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PDBsum entry 1thf
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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.4.3.2.10
- imidazole glycerol-phosphate synthase.
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Reaction:
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5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta- D-ribosyl)imidazole-4-carboxamide + L-glutamine = D-erythro-1-(imidazol- 4-yl)glycerol 3-phosphate + 5-amino-1-(5-phospho-beta-D- ribosyl)imidazole-4-carboxamide + L-glutamate + H+
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5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta- D-ribosyl)imidazole-4-carboxamide
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+
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L-glutamine
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=
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D-erythro-1-(imidazol- 4-yl)glycerol 3-phosphate
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+
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5-amino-1-(5-phospho-beta-D- ribosyl)imidazole-4-carboxamide
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L-glutamate
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+
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H(+)
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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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Science
289:1546-1550
(2000)
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PubMed id:
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Structural evidence for evolution of the beta/alpha barrel scaffold by gene duplication and fusion.
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D.Lang,
R.Thoma,
M.Henn-Sax,
R.Sterner,
M.Wilmanns.
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ABSTRACT
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The atomic structures of two proteins in the histidine biosynthesis pathway
consist of beta/alpha barrels with a twofold repeat pattern. It is likely that
these proteins evolved by twofold gene duplication and gene fusion from a common
half-barrel ancestor. These ancestral domains are not visible as independent
domains in the extant proteins but can be inferred from a combination of
sequence and structural analysis. The detection of subdomain structures may be
useful in efforts to search genome sequences for functionally and structurally
related proteins.
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Selected figure(s)
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Figure 1.
Fig. 1. Atomic structures of HisA (upper panel) and HisF (lower
panel) from Thermotoga maritima in ribbon presentations (29).
View from the COOH-terminal face of the central  barrel,
left; side view, center; and view from the NH[2]-terminal face
of the barrel, right. HisF contains two phosphate ions bound to
the active site, shown as space-filling models (red). The strands
and  helices
of the central eightfold / barrel are
in orange and yellow, respectively. Loops at the NH[2]- and
COOH-terminal faces of the barrel are in cyan and green,
respectively. Some loops contain additional secondary structural
elements. The NH[2]- and COOH-termini are labeled when visible.
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Figure 3.
Fig. 3. Model for the evolution of the / barrel
scaffold by twofold gene duplication. The first gene duplication
generates two initially identical half-barrels that are then
fused and adapted into an ancestral / barrel. A
second gene duplication step leads to the diversification of the
ancestral / barrel
into two enzymes with distinct catalytic activities.
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The above figures are
reprinted
by permission from the AAAs:
Science
(2000,
289,
1546-1550)
copyright 2000.
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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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A.V.Due,
J.Kuper,
A.Geerlof,
J.P.Kries,
and
M.Wilmanns
(2011).
Bisubstrate specificity in histidine/tryptophan biosynthesis isomerase from Mycobacterium tuberculosis by active site metamorphosis.
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Proc Natl Acad Sci U S A,
108,
3554-3559.
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PDB codes:
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S.Setiyaputra,
J.P.Mackay,
and
W.M.Patrick
(2011).
The structure of a truncated phosphoribosylanthranilate isomerase suggests a unified model for evolution of the (βα)8 barrel fold.
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J Mol Biol,
408,
291-303.
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PDB code:
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C.Liebold,
F.List,
H.R.Kalbitzer,
R.Sterner,
and
E.Brunner
(2010).
The interaction of ammonia and xenon with the imidazole glycerol phosphate synthase from Thermotoga maritima as detected by NMR spectroscopy.
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Protein Sci,
19,
1774-1782.
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C.Nagao,
N.Nagano,
and
K.Mizuguchi
(2010).
Relationships between functional subclasses and information contained in active-site and ligand-binding residues in diverse superfamilies.
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Proteins,
78,
2369-2384.
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I.Yadid,
N.Kirshenbaum,
M.Sharon,
O.Dym,
and
D.S.Tawfik
(2010).
Metamorphic proteins mediate evolutionary transitions of structure.
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Proc Natl Acad Sci U S A,
107,
7287-7292.
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PDB codes:
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J.Feng,
M.Li,
Y.Huang,
and
Y.Xiao
(2010).
Symmetric key structural residues in symmetric proteins with beta-trefoil fold.
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PLoS One,
5,
e14138.
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S.Akanuma,
T.Matsuba,
E.Ueno,
N.Umeda,
and
A.Yamagishi
(2010).
Mimicking the evolution of a thermally stable monomeric four-helix bundle by fusion of four identical single-helix peptides.
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J Biochem,
147,
371-379.
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S.Eisenbeis,
and
B.Höcker
(2010).
Evolutionary mechanism as a template for protein engineering.
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J Pept Sci,
16,
538-544.
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A.Fischer,
N.Enkler,
G.Neudert,
M.Bocola,
R.Sterner,
and
R.Merkl
(2009).
TransCent: computational enzyme design by transferring active sites and considering constraints relevant for catalysis.
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BMC Bioinformatics,
10,
54.
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H.Li,
W.Fast,
and
S.J.Benkovic
(2009).
Structural and functional modularity of proteins in the de novo purine biosynthetic pathway.
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Protein Sci,
18,
881-892.
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J.Claren,
C.Malisi,
B.Höcker,
and
R.Sterner
(2009).
Establishing wild-type levels of catalytic activity on natural and artificial (beta alpha)8-barrel protein scaffolds.
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Proc Natl Acad Sci U S A,
106,
3704-3709.
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PDB code:
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J.Lipchock,
and
J.P.Loria
(2009).
Millisecond dynamics in the allosteric enzyme imidazole glycerol phosphate synthase (IGPS) from Thermotoga maritima.
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J Biomol NMR,
45,
73-84.
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M.Hidaka,
M.Nishimoto,
M.Kitaoka,
T.Wakagi,
H.Shoun,
and
S.Fushinobu
(2009).
The crystal structure of galacto-N-biose/lacto-N-biose I phosphorylase: a large deformation of a TIM barrel scaffold.
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J Biol Chem,
284,
7273-7283.
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PDB codes:
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A.Biegert,
and
J.Söding
(2008).
De novo identification of highly diverged protein repeats by probabilistic consistency.
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Bioinformatics,
24,
807-814.
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A.N.Alexandrova,
D.Röthlisberger,
D.Baker,
and
W.L.Jorgensen
(2008).
Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination.
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J Am Chem Soc,
130,
15907-15915.
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F.Birzele,
G.Csaba,
and
R.Zimmer
(2008).
Alternative splicing and protein structure evolution.
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Nucleic Acids Res,
36,
550-558.
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I.Chaudhuri,
J.Söding,
and
A.N.Lupas
(2008).
Evolution of the beta-propeller fold.
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Proteins,
71,
795-803.
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J.J.Graziano,
W.Liu,
R.Perera,
B.H.Geierstanger,
S.A.Lesley,
and
P.G.Schultz
(2008).
Selecting folded proteins from a library of secondary structural elements.
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J Am Chem Soc,
130,
176-185.
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J.M.Lipchock,
and
J.P.Loria
(2008).
1H, 15N and 13C resonance assignment of imidazole glycerol phosphate (IGP) synthase protein HisF from Thermotoga maritima.
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Biomol NMR Assign,
2,
219-221.
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K.K.Chan,
A.A.Fedorov,
E.V.Fedorov,
S.C.Almo,
and
J.A.Gerlt
(2008).
Structural basis for substrate specificity in phosphate binding (beta/alpha)8-barrels: D-allulose 6-phosphate 3-epimerase from Escherichia coli K-12.
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Biochemistry,
47,
9608-9617.
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PDB codes:
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M.Li,
Y.Huang,
and
Y.Xiao
(2008).
Effects of external interactions on protein sequence-structure relations of beta-trefoil fold.
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Proteins,
72,
1161-1170.
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M.T.Reetz,
M.Rentzsch,
A.Pletsch,
A.Taglieber,
F.Hollmann,
R.J.Mondière,
N.Dickmann,
B.Höcker,
S.Cerrone,
M.C.Haeger,
and
R.Sterner
(2008).
A robust protein host for anchoring chelating ligands and organocatalysts.
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Chembiochem,
9,
552-564.
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T.A.Bharat,
S.Eisenbeis,
K.Zeth,
and
B.Höcker
(2008).
A beta alpha-barrel built by the combination of fragments from different folds.
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Proc Natl Acad Sci U S A,
105,
9942-9947.
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PDB code:
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J.Payandeh,
and
E.F.Pai
(2007).
Enzyme-driven speciation: crystallizing Archaea via lipid capture.
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J Mol Evol,
64,
364-374.
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N.Lartillot,
H.Brinkmann,
and
H.Philippe
(2007).
Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model.
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BMC Evol Biol,
7,
S4.
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P.L.Nester,
E.Gayó,
C.Latorre,
T.E.Jordan,
and
N.Blanco
(2007).
Perennial stream discharge in the hyperarid Atacama Desert of northern Chile during the latest Pleistocene.
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Proc Natl Acad Sci U S A,
104,
19724-19729.
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R.Fani,
M.Brilli,
M.Fondi,
and
P.Lió
(2007).
The role of gene fusions in the evolution of metabolic pathways: the histidine biosynthesis case.
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BMC Evol Biol,
7,
S4.
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T.Ke,
X.D.Ma,
P.H.Mao,
X.Jin,
S.J.Chen,
Y.Li,
L.X.Ma,
and
G.Y.He
(2007).
A mutant alpha-amylase with only part of the catalytic domain and its structural implication.
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Biotechnol Lett,
29,
117-122.
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Y.Huang,
and
Y.Xiao
(2007).
Detection of gene duplication signals of Ig folds from their amino acid sequences.
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Proteins,
68,
267-272.
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C.Mir,
E.Lopez-Viñas,
R.Aledo,
B.Puisac,
C.Rizzo,
C.Dionisi-Vici,
F.Deodato,
J.Pié,
P.Gomez-Puertas,
F.G.Hegardt,
and
N.Casals
(2006).
A single-residue mutation, G203E, causes 3-hydroxy-3-methylglutaric aciduria by occluding the substrate channel in the 3D structural model of HMG-CoA lyase.
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J Inherit Metab Dis,
29,
64-70.
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J.Söding,
M.Remmert,
and
A.Biegert
(2006).
HHrep: de novo protein repeat detection and the origin of TIM barrels.
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Nucleic Acids Res,
34,
W137-W142.
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S.Quevillon-Cheruel,
N.Leulliot,
M.Graille,
K.Blondeau,
J.Janin,
and
H.van Tilbeurgh
(2006).
Crystal structure of the yeast His6 enzyme suggests a reaction mechanism.
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Protein Sci,
15,
1516-1521.
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PDB code:
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B.Höcker
(2005).
Directed evolution of (betaalpha)(8)-barrel enzymes.
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Biomol Eng,
22,
31-38.
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D.G.Naumoff
(2005).
GH97 is a new family of glycoside hydrolases, which is related to the alpha-galactosidase superfamily.
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BMC Genomics,
6,
112.
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J.A.Gaspar,
C.Liu,
K.A.Vassall,
G.Meglei,
R.Stephen,
P.B.Stathopulos,
A.Pineda-Lucena,
B.Wu,
A.Yee,
C.H.Arrowsmith,
and
E.M.Meiering
(2005).
A novel member of the YchN-like fold: solution structure of the hypothetical protein Tm0979 from Thermotoga maritima.
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Protein Sci,
14,
216-223.
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PDB code:
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J.Kuper,
C.Doenges,
and
M.Wilmanns
(2005).
Two-fold repeated (betaalpha)4 half-barrels may provide a molecular tool for dual substrate specificity.
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EMBO Rep,
6,
134-139.
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PDB code:
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M.C.Vega,
P.Zou,
F.J.Fernandez,
G.E.Murphy,
R.Sterner,
A.Popov,
and
M.Wilmanns
(2005).
Regulation of the hetero-octameric ATP phosphoribosyl transferase complex from Thermotoga maritima by a tRNA synthetase-like subunit.
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Mol Microbiol,
55,
675-686.
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PDB code:
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R.E.Amaro,
R.S.Myers,
V.J.Davisson,
and
Z.A.Luthey-Schulten
(2005).
Structural elements in IGP synthase exclude water to optimize ammonia transfer.
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Biophys J,
89,
475-487.
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V.K.Dubey,
J.Lee,
and
M.Blaber
(2005).
Redesigning symmetry-related "mini-core" regions of FGF-1 to increase primary structure symmetry: thermodynamic and functional consequences of structural symmetry.
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Protein Sci,
14,
2315-2323.
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W.M.Patrick,
and
J.M.Blackburn
(2005).
In vitro selection and characterization of a stable subdomain of phosphoribosylanthranilate isomerase.
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FEBS J,
272,
3684-3697.
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A.Shukla,
and
P.Guptasarma
(2004).
Folding of beta/alpha-unit scrambled forms of S. cerevisiae triosephosphate isomerase: Evidence for autonomy of substructure formation and plasticity of hydrophobic and hydrogen bonding interactions in core of (beta/alpha)8-barrel.
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Proteins,
55,
548-557.
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B.Höcker,
J.Claren,
and
R.Sterner
(2004).
Mimicking enzyme evolution by generating new (betaalpha)8-barrels from (betaalpha)4-half-barrels.
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Proc Natl Acad Sci U S A,
101,
16448-16453.
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H.Wright,
F.Barona-Gómez,
D.A.Hodgson,
and
V.Fülöp
(2004).
Expression, purification and preliminary crystallographic analysis of phosphoribosyl isomerase (PriA) from Streptomyces coelicolor.
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Acta Crystallogr D Biol Crystallogr,
60,
534-536.
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K.B.Murray,
W.R.Taylor,
and
J.M.Thornton
(2004).
Toward the detection and validation of repeats in protein structure.
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Proteins,
57,
365-380.
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K.J.Woycechowsky
(2004).
Recombination of fragmented proteins.
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Chem Biol,
11,
589-591.
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M.H.Ali,
E.Peisach,
K.N.Allen,
and
B.Imperiali
(2004).
X-ray structure analysis of a designed oligomeric miniprotein reveals a discrete quaternary architecture.
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Proc Natl Acad Sci U S A,
101,
12183-12188.
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PDB codes:
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M.J.Bernett,
T.Somasundaram,
and
M.Blaber
(2004).
An atomic resolution structure for human fibroblast growth factor 1.
|
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Proteins,
57,
626-634.
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PDB code:
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Y.Nicolet,
and
C.L.Drennan
(2004).
AdoMet radical proteins--from structure to evolution--alignment of divergent protein sequences reveals strong secondary structure element conservation.
|
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Nucleic Acids Res,
32,
4015-4025.
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A.C.Joerger,
S.Mayer,
and
A.R.Fersht
(2003).
Mimicking natural evolution in vitro: an N-acetylneuraminate lyase mutant with an increased dihydrodipicolinate synthase activity.
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Proc Natl Acad Sci U S A,
100,
5694-5699.
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PDB code:
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A.Matte,
J.Sivaraman,
I.Ekiel,
K.Gehring,
Z.Jia,
and
M.Cygler
(2003).
Contribution of structural genomics to understanding the biology of Escherichia coli.
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J Bacteriol,
185,
3994-4002.
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B.A.Manjasetty,
J.Powlowski,
and
A.Vrielink
(2003).
Crystal structure of a bifunctional aldolase-dehydrogenase: sequestering a reactive and volatile intermediate.
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Proc Natl Acad Sci U S A,
100,
6992-6997.
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PDB code:
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B.N.Chaudhuri,
M.R.Sawaya,
C.Y.Kim,
G.S.Waldo,
M.S.Park,
T.C.Terwilliger,
and
T.O.Yeates
(2003).
The crystal structure of the first enzyme in the pantothenate biosynthetic pathway, ketopantoate hydroxymethyltransferase, from M tuberculosis.
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Structure,
11,
753-764.
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PDB code:
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F.Barona-Gómez,
and
D.A.Hodgson
(2003).
Occurrence of a putative ancient-like isomerase involved in histidine and tryptophan biosynthesis.
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EMBO Rep,
4,
296-300.
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M.Hartmann,
T.R.Schneider,
A.Pfeil,
G.Heinrich,
W.N.Lipscomb,
and
G.H.Braus
(2003).
Evolution of feedback-inhibited beta /alpha barrel isoenzymes by gene duplication and a single mutation.
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Proc Natl Acad Sci U S A,
100,
862-867.
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PDB code:
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S.R.Brych,
J.Kim,
T.M.Logan,
and
M.Blaber
(2003).
Accommodation of a highly symmetric core within a symmetric protein superfold.
|
| |
Protein Sci,
12,
2704-2718.
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PDB codes:
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A.Douangamath,
M.Walker,
S.Beismann-Driemeyer,
M.C.Vega-Fernandez,
R.Sterner,
and
M.Wilmanns
(2002).
Structural evidence for ammonia tunneling across the (beta alpha)(8) barrel of the imidazole glycerol phosphate synthase bienzyme complex.
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Structure,
10,
185-193.
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PDB codes:
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J.A.Barbosa,
J.Sivaraman,
Y.Li,
R.Larocque,
A.Matte,
J.D.Schrag,
and
M.Cygler
(2002).
Mechanism of action and NAD+-binding mode revealed by the crystal structure of L-histidinol dehydrogenase.
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Proc Natl Acad Sci U S A,
99,
1859-1864.
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PDB codes:
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O.Mayans,
A.Ivens,
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and
M.Wilmanns
(2002).
Structural analysis of two enzymes catalysing reverse metabolic reactions implies common ancestry.
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| |
EMBO J,
21,
3245-3254.
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PDB codes:
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S.Korolev,
T.Skarina,
E.Evdokimova,
S.Beasley,
A.Edwards,
A.Joachimiak,
and
A.Savchenko
(2002).
Crystal structure of glutamine amidotransferase from Thermotoga maritima.
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| |
Proteins,
49,
420-422.
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PDB code:
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B.Höcker,
C.Jürgens,
M.Wilmanns,
and
R.Sterner
(2001).
Stability, catalytic versatility and evolution of the (beta alpha)(8)-barrel fold.
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Curr Opin Biotechnol,
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F.Forcellino,
and
P.Derreumaux
(2001).
Computer simulations aimed at structure prediction of supersecondary motifs in proteins.
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Proteins,
45,
159-166.
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J.A.Gerlt,
and
P.C.Babbitt
(2001).
Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies.
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Annu Rev Biochem,
70,
209-246.
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J.D.Stevenson,
S.Lutz,
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(2001).
Retracing Enzyme Evolution in the (betaalpha)(8)-Barrel Scaffold.
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Angew Chem Int Ed Engl,
40,
1854-1856.
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J.Jung,
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Circularly permuted proteins in the protein structure database.
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Protein Sci,
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J.M.Petock,
I.Y.Torshin,
Y.F.Wang,
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C.M.Croce,
R.W.Harrison,
and
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(2001).
Structure of murine Tcl1 at 2.5 A resolution and implications for the TCL oncogene family.
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| |
Acta Crystallogr D Biol Crystallogr,
57,
1545-1551.
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PDB code:
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|
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|
|
M.Henn-Sax,
B.Höcker,
M.Wilmanns,
and
R.Sterner
(2001).
Divergent evolution of (betaalpha)8-barrel enzymes.
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Biol Chem,
382,
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M.J.Banfield,
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V.L.Arcus,
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and
E.N.Baker
(2001).
Structure of HisF, a histidine biosynthetic protein from Pyrobaculum aerophilum.
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| |
Acta Crystallogr D Biol Crystallogr,
57,
1518-1525.
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PDB code:
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T.J.Klem,
Y.Chen,
and
V.J.Davisson
(2001).
Subunit interactions and glutamine utilization by Escherichia coli imidazole glycerol phosphate synthase.
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J Bacteriol,
183,
989-996.
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C.Binda,
R.T.Bossi,
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(2000).
Cross-talk and ammonia channeling between active centers in the unexpected domain arrangement of glutamate synthase.
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| |
Structure,
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PDB code:
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|
J.A.Gerlt,
and
P.C.Babbitt
(2000).
Can sequence determine function?
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| |
Genome Biol,
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REVIEWS0005.
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J.Stubbe,
and
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(2000).
Clarity through structures. Editorial overview.
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Curr Opin Struct Biol,
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only a partial list as not all journals are covered by
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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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