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PDBsum entry 1dcs
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Oxidoreductase
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PDB id
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1dcs
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* Residue conservation analysis
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PDB id:
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Oxidoreductase
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Title:
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Deacetoxycephalosporin c synthase from s. Clavuligerus
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Structure:
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Deacetoxycephalosporin c synthase. Chain: a. Synonym: ring expanding enzyme, ring expandase. Engineered: yes
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Source:
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Streptomyces clavuligerus. Organism_taxid: 1901. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Biol. unit:
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Trimer (from
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Resolution:
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1.30Å
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R-factor:
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0.129
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R-free:
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0.150
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Authors:
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K.Valegard,A.C.Terwisscha Van Scheltinga,M.D.Lloyd,T.Hara, S.Ramaswamy,A.Perrakis,A.Thompson,H.J.Lee,J.E.Baldwin,C.J.Schofield, J.Hajdu,I.Andersson
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Key ref:
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K.Valegård
et al.
(1998).
Structure of a cephalosporin synthase.
Nature,
394,
805-809.
PubMed id:
DOI:
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Date:
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05-Jun-98
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Release date:
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08-Jun-99
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PROCHECK
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Headers
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References
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P18548
(CEFE_STRCL) -
Deacetoxycephalosporin C synthase from Streptomyces clavuligerus
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Seq:
Struc:
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311 a.a.
279 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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Nature
394:805-809
(1998)
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PubMed id:
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Structure of a cephalosporin synthase.
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K.Valegård,
A.C.van Scheltinga,
M.D.Lloyd,
T.Hara,
S.Ramaswamy,
A.Perrakis,
A.Thompson,
H.J.Lee,
J.E.Baldwin,
C.J.Schofield,
J.Hajdu,
I.Andersson.
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ABSTRACT
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Penicillins and cephalosporins are among the most widely used therapeutic
agents. These antibiotics are produced from fermentation-derived materials as
their chemical synthesis is not commercially viable. Unconventional steps in
their biosynthesis are catalysed by Fe(II)-dependent oxidases/oxygenases;
isopenicillin N synthase (IPNS) creates in one step the bicyclic nucleus of
penicillins, and deacetoxycephalosporin C synthase (DAOCS) catalyses the
expansion of the penicillin nucleus into the nucleus of cephalosporins. Both
enzymes use dioxygen-derived ferryl intermediates in catalysis but, in contrast
to IPNS, the ferryl form of DAOCS is produced by the oxidative splitting of a
co-substrate, 2-oxoglutarate (alpha-ketoglutarate). This route of controlled
ferryl formation and reaction is common to many mononuclear ferrous enzymes,
which participate in a broader range of reactions than their well-characterized
counterparts, the haem enzymes. Here we report the first crystal structure of a
2-oxoacid-dependent oxygenase. High-resolution structures for apo-DAOCS, the
enzyme complexed with Fe(II), and with Fe(II) and 2-oxoglutarate, were obtained
from merohedrally twinned crystals. Using a model based on these structures, we
propose a mechanism for ferryl formation.
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Selected figure(s)
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Figure 1.
Figure 1 Scheme to show the key steps in the biosynthesis of
penicillins and cephalosporins.
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Figure 2.
Figure 2 Comparison of the structures of
deacetoxycephalosporin C synthase (DAOCS) and isopenicillin N
synthase (IPNS). DAOCS (a) is a 2-oxoacid-dependent enzyme,
whereas IPNS (b) is not. The two sequences show only 19%
identity. Major departures from the IPNS structure can be found
in the amino-terminal loop, in the region between residues 272
and 292 where two strands and a helix are inserted, in the
active site and its environment, and at the C-terminal arm
(highlighted in red in DAOCS).
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(1998,
394,
805-809)
copyright 1998.
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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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C.Loenarz,
and
C.J.Schofield
(2011).
Physiological and biochemical aspects of hydroxylations and demethylations catalyzed by human 2-oxoglutarate oxygenases.
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Trends Biochem Sci,
36,
7.
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L.G.Bjørnstad,
G.Zoppellaro,
A.B.Tomter,
P.Ã.˜.Falnes,
and
K.K.Andersson
(2011).
Spectroscopic and magnetic studies of wild-type and mutant forms of the Fe(II)- and 2-oxoglutarate-dependent decarboxylase ALKBH4.
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Biochem J,
434,
391-398.
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C.T.Walsh,
and
M.A.Fischbach
(2010).
Natural products version 2.0: connecting genes to molecules.
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J Am Chem Soc,
132,
2469-2493.
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D.Khare,
B.Wang,
L.Gu,
J.Razelun,
D.H.Sherman,
W.H.Gerwick,
K.Håkansson,
and
J.L.Smith
(2010).
Conformational switch triggered by alpha-ketoglutarate in a halogenase of curacin A biosynthesis.
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Proc Natl Acad Sci U S A,
107,
14099-14104.
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PDB codes:
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E.Flashman,
L.M.Hoffart,
R.B.Hamed,
J.M.Bollinger,
C.Krebs,
and
C.J.Schofield
(2010).
Evidence for the slow reaction of hypoxia-inducible factor prolyl hydroxylase 2 with oxygen.
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FEBS J,
277,
4089-4099.
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F.Dahmani-Mardas,
C.Troadec,
A.Boualem,
S.Lévêque,
A.A.Alsadon,
A.A.Aldoss,
C.Dogimont,
and
A.Bendahmane
(2010).
Engineering melon plants with improved fruit shelf life using the TILLING approach.
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PLoS One,
5,
e15776.
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K.Reuter,
M.Pittelkow,
J.Bursy,
A.Heine,
T.Craan,
and
E.Bremer
(2010).
Synthesis of 5-hydroxyectoine from ectoine: crystal structure of the non-heme iron(II) and 2-oxoglutarate-dependent dioxygenase EctD.
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PLoS One,
5,
e10647.
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PDB code:
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M.A.Culpepper,
E.E.Scott,
and
J.Limburg
(2010).
Crystal structure of prolyl 4-hydroxylase from Bacillus anthracis.
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Biochemistry,
49,
124-133.
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PDB code:
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E.M.Nolan,
and
C.T.Walsh
(2009).
How nature morphs peptide scaffolds into antibiotics.
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Chembiochem,
10,
34-53.
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E.G.Kovaleva,
and
J.D.Lipscomb
(2008).
Versatility of biological non-heme Fe(II) centers in oxygen activation reactions.
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Nat Chem Biol,
4,
186-193.
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K.S.Goo,
C.S.Chua,
and
T.S.Sim
(2008).
Relevant double mutations in bioengineered Streptomyces clavuligerus deacetoxycephalosporin C synthase result in higher binding specificities which improve penicillin bioconversion.
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Appl Environ Microbiol,
74,
1167-1175.
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K.Sim Goo,
C.Song Chua,
and
T.S.Sim
(2008).
A complete library of amino acid alterations at R306 in Streptomyces clavuligerus deacetoxycephalosporin C synthase demonstrates its structural role in the ring-expansion activity.
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Proteins,
70,
739-747.
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K.Watanabe
(2008).
Exploring the biosynthesis of natural products and their inherent suitability for the rational design of desirable compounds through genetic engineering.
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Biosci Biotechnol Biochem,
72,
2491-2506.
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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.
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Chem Soc Rev,
37,
2716-2744.
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D.Hoffmeister,
and
N.P.Keller
(2007).
Natural products of filamentous fungi: enzymes, genes, and their regulation.
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Nat Prod Rep,
24,
393-416.
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M.L.Neidig,
C.D.Brown,
K.M.Light,
D.G.Fujimori,
E.M.Nolan,
J.C.Price,
E.W.Barr,
J.M.Bollinger,
C.Krebs,
C.T.Walsh,
and
E.I.Solomon
(2007).
CD and MCD of CytC3 and taurine dioxygenase: role of the facial triad in alpha-KG-dependent oxygenases.
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J Am Chem Soc,
129,
14224-14231.
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T.Gerken,
C.A.Girard,
Y.C.Tung,
C.J.Webby,
V.Saudek,
K.S.Hewitson,
G.S.Yeo,
M.A.McDonough,
S.Cunliffe,
L.A.McNeill,
J.Galvanovskis,
P.Rorsman,
P.Robins,
X.Prieur,
A.P.Coll,
M.Ma,
Z.Jovanovic,
I.S.Farooqi,
B.Sedgwick,
I.Barroso,
T.Lindahl,
C.P.Ponting,
F.M.Ashcroft,
S.O'Rahilly,
and
C.J.Schofield
(2007).
The obesity-associated FTO gene encodes a 2-oxoglutarate-dependent nucleic acid demethylase.
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Science,
318,
1469-1472.
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V.Purpero,
and
G.R.Moran
(2007).
The diverse and pervasive chemistries of the alpha-keto acid dependent enzymes.
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J Biol Inorg Chem,
12,
587-601.
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J.Nakajima,
Y.Sato,
T.Hoshino,
M.Yamazaki,
and
K.Saito
(2006).
Mechanistic study on the oxidation of anthocyanidin synthase by quantum mechanical calculation.
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J Biol Chem,
281,
21387-21398.
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K.D.Koehntop,
S.Marimanikkuppam,
M.J.Ryle,
R.P.Hausinger,
and
L.Que
(2006).
Self-hydroxylation of taurine/alpha-ketoglutarate dioxygenase: evidence for more than one oxygen activation mechanism.
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J Biol Inorg Chem,
11,
63-72.
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M.A.McDonough,
V.Li,
E.Flashman,
R.Chowdhury,
C.Mohr,
B.M.Liénard,
J.Zondlo,
N.J.Oldham,
I.J.Clifton,
J.Lewis,
L.A.McNeill,
R.J.Kurzeja,
K.S.Hewitson,
E.Yang,
S.Jordan,
R.S.Syed,
and
C.J.Schofield
(2006).
Cellular oxygen sensing: Crystal structure of hypoxia-inducible factor prolyl hydroxylase (PHD2).
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Proc Natl Acad Sci U S A,
103,
9814-9819.
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PDB codes:
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R.C.Hillig,
and
L.Renault
(2006).
Detecting and overcoming hemihedral twinning during the MIR structure determination of Rna1p.
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Acta Crystallogr D Biol Crystallogr,
62,
750-765.
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PDB code:
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T.A.Müller,
M.I.Zavodszky,
M.Feig,
L.A.Kuhn,
and
R.P.Hausinger
(2006).
Structural basis for the enantiospecificities of R- and S-specific phenoxypropionate/alpha-ketoglutarate dioxygenases.
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Protein Sci,
15,
1356-1368.
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E.Bitto,
C.A.Bingman,
S.T.Allard,
G.E.Wesenberg,
D.J.Aceti,
R.L.Wrobel,
R.O.Frederick,
H.Sreenath,
F.C.Vojtik,
W.B.Jeon,
C.S.Newman,
J.Primm,
M.R.Sussman,
B.G.Fox,
J.L.Markley,
and
G.N.Phillips
(2005).
The structure at 2.4 A resolution of the protein from gene locus At3g21360, a putative Fe(II)/2-oxoglutarate-dependent enzyme from Arabidopsis thaliana.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
61,
469-472.
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PDB code:
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K.D.Koehntop,
J.P.Emerson,
and
L.Que
(2005).
The 2-His-1-carboxylate facial triad: a versatile platform for dioxygen activation by mononuclear non-heme iron(II) enzymes.
|
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J Biol Inorg Chem,
10,
87-93.
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L.A.McNeill,
E.Flashman,
M.R.Buck,
K.S.Hewitson,
I.J.Clifton,
G.Jeschke,
T.D.Claridge,
D.Ehrismann,
N.J.Oldham,
and
C.J.Schofield
(2005).
Hypoxia-inducible factor prolyl hydroxylase 2 has a high affinity for ferrous iron and 2-oxoglutarate.
|
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Mol Biosyst,
1,
321-324.
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M.A.McDonough,
K.L.Kavanagh,
D.Butler,
T.Searls,
U.Oppermann,
and
C.J.Schofield
(2005).
Structure of human phytanoyl-CoA 2-hydroxylase identifies molecular mechanisms of Refsum disease.
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J Biol Chem,
280,
41101-41110.
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PDB code:
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M.L.Neidig,
and
E.I.Solomon
(2005).
Structure-function correlations in oxygen activating non-heme iron enzymes.
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Chem Commun (Camb),
(),
5843-5863.
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N.J.Kershaw,
M.E.Caines,
M.C.Sleeman,
and
C.J.Schofield
(2005).
The enzymology of clavam and carbapenem biosynthesis.
|
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Chem Commun (Camb),
(),
4251-4263.
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S.H.Park,
M.Nakajima,
M.Sakane,
Z.J.Xu,
K.Tomioka,
and
I.Yamaguchi
(2005).
Gibberellin 2-oxidases from seedlings of adzuki bean (Vigna angularis) show high gibberellin-binding activity in the presence of 2-oxoglutarate and Co2+.
|
| |
Biosci Biotechnol Biochem,
69,
1498-1507.
|
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T.R.Barends,
R.M.de Jong,
K.E.van Straaten,
A.M.Thunnissen,
and
B.W.Dijkstra
(2005).
Escherichia coli MltA: MAD phasing and refinement of a tetartohedrally twinned protein crystal structure.
|
| |
Acta Crystallogr D Biol Crystallogr,
61,
613-621.
|
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X.B.Wu,
K.Q.Fan,
Q.H.Wang,
and
K.Q.Yang
(2005).
C-terminus mutations of Acremonium chrysogenum deacetoxy/deacetylcephalosporin C synthase with improved activity toward penicillin analogs.
|
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FEMS Microbiol Lett,
246,
103-110.
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C.J.Schofield,
and
P.J.Ratcliffe
(2004).
Oxygen sensing by HIF hydroxylases.
|
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Nat Rev Mol Cell Biol,
5,
343-354.
|
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E.Metzen,
and
P.J.Ratcliffe
(2004).
HIF hydroxylation and cellular oxygen sensing.
|
| |
Biol Chem,
385,
223-230.
|
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K.Valegård,
A.C.Terwisscha van Scheltinga,
A.Dubus,
G.Ranghino,
L.M.Oster,
J.Hajdu,
and
I.Andersson
(2004).
The structural basis of cephalosporin formation in a mononuclear ferrous enzyme.
|
| |
Nat Struct Mol Biol,
11,
95.
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PDB codes:
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M.D.Lloyd,
S.J.Lipscomb,
K.S.Hewitson,
C.M.Hensgens,
J.E.Baldwin,
and
C.J.Schofield
(2004).
Controlling the substrate selectivity of deacetoxycephalosporin/deacetylcephalosporin C synthase.
|
| |
J Biol Chem,
279,
15420-15426.
|
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|
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Z.Zhang,
J.S.Ren,
I.J.Clifton,
and
C.J.Schofield
(2004).
Crystal structure and mechanistic implications of 1-aminocyclopropane-1-carboxylic acid oxidase--the ethylene-forming enzyme.
|
| |
Chem Biol,
11,
1383-1394.
|
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PDB codes:
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A.C.Terwisscha van Scheltinga,
K.Valegård,
J.Hajdu,
and
I.Andersson
(2003).
MIR phasing using merohedrally twinned crystals.
|
| |
Acta Crystallogr D Biol Crystallogr,
59,
2017-2022.
|
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C.L.Wei,
Y.B.Yang,
W.C.Wang,
W.C.Liu,
J.S.Hsu,
and
Y.C.Tsai
(2003).
Engineering Streptomyces clavuligerus deacetoxycephalosporin C synthase for optimal ring expansion activity toward penicillin G.
|
| |
Appl Environ Microbiol,
69,
2306-2312.
|
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|
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C.Lee,
S.J.Kim,
D.G.Jeong,
S.M.Lee,
and
S.E.Ryu
(2003).
Structure of human FIH-1 reveals a unique active site pocket and interaction sites for HIF-1 and von Hippel-Lindau.
|
| |
J Biol Chem,
278,
7558-7563.
|
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PDB code:
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H.J.Lee,
Y.F.Dai,
C.Y.Shiau,
C.J.Schofield,
and
M.D.Lloyd
(2003).
The kinetic properties of various R258 mutants of deacetoxycephalosporin C synthase.
|
| |
Eur J Biochem,
270,
1301-1307.
|
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M.J.Ryle,
K.D.Koehntop,
A.Liu,
L.Que,
and
R.P.Hausinger
(2003).
Interconversion of two oxidized forms of taurine/alpha-ketoglutarate dioxygenase, a non-heme iron hydroxylase: evidence for bicarbonate binding.
|
| |
Proc Natl Acad Sci U S A,
100,
3790-3795.
|
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M.Mukherji,
C.J.Schofield,
A.S.Wierzbicki,
G.A.Jansen,
R.J.Wanders,
and
M.D.Lloyd
(2003).
The chemical biology of branched-chain lipid metabolism.
|
| |
Prog Lipid Res,
42,
359-376.
|
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|
|
|
|
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P.A.Aas,
M.Otterlei,
P.O.Falnes,
C.B.Vågbø,
F.Skorpen,
M.Akbari,
O.Sundheim,
M.Bjørås,
G.Slupphaug,
E.Seeberg,
and
H.E.Krokan
(2003).
Human and bacterial oxidative demethylases repair alkylation damage in both RNA and DNA.
|
| |
Nature,
421,
859-863.
|
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|
|
|
|
|
P.Liu,
A.Liu,
F.Yan,
M.D.Wolfe,
J.D.Lipscomb,
and
H.W.Liu
(2003).
Biochemical and spectroscopic studies on (S)-2-hydroxypropylphosphonic acid epoxidase: a novel mononuclear non-heme iron enzyme.
|
| |
Biochemistry,
42,
11577-11586.
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PDB codes:
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C.M.Hensgens,
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Purification, crystallization and preliminary X-ray diffraction of Cys103Ala acyl coenzyme A: isopenicillin N acyltransferase from Penicillium chrysogenum.
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Genes Dev,
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Functional expression and mutational analysis of flavonol synthase from Citrus unshiu.
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Tyrosinemia I, a model for human diseases mediated by 2-oxoacid-utilizing dioxygenases: hepatotoxin suppression by NTBC does not normalize hepatic collagen metabolism.
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Biochemistry,
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PDB code:
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J Biol Chem,
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The role of arginine residues in substrate binding and catalysis by deacetoxycephalosporin C synthase.
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Eur J Biochem,
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Multiple isomorphous replacement on merohedral twins: structure determination of deacetoxycephalosporin C synthase.
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Crystallization and 2.2 A resolution structure of R-phycoerythrin from Gracilaria chilensis: a case of perfect hemihedral twinning.
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Acta Crystallogr D Biol Crystallogr,
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PDB code:
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I.J.Clifton,
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PDB codes:
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J.A.Gerlt,
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Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies.
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Purification, crystallization and preliminary X-ray diffraction of anthocyanidin synthase from Arabidopsis thaliana.
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Acta Crystallogr D Biol Crystallogr,
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Alternative oxidation by isopenicillin N synthase observed by X-ray diffraction.
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Chem Biol,
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PDB codes:
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L.Aravind,
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The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases.
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Genome Biol,
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Site-directed mutagenesis of 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate dioxygenase. Identification of residues involved in metallocenter formation and substrate binding.
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J Biol Chem,
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Effects of crystal twinning on the ability to solve a macromolecular structure using multiwavelength anomalous diffraction.
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Mutational evidence supporting the involvement of tripartite residues His183, Asp185, and His243 in Streptomyces clavuligerus deacetoxycephalosporin C synthase for catalysis.
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Site-directed mutagenesis and biochemical analysis of the endogenous ligands in the ferrous active site of clavaminate synthase. The His-3 variant of the 2-His-1-carboxylate model.
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Biochemistry,
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Role of the nonheme Fe(II) center in the biosynthesis of the plant hormone ethylene.
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Structural and mechanistic studies on 2-oxoglutarate-dependent oxygenases and related enzymes.
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Microbial proline 4-hydroxylase screening and gene cloning.
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Disorder and twin refinement of RNA heptamer double helices.
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Acta Crystallogr D Biol Crystallogr,
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|
PDB codes:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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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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