouchier,
E.Dittmann,
C.Hertweck,
and
N.Tandeau de Marsac
(2009).
Plasticity and evolution of aeruginosin biosynthesis in cyanobacteria.
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Appl Environ Microbiol,
75,
2017-2026.
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M.B.Shah,
C.Ingram-Smith,
L.L.Cooper,
J.Qu,
Y.Meng,
K.S.Smith,
and
A.M.Gulick
(2009).
The 2.1 A crystal structure of an acyl-CoA synthetase from Methanosarcina acetivorans reveals an alternate acyl-binding pocket for small branched acyl substrates.
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Proteins,
77,
685-698.
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PDB code:
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P.Arora,
A.Goyal,
V.T.Natarajan,
E.Rajakumara,
P.Verma,
R.Gupta,
M.Yousuf,
O.A.Trivedi,
D.Mohanty,
A.Tyagi,
R.Sankaranarayanan,
and
R.S.Gokhale
(2009).
Mechanistic and functional insights into fatty acid activation in Mycobacterium tuberculosis.
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Nat Chem Biol,
5,
166-173.
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PDB code:
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R.E.Frederick,
J.A.Mayfield,
and
J.L.DuBois
(2009).
Iron trafficking as an antimicrobial target.
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Biometals,
22,
583-593.
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R.Wu,
A.S.Reger,
X.Lu,
A.M.Gulick,
and
D.Dunaway-Mariano
(2009).
The mechanism of domain alternation in the acyl-adenylate forming ligase superfamily member 4-chlorobenzoate: coenzyme A ligase.
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Biochemistry,
48,
4115-4125.
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PDB code:
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S.Schmelz,
N.Kadi,
S.A.McMahon,
L.Song,
D.Oves-Costales,
M.Oke,
H.Liu,
K.A.Johnson,
L.G.Carter,
C.H.Botting,
M.F.White,
G.L.Challis,
and
J.H.Naismith
(2009).
AcsD catalyzes enantioselective citrate desymmetrization in siderophore biosynthesis.
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Nat Chem Biol,
5,
174-182.
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PDB codes:
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A.Gupte,
H.I.Boshoff,
D.J.Wilson,
J.Neres,
N.P.Labello,
R.V.Somu,
C.Xing,
C.E.Barry,
and
C.C.Aldrich
(2008).
Inhibition of siderophore biosynthesis by 2-triazole substituted analogues of 5'-O-[N-(salicyl)sulfamoyl]adenosine: antibacterial nucleosides effective against Mycobacterium tuberculosis.
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J Med Chem,
51,
7495-7507.
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A.S.Reger,
R.Wu,
D.Dunaway-Mariano,
and
A.M.Gulick
(2008).
Structural characterization of a 140 degrees domain movement in the two-step reaction catalyzed by 4-chlorobenzoate:CoA ligase.
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Biochemistry,
47,
8016-8025.
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PDB codes:
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A.Tanovic,
S.A.Samel,
L.O.Essen,
and
M.A.Marahiel
(2008).
Crystal structure of the termination module of a nonribosomal peptide synthetase.
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Science,
321,
659-663.
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PDB code:
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G.Mercado,
M.Tello,
M.Marín,
O.Monasterio,
and
R.Lagos
(2008).
The production in vivo of microcin E492 with antibacterial activity depends on salmochelin and EntF.
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J Bacteriol,
190,
5464-5471.
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H.Fraga
(2008).
Firefly luminescence: a historical perspective and recent developments.
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Photochem Photobiol Sci,
7,
146-158.
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J.A.Ferreras,
K.L.Stirrett,
X.Lu,
J.S.Ryu,
C.E.Soll,
D.S.Tan,
and
L.E.Quadri
(2008).
Mycobacterial phenolic glycolipid virulence factor biosynthesis: mechanism and small-molecule inhibition of polyketide chain initiation.
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Chem Biol,
15,
51-61.
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J.Neres,
D.J.Wilson,
L.Celia,
B.J.Beck,
and
C.C.Aldrich
(2008).
Aryl acid adenylating enzymes involved in siderophore biosynthesis: fluorescence polarization assay, ligand specificity, and discovery of non-nucleoside inhibitors via high-throughput screening.
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Biochemistry,
47,
11735-11749.
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J.Neres,
N.P.Labello,
R.V.Somu,
H.I.Boshoff,
D.J.Wilson,
J.Vannada,
L.Chen,
C.E.Barry,
E.M.Bennett,
and
C.C.Aldrich
(2008).
Inhibition of siderophore biosynthesis in Mycobacterium tuberculosis with nucleoside bisubstrate analogues: structure-activity relationships of the nucleobase domain of 5'-O-[N-(salicyl)sulfamoyl]adenosine.
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J Med Chem,
51,
5349-5370.
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J.S.Cisar,
and
D.S.Tan
(2008).
Small molecule inhibition of microbial natural product biosynthesis-an emerging antibiotic strategy.
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Chem Soc Rev,
37,
1320-1329.
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N.P.Labello,
E.M.Bennett,
D.M.Ferguson,
and
C.C.Aldrich
(2008).
Quantitative three dimensional structure linear interaction energy model of 5'-O-[N-(salicyl)sulfamoyl]adenosine and the aryl acid adenylating enzyme MbtA.
|
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J Med Chem,
51,
7154-7160.
|
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V.Viviani
(2008).
Introduction to the themed issue on bioluminescence.
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Photochem Photobiol Sci,
7,
145.
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X.Lu,
H.Zhang,
P.J.Tonge,
and
D.S.Tan
(2008).
Mechanism-based inhibitors of MenE, an acyl-CoA synthetase involved in bacterial menaquinone biosynthesis.
|
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Bioorg Med Chem Lett,
18,
5963-5966.
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Y.Tian,
D.H.Suk,
F.Cai,
D.Crich,
and
A.D.Mesecar
(2008).
Bacillus anthracis o-succinylbenzoyl-CoA synthetase: reaction kinetics and a novel inhibitor mimicking its reaction intermediate.
|
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Biochemistry,
47,
12434-12447.
|
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Z.Heather,
M.T.Holden,
K.F.Steward,
J.Parkhill,
L.Song,
G.L.Challis,
C.Robinson,
N.Davis-Poynter,
and
A.S.Waller
(2008).
A novel streptococcal integrative conjugative element involved in iron acquisition.
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Mol Microbiol,
70,
1274-1292.
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A.D.Berti,
N.J.Greve,
Q.H.Christensen,
and
M.G.Thomas
(2007).
Identification of a biosynthetic gene cluster and the six associated lipopeptides involved in swarming motility of Pseudomonas syringae pv. tomato DC3000.
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J Bacteriol,
189,
6312-6323.
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A.Renier,
E.Vivien,
S.Cociancich,
P.Letourmy,
X.Perrier,
P.C.Rott,
and
M.Royer
(2007).
Substrate specificity-conferring regions of the nonribosomal peptide synthetase adenylation domains involved in albicidin pathotoxin biosynthesis are highly conserved within the species Xanthomonas albilineans.
|
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Appl Environ Microbiol,
73,
5523-5530.
|
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A.S.Reger,
J.M.Carney,
and
A.M.Gulick
(2007).
Biochemical and crystallographic analysis of substrate binding and conformational changes in acetyl-CoA synthetase.
|
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Biochemistry,
46,
6536-6546.
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PDB codes:
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A.Szarecka,
Y.Xu,
and
P.Tang
(2007).
Dynamics of firefly luciferase inhibition by general anesthetics: Gaussian and anisotropic network analyses.
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Biophys J,
93,
1895-1905.
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C.Ingram-Smith,
and
K.S.Smith
(2007).
AMP-forming acetyl-CoA synthetases in Archaea show unexpected diversity in substrate utilization.
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Archaea,
2,
95.
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C.Qiao,
A.Gupte,
H.I.Boshoff,
D.J.Wilson,
E.M.Bennett,
R.V.Somu,
C.E.Barry,
and
C.C.Aldrich
(2007).
5'-O-[(N-acyl)sulfamoyl]adenosines as antitubercular agents that inhibit MbtA: an adenylation enzyme required for siderophore biosynthesis of the mycobactins.
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J Med Chem,
50,
6080-6094.
|
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J.S.Cisar,
J.A.Ferreras,
R.K.Soni,
L.E.Quadri,
and
D.S.Tan
(2007).
Exploiting ligand conformation in selective inhibition of non-ribosomal peptide synthetase amino acid adenylation with designed macrocyclic small molecules.
|
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J Am Chem Soc,
129,
7752-7753.
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M.Miethke,
and
M.A.Marahiel
(2007).
Siderophore-based iron acquisition and pathogen control.
|
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Microbiol Mol Biol Rev,
71,
413-451.
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P.Schneider,
M.Weber,
K.Rosenberger,
and
D.Hoffmeister
(2007).
A one-pot chemoenzymatic synthesis for the universal precursor of antidiabetes and antiviral bis-indolylquinones.
|
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Chem Biol,
14,
635-644.
|
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E.J.Drake,
D.A.Nicolai,
and
A.M.Gulick
(2006).
Structure of the EntB multidomain nonribosomal peptide synthetase and functional analysis of its interaction with the EntE adenylation domain.
|
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Chem Biol,
13,
409-419.
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PDB code:
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G.Niu,
G.Liu,
Y.Tian,
and
H.Tan
(2006).
SanJ, an ATP-dependent picolinate-CoA ligase, catalyzes the conversion of picolinate to picolinate-CoA during nikkomycin biosynthesis in Streptomyces ansochromogenes.
|
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Metab Eng,
8,
183-195.
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J.Grünewald,
and
M.A.Marahiel
(2006).
Chemoenzymatic and template-directed synthesis of bioactive macrocyclic peptides.
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Microbiol Mol Biol Rev,
70,
121-146.
|
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J.Vannada,
E.M.Bennett,
D.J.Wilson,
H.I.Boshoff,
C.E.Barry,
and
C.C.Aldrich
(2006).
Design, synthesis, and biological evaluation of beta-ketosulfonamide adenylation inhibitors as potential antitubercular agents.
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| |
Org Lett,
8,
4707-4710.
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M.Ehling-Schulz,
M.Fricker,
H.Grallert,
P.Rieck,
M.Wagner,
and
S.Scherer
(2006).
Cereulide synthetase gene cluster from emetic Bacillus cereus: structure and location on a mega virulence plasmid related to Bacillus anthracis toxin plasmid pXO1.
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BMC Microbiol,
6,
20.
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M.Miethke,
O.Klotz,
U.Linne,
J.J.May,
C.L.Beckering,
and
M.A.Marahiel
(2006).
Ferri-bacillibactin uptake and hydrolysis in Bacillus subtilis.
|
| |
Mol Microbiol,
61,
1413-1427.
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M.Miethke,
P.Bisseret,
C.L.Beckering,
D.Vignard,
J.Eustache,
and
M.A.Marahiel
(2006).
Inhibition of aryl acid adenylation domains involved in bacterial siderophore synthesis.
|
| |
FEBS J,
273,
409-419.
|
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R.V.Somu,
D.J.Wilson,
E.M.Bennett,
H.I.Boshoff,
L.Celia,
B.J.Beck,
C.E.Barry,
and
C.C.Aldrich
(2006).
Antitubercular nucleosides that inhibit siderophore biosynthesis: SAR of the glycosyl domain.
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J Med Chem,
49,
7623-7635.
|
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T.Nakatsu,
S.Ichiyama,
J.Hiratake,
A.Saldanha,
N.Kobashi,
K.Sakata,
and
H.Kato
(2006).
Structural basis for the spectral difference in luciferase bioluminescence.
|
| |
Nature,
440,
372-376.
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PDB codes:
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C.Chutrakul,
and
J.F.Peberdy
(2005).
Isolation and characterisation of a partial peptide synthetase gene from Trichoderma asperellum.
|
| |
FEMS Microbiol Lett,
252,
257-265.
|
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J.A.Ferreras,
J.S.Ryu,
F.Di Lello,
D.S.Tan,
and
L.E.Quadri
(2005).
Small-molecule inhibition of siderophore biosynthesis in Mycobacterium tuberculosis and Yersinia pestis.
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Nat Chem Biol,
1,
29-32.
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J.J.May,
R.Finking,
F.Wiegeshoff,
T.T.Weber,
N.Bandur,
U.Koert,
and
M.A.Marahiel
(2005).
Inhibition of the D-alanine:D-alanyl carrier protein ligase from Bacillus subtilis increases the bacterium's susceptibility to antibiotics that target the cell wall.
|
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FEBS J,
272,
2993-3003.
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