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PDBsum entry 1tht
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Contents |
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* Residue conservation analysis
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PDB id:
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Thioesterase
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Title:
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Structure of a myristoyl-acp-specific thioesterase from vibrio harveyi
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Structure:
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Thioesterase. Chain: a, b. Engineered: yes
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Source:
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Vibrio harveyi. Organism_taxid: 669
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Resolution:
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Authors:
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D.M.Lawson,U.Derewenda,L.Serre,S.Ferri,R.Szitter,Y.Wei,E.A.Meighen, Z.S.Derewenda
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Key ref:
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D.M.Lawson
et al.
(1994).
Structure of a myristoyl-ACP-specific thioesterase from Vibrio harveyi.
Biochemistry,
33,
9382-9388.
PubMed id:
DOI:
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Date:
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19-Apr-94
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Release date:
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07-Jun-95
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PROCHECK
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Headers
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References
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P05521
(LUXD_VIBHA) -
Acyl transferase from Vibrio harveyi
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Seq:
Struc:
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305 a.a.
294 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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*
PDB and UniProt seqs differ
at 2 residue positions (black
crosses)
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DOI no:
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Biochemistry
33:9382-9388
(1994)
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PubMed id:
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Structure of a myristoyl-ACP-specific thioesterase from Vibrio harveyi.
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D.M.Lawson,
U.Derewenda,
L.Serre,
S.Ferri,
R.Szittner,
Y.Wei,
E.A.Meighen,
Z.S.Derewenda.
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ABSTRACT
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The crystal structure of a myristoyl acyl carrier protein specific thioesterase
(C14ACP-TE) from a bioluminescent bacterium, Vibrio harveyi, was solved by
multiple isomorphous replacement methods and refined to an R factor of 22% at
2.1-A resolution. This is the first elucidation of a three-dimensional structure
of a thioesterase. The overall tertiary architecture of the enzyme resembles
closely the consensus fold of the rapidly expanding superfamily of alpha/beta
hydrolases, although there is no detectable homology with any of its members at
the amino acid sequence level. Particularly striking similarity exists between
the C14ACP-TE structure and that of haloalkane dehalogenase from Xanthobacter
autotrophicus. Contrary to the conclusions of earlier studies [Ferri, S. R.,
& Meighen, E. A. (1991) J. Biol. Chem. 266, 12852-12857] which implicated
Ser77 in catalysis, the crystal structure of C14ACP-TE reveals a lipase-like
catalytic triad made up of Ser114, His241, and Asp211. Surprisingly, the
gamma-turn with Ser114 in a strained secondary conformation (phi = 53 degrees,
psi = -127 degrees), characteristic of the so-called nucleophilic elbow, does
not conform to the frequently invoked lipase/esterase consensus sequence
(Gly-X-Ser-X-Gly), as the positions of both glycines are occupied by larger
amino acids. Site-directed mutagenesis and radioactive labeling support the
catalytic function of Ser114. Crystallographic analysis of the Ser77-->Gly
mutant at 2.5-A resolution revealed no structural changes; in both cases the
loop containing the residue in position 77 is disordered.(ABSTRACT TRUNCATED AT
250 WORDS)
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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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Y.Jiang,
K.L.Morley,
J.D.Schrag,
and
R.J.Kazlauskas
(2011).
Different active-site loop orientation in serine hydrolases versus acyltransferases.
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Chembiochem,
12,
768-776.
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PDB code:
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A.C.Mercer,
and
M.D.Burkart
(2007).
The ubiquitous carrier protein--a window to metabolite biosynthesis.
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Nat Prod Rep,
24,
750-773.
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B.M.Harvey,
H.Hong,
M.A.Jones,
Z.A.Hughes-Thomas,
R.M.Goss,
M.L.Heathcote,
V.M.Bolanos-Garcia,
W.Kroutil,
J.Staunton,
P.F.Leadlay,
and
J.B.Spencer
(2006).
Evidence that a novel thioesterase is responsible for polyketide chain release during biosynthesis of the polyether ionophore monensin.
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Chembiochem,
7,
1435-1442.
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J.W.Giraldes,
D.L.Akey,
J.D.Kittendorf,
D.H.Sherman,
J.L.Smith,
and
R.A.Fecik
(2006).
Structural and mechanistic insights into polyketide macrolactonization from polyketide-based affinity labels.
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Nat Chem Biol,
2,
531-536.
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PDB codes:
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K.M.Mayer,
and
J.Shanklin
(2005).
A structural model of the plant acyl-acyl carrier protein thioesterase FatB comprises two helix/4-stranded sheet domains, the N-terminal domain containing residues that affect specificity and the C-terminal domain containing catalytic residues.
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J Biol Chem,
280,
3621-3627.
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PDB code:
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I.Janda,
Y.Devedjiev,
D.Cooper,
M.Chruszcz,
U.Derewenda,
A.Gabrys,
W.Minor,
A.Joachimiak,
and
Z.S.Derewenda
(2004).
Harvesting the high-hanging fruit: the structure of the YdeN gene product from Bacillus subtilis at 1.8 angstroms resolution.
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Acta Crystallogr D Biol Crystallogr,
60,
1101-1107.
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PDB code:
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K.Huhtinen,
J.O'Byrne,
P.J.Lindquist,
J.A.Contreras,
and
S.E.Alexson
(2002).
The peroxisome proliferator-induced cytosolic type I acyl-CoA thioesterase (CTE-I) is a serine-histidine-aspartic acid alpha /beta hydrolase.
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J Biol Chem,
277,
3424-3432.
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R.M.Kohli,
J.Takagi,
and
C.T.Walsh
(2002).
The thioesterase domain from a nonribosomal peptide synthetase as a cyclization catalyst for integrin binding peptides.
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Proc Natl Acad Sci U S A,
99,
1247-1252.
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S.D.Bruner,
T.Weber,
R.M.Kohli,
D.Schwarzer,
M.A.Marahiel,
C.T.Walsh,
and
M.T.Stubbs
(2002).
Structural basis for the cyclization of the lipopeptide antibiotic surfactin by the thioesterase domain SrfTE.
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Structure,
10,
301-310.
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PDB code:
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Z.Zhuang,
F.Song,
W.Zhang,
K.Taylor,
A.Archambault,
D.Dunaway-Mariano,
J.Dong,
and
P.R.Carey
(2002).
Kinetic, Raman, NMR, and site-directed mutagenesis studies of the Pseudomonas sp. strain CBS3 4-hydroxybenzoyl-CoA thioesterase active site.
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Biochemistry,
41,
11152-11160.
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F.Bordusa
(2001).
Enzymes for peptide cyclization.
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Chembiochem,
2,
405-409.
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M.L.Schaeffer,
G.Agnihotri,
H.Kallender,
P.J.Brennan,
and
J.T.Lonsdale
(2001).
Expression, purification, and characterization of the Mycobacterium tuberculosis acyl carrier protein, AcpM.
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Biochim Biophys Acta,
1532,
67-78.
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S.C.Tsai,
L.J.Miercke,
J.Krucinski,
R.Gokhale,
J.C.Chen,
P.G.Foster,
D.E.Cane,
C.Khosla,
and
R.M.Stroud
(2001).
Crystal structure of the macrocycle-forming thioesterase domain of the erythromycin polyketide synthase: versatility from a unique substrate channel.
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Proc Natl Acad Sci U S A,
98,
14808-14813.
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PDB code:
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D.V.Debabov,
M.Y.Kiriukhin,
and
F.C.Neuhaus
(2000).
Biosynthesis of lipoteichoic acid in Lactobacillus rhamnosus: role of DltD in D-alanylation.
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J Bacteriol,
182,
2855-2864.
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J.J.Bellizzi,
J.Widom,
C.Kemp,
J.Y.Lu,
A.K.Das,
S.L.Hofmann,
and
J.Clardy
(2000).
The crystal structure of palmitoyl protein thioesterase 1 and the molecular basis of infantile neuronal ceroid lipofuscinosis.
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Proc Natl Acad Sci U S A,
97,
4573-4578.
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PDB codes:
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J.Li,
R.Szittner,
and
E.A.Meighen
(2000).
Hyperactivity and interactions of a chimeric myristoryl-ACP thioesterase from the lux system of luminescent bacteria.
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Biochim Biophys Acta,
1481,
237-246.
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P.C.Bourne,
M.N.Isupov,
and
J.A.Littlechild
(2000).
The atomic-resolution structure of a novel bacterial esterase.
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Structure,
8,
143-151.
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PDB codes:
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V.Z.Pletnev,
T.S.Zamolodchikova,
W.A.Pangborn,
and
W.L.Duax
(2000).
Crystal structure of bovine duodenase, a serine protease, with dual trypsin and chymotrypsin-like specificities.
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Proteins,
41,
8.
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PDB code:
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Y.Devedjiev,
Z.Dauter,
S.R.Kuznetsov,
T.L.Jones,
and
Z.S.Derewenda
(2000).
Crystal structure of the human acyl protein thioesterase I from a single X-ray data set to 1.5 A.
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Structure,
8,
1137-1146.
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PDB code:
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Y.Jia,
T.J.Kappock,
T.Frick,
A.J.Sinskey,
and
J.Stubbe
(2000).
Lipases provide a new mechanistic model for polyhydroxybutyrate (PHB) synthases: characterization of the functional residues in Chromatium vinosum PHB synthase.
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Biochemistry,
39,
3927-3936.
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C.A.Shaw-Reid,
N.L.Kelleher,
H.C.Losey,
A.M.Gehring,
C.Berg,
and
C.T.Walsh
(1999).
Assembly line enzymology by multimodular nonribosomal peptide synthetases: the thioesterase domain of E. coli EntF catalyzes both elongation and cyclolactonization.
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Chem Biol,
6,
385-400.
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K.E.Jaeger,
B.W.Dijkstra,
and
M.T.Reetz
(1999).
Bacterial biocatalysts: molecular biology, three-dimensional structures, and biotechnological applications of lipases.
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Annu Rev Microbiol,
53,
315-351.
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P.C.Bourne,
M.N.Isupov,
and
J.A.Littlechild
(1999).
Crystallization and preliminary x-ray diffraction studies of a novel bacterial esterase.
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Acta Crystallogr D Biol Crystallogr,
55,
915-917.
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R.S.Gokhale,
D.Hunziker,
D.E.Cane,
and
C.Khosla
(1999).
Mechanism and specificity of the terminal thioesterase domain from the erythromycin polyketide synthase.
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Chem Biol,
6,
117-125.
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A.M.Gehring,
I.Mori,
and
C.T.Walsh
(1998).
Reconstitution and characterization of the Escherichia coli enterobactin synthetase from EntB, EntE, and EntF.
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Biochemistry,
37,
2648-2659.
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B.J.Rawlings
(1998).
Biosynthesis of fatty acids and related metabolites.
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Nat Prod Rep,
15,
275-308.
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J.Pleiss,
M.Fischer,
and
R.D.Schmid
(1998).
Anatomy of lipase binding sites: the scissile fatty acid binding site.
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Chem Phys Lipids,
93,
67-80.
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M.M.Benning,
G.Wesenberg,
R.Liu,
K.L.Taylor,
D.Dunaway-Mariano,
and
H.M.Holden
(1998).
The three-dimensional structure of 4-hydroxybenzoyl-CoA thioesterase from Pseudomonas sp. Strain CBS-3.
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J Biol Chem,
273,
33572-33579.
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PDB code:
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Y.Wei,
L.Swenson,
C.Castro,
U.Derewenda,
W.Minor,
H.Arai,
J.Aoki,
K.Inoue,
L.Servin-Gonzalez,
and
Z.S.Derewenda
(1998).
Structure of a microbial homologue of mammalian platelet-activating factor acetylhydrolases: Streptomyces exfoliatus lipase at 1.9 A resolution.
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Structure,
6,
511-519.
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PDB code:
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A.A.Soyombo,
and
S.L.Hofmann
(1997).
Molecular cloning and expression of palmitoyl-protein thioesterase 2 (PPT2), a homolog of lysosomal palmitoyl-protein thioesterase with a distinct substrate specificity.
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J Biol Chem,
272,
27456-27463.
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K.K.Kim,
H.K.Song,
D.H.Shin,
K.Y.Hwang,
and
S.W.Suh
(1997).
The crystal structure of a triacylglycerol lipase from Pseudomonas cepacia reveals a highly open conformation in the absence of a bound inhibitor.
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Structure,
5,
173-185.
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PDB code:
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P.A.Kroon,
C.B.Faulds,
C.Brézillon,
and
G.Williamson
(1997).
Methyl phenylalkanoates as substrates to probe the active sites of esterases.
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Eur J Biochem,
248,
245-251.
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V.de Crécy-Lagard,
W.Saurin,
D.Thibaut,
P.Gil,
L.Naudin,
J.Crouzet,
and
V.Blanc
(1997).
Streptogramin B biosynthesis in Streptomyces pristinaespiralis and Streptomyces virginiae: molecular characterization of the last structural peptide synthetase gene.
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Antimicrob Agents Chemother,
41,
1904-1909.
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J.Li,
R.Szittner,
Z.S.Derewenda,
and
E.A.Meighen
(1996).
Conversion of serine-114 to cysteine-114 and the role of the active site nucleophile in acyl transfer by myristoyl-ACP thioesterase from Vibrio harveyi.
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Biochemistry,
35,
9967-9973.
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L.Yuan,
B.A.Nelson,
and
G.Caryl
(1996).
The catalytic cysteine and histidine in the plant acyl-acyl carrier protein thioesterases.
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J Biol Chem,
271,
3417-3419.
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M.J.Guimarães,
J.F.Bazan,
J.Castagnola,
S.Diaz,
N.G.Copeland,
D.J.Gilbert,
N.A.Jenkins,
A.Varki,
and
A.Zlotnik
(1996).
Molecular cloning and characterization of lysosomal sialic acid O-acetylesterase.
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J Biol Chem,
271,
13697-13705.
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T.Hisano,
Y.Hata,
T.Fujii,
J.Q.Liu,
T.Kurihara,
N.Esaki,
and
K.Soda
(1996).
Crystal structure of L-2-haloacid dehalogenase from Pseudomonas sp. YL. An alpha/beta hydrolase structure that is different from the alpha/beta hydrolase fold.
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J Biol Chem,
271,
20322-20330.
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PDB code:
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U.G.Wagner,
M.Hasslacher,
H.Griengl,
H.Schwab,
and
C.Kratky
(1996).
Mechanism of cyanogenesis: the crystal structure of hydroxynitrile lyase from Hevea brasiliensis.
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Structure,
4,
811-822.
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PDB code:
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G.Meurer,
and
C.R.Hutchinson
(1995).
Functional analysis of putative beta-ketoacyl:acyl carrier protein synthase and acyltransferase active site motifs in a type II polyketide synthase of Streptomyces glaucescens.
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J Bacteriol,
177,
477-481.
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J.L.Buchbinder,
A.Witkowski,
S.Smith,
and
R.J.Fletterick
(1995).
Crystallization and preliminary diffraction studies of thioesterase II from rat mammary gland.
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Proteins,
22,
73-75.
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L.Yuan,
T.A.Voelker,
and
D.J.Hawkins
(1995).
Modification of the substrate specificity of an acyl-acyl carrier protein thioesterase by protein engineering.
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Proc Natl Acad Sci U S A,
92,
10639-10643.
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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
code is
shown on the right.
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Links
