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PDBsum entry 1bnc
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Fatty acid biosynthesis
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PDB id
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1bnc
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* Residue conservation analysis
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Enzyme class:
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E.C.6.3.4.14
- biotin carboxylase.
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Reaction:
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N6-biotinyl-L-lysyl-[protein] + hydrogencarbonate + ATP = N6- carboxybiotinyl-L-lysyl-[protein] + ADP + phosphate + H+
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N(6)-biotinyl-L-lysyl-[protein]
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+
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hydrogencarbonate
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+
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ATP
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=
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N(6)- carboxybiotinyl-L-lysyl-[protein]
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+
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ADP
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+
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phosphate
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+
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H(+)
Bound ligand (Het Group name = )
corresponds exactly
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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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Biochemistry
33:10249-10256
(1994)
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PubMed id:
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Three-dimensional structure of the biotin carboxylase subunit of acetyl-CoA carboxylase.
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G.L.Waldrop,
I.Rayment,
H.M.Holden.
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ABSTRACT
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Acetyl-CoA carboxylase is found in all animals, plants, and bacteria and
catalyzes the first committed step in fatty acid synthesis. It is a
multicomponent enzyme containing a biotin carboxylase activity, a biotin
carboxyl carrier protein, and a carboxyltransferase functionality. Here we
report the X-ray structure of the biotin carboxylase component from Escherichia
coli determined to 2.4-A resolution. The structure was solved by a combination
of multiple isomorphous replacement and electron density modification
procedures. The overall fold of the molecule may be described in terms of three
structural domains. The N-terminal region, formed by Met 1-Ile 103, adopts a
dinucleotide binding motif with five strands of parallel beta-sheet flanked on
either side by alpha-helices. The "B-domain" extends from the main body of the
subunit where it folds into two alpha-helical regions and three strands of
beta-sheet. Following the excursion into the B-domain, the polypeptide chain
folds back into the body of the protein where it forms an eight-stranded
antiparallel beta-sheet. In addition to this major secondary structural element,
the C-terminal domain also contains a smaller three-stranded antiparallel
beta-sheet and seven alpha-helices. The active site of the enzyme has been
identified tentatively by a difference Fourier map calculated between X-ray data
from the native crystals and from crystals soaked in a Ag+/biotin complex. Those
amino acid residues believed to form part of the active site pocket include His
209-Glu 211, His 236-Glu 241, Glu 276, Ile 287-Glu 296, and Arg 338.2+
represents the first X-ray model of a biotin-dependent carboxylase.
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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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G.Gago,
L.Diacovich,
A.Arabolaza,
S.C.Tsai,
and
H.Gramajo
(2011).
Fatty acid biosynthesis in actinomycetes.
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FEMS Microbiol Rev,
35,
475-497.
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U.Pieper,
B.M.Webb,
D.T.Barkan,
D.Schneidman-Duhovny,
A.Schlessinger,
H.Braberg,
Z.Yang,
E.C.Meng,
E.F.Pettersen,
C.C.Huang,
R.S.Datta,
P.Sampathkumar,
M.S.Madhusudhan,
K.Sjölander,
T.E.Ferrin,
S.K.Burley,
and
A.Sali
(2011).
ModBase, a database of annotated comparative protein structure models, and associated resources.
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Nucleic Acids Res,
39,
D465-D474.
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C.L.Colbert,
C.W.Kim,
Y.A.Moon,
L.Henry,
M.Palnitkar,
W.B.McKean,
K.Fitzgerald,
J.Deisenhofer,
J.D.Horton,
and
H.J.Kwon
(2010).
Crystal structure of Spot 14, a modulator of fatty acid synthesis.
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Proc Natl Acad Sci U S A,
107,
18820-18825.
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PDB code:
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C.S.Huang,
K.Sadre-Bazzaz,
Y.Shen,
B.Deng,
Z.H.Zhou,
and
L.Tong
(2010).
Crystal structure of the alpha(6)beta(6) holoenzyme of propionyl-coenzyme A carboxylase.
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Nature,
466,
1001-1005.
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PDB code:
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S.A.Borisova,
B.T.Circello,
J.K.Zhang,
W.A.van der Donk,
and
W.W.Metcalf
(2010).
Biosynthesis of rhizocticins, antifungal phosphonate oligopeptides produced by Bacillus subtilis ATCC6633.
|
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Chem Biol,
17,
28-37.
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S.Duangpan,
S.Jitrapakdee,
A.Adina-Zada,
L.Byrne,
T.N.Zeczycki,
M.St Maurice,
W.W.Cleland,
J.C.Wallace,
and
P.V.Attwood
(2010).
Probing the catalytic roles of Arg548 and Gln552 in the carboxyl transferase domain of the Rhizobium etli pyruvate carboxylase by site-directed mutagenesis.
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Biochemistry,
49,
3296-3304.
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C.Y.Chou,
L.P.Yu,
and
L.Tong
(2009).
Crystal structure of biotin carboxylase in complex with substrates and implications for its catalytic mechanism.
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J Biol Chem,
284,
11690-11697.
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PDB codes:
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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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I.Mochalkin,
J.R.Miller,
A.Evdokimov,
S.Lightle,
C.Yan,
C.K.Stover,
and
G.L.Waldrop
(2008).
Structural evidence for substrate-induced synergism and half-sites reactivity in biotin carboxylase.
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Protein Sci,
17,
1706-1718.
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PDB codes:
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S.Jitrapakdee,
M.St Maurice,
I.Rayment,
W.W.Cleland,
J.C.Wallace,
and
P.V.Attwood
(2008).
Structure, mechanism and regulation of pyruvate carboxylase.
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Biochem J,
413,
369-387.
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S.O.Nilsson Lill,
J.Gao,
and
G.L.Waldrop
(2008).
Molecular dynamics simulations of biotin carboxylase.
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J Phys Chem B,
112,
3149-3156.
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Y.S.Cho,
J.I.Lee,
D.Shin,
H.T.Kim,
Y.H.Cheon,
C.I.Seo,
Y.E.Kim,
Y.L.Hyun,
Y.S.Lee,
K.Sugiyama,
S.Y.Park,
S.Ro,
J.M.Cho,
T.G.Lee,
and
Y.S.Heo
(2008).
Crystal structure of the biotin carboxylase domain of human acetyl-CoA carboxylase 2.
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Proteins,
70,
268-272.
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PDB code:
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Y.Zhang,
M.Morar,
and
S.E.Ealick
(2008).
Structural biology of the purine biosynthetic pathway.
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Cell Mol Life Sci,
65,
3699-3724.
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Y.Zhang,
R.H.White,
and
S.E.Ealick
(2008).
Crystal structure and function of 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase from Methanocaldococcus jannaschii.
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Biochemistry,
47,
205-217.
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PDB codes:
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R.Gande,
L.G.Dover,
K.Krumbach,
G.S.Besra,
H.Sahm,
T.Oikawa,
and
L.Eggeling
(2007).
The two carboxylases of Corynebacterium glutamicum essential for fatty acid and mycolic acid synthesis.
|
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J Bacteriol,
189,
5257-5264.
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S.Jitrapakdee,
K.H.Surinya,
A.Adina-Zada,
S.W.Polyak,
C.Stojkoski,
R.Smyth,
G.W.Booker,
W.W.Cleland,
P.V.Attwood,
and
J.C.Wallace
(2007).
Conserved Glu40 and Glu433 of the biotin carboxylase domain of yeast pyruvate carboxylase I isoenzyme are essential for the association of tetramers.
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Int J Biochem Cell Biol,
39,
2120-2134.
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L.Tong,
and
H.J.Harwood
(2006).
Acetyl-coenzyme A carboxylases: versatile targets for drug discovery.
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J Cell Biochem,
99,
1476-1488.
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M.E.Fraser,
K.Hayakawa,
M.S.Hume,
D.G.Ryan,
and
E.R.Brownie
(2006).
Interactions of GTP with the ATP-grasp domain of GTP-specific succinyl-CoA synthetase.
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J Biol Chem,
281,
11058-11065.
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PDB codes:
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M.Seki
(2006).
Biological significance and development of practical synthesis of biotin.
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Med Res Rev,
26,
434-482.
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Y.Shen,
C.Y.Chou,
G.G.Chang,
and
L.Tong
(2006).
Is dimerization required for the catalytic activity of bacterial biotin carboxylase?
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Mol Cell,
22,
807-818.
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PDB codes:
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J.Jeyakanthan,
E.Inagaki,
C.Kuroishi,
and
T.H.Tahirov
(2005).
Structure of PIN-domain protein PH0500 from Pyrococcus horikoshii.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
61,
463-468.
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PDB codes:
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J.M.Rodríguez,
P.Ruíz-Sala,
M.Ugarte,
and
M.A.Peñalva
(2004).
Fungal metabolic model for 3-methylcrotonyl-CoA carboxylase deficiency.
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J Biol Chem,
279,
4578-4587.
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R.J.Heath,
and
C.O.Rock
(2004).
Fatty acid biosynthesis as a target for novel antibacterials.
|
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Curr Opin Investig Drugs,
5,
146-153.
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S.Sueda,
M.N.Islam,
and
H.Kondo
(2004).
Protein engineering of pyruvate carboxylase: investigation on the function of acetyl-CoA and the quaternary structure.
|
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Eur J Biochem,
271,
1391-1400.
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T.Kanamori,
N.Kanou,
H.Atomi,
and
T.Imanaka
(2004).
Enzymatic characterization of a prokaryotic urea carboxylase.
|
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J Bacteriol,
186,
2532-2539.
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V.Sloane,
and
G.L.Waldrop
(2004).
Kinetic characterization of mutations found in propionic acidemia and methylcrotonylglycinuria: evidence for cooperativity in biotin carboxylase.
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J Biol Chem,
279,
15772-15778.
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Y.Sasaki,
and
Y.Nagano
(2004).
Plant acetyl-CoA carboxylase: structure, biosynthesis, regulation, and gene manipulation for plant breeding.
|
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Biosci Biotechnol Biochem,
68,
1175-1184.
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Y.Shen,
S.L.Volrath,
S.C.Weatherly,
T.D.Elich,
and
L.Tong
(2004).
A mechanism for the potent inhibition of eukaryotic acetyl-coenzyme A carboxylase by soraphen A, a macrocyclic polyketide natural product.
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Mol Cell,
16,
881-891.
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PDB codes:
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E.Choi-Rhee,
and
J.E.Cronan
(2003).
The biotin carboxylase-biotin carboxyl carrier protein complex of Escherichia coli acetyl-CoA carboxylase.
|
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J Biol Chem,
278,
30806-30812.
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S.Chuakrut,
H.Arai,
M.Ishii,
and
Y.Igarashi
(2003).
Characterization of a bifunctional archaeal acyl coenzyme A carboxylase.
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J Bacteriol,
185,
938-947.
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J.E.Cronan,
and
G.L.Waldrop
(2002).
Multi-subunit acetyl-CoA carboxylases.
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Prog Lipid Res,
41,
407-435.
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S.Ramón-Maiques,
A.Marina,
F.Gil-Ortiz,
I.Fita,
and
V.Rubio
(2002).
Structure of acetylglutamate kinase, a key enzyme for arginine biosynthesis and a prototype for the amino acid kinase enzyme family, during catalysis.
|
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Structure,
10,
329-342.
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PDB codes:
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L.H.Weaver,
K.Kwon,
D.Beckett,
and
B.W.Matthews
(2001).
Competing protein:protein interactions are proposed to control the biological switch of the E coli biotin repressor.
|
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Protein Sci,
10,
2618-2622.
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PDB codes:
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M.E.Gallardo,
L.R.Desviat,
J.M.Rodríguez,
J.Esparza-Gordillo,
C.Pérez-Cerdá,
B.Pérez,
P.Rodríguez-Pombo,
O.Criado,
R.Sanz,
D.H.Morton,
K.M.Gibson,
T.P.Le,
A.Ribes,
S.R.de Córdoba,
M.Ugarte,
and
M.A.Peñalva
(2001).
The molecular basis of 3-methylcrotonylglycinuria, a disorder of leucine catabolism.
|
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Am J Hum Genet,
68,
334-346.
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M.R.Baumgartner,
S.Almashanu,
T.Suormala,
C.Obie,
R.N.Cole,
S.Packman,
E.R.Baumgartner,
and
D.Valle
(2001).
The molecular basis of human 3-methylcrotonyl-CoA carboxylase deficiency.
|
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J Clin Invest,
107,
495-504.
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R.J.Heath,
S.W.White,
and
C.O.Rock
(2001).
Lipid biosynthesis as a target for antibacterial agents.
|
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Prog Lipid Res,
40,
467-497.
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I.N.Shindyalov,
and
P.E.Bourne
(2000).
An alternative view of protein fold space.
|
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Proteins,
38,
247-260.
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J.B.Thoden,
C.Z.Blanchard,
H.M.Holden,
and
G.L.Waldrop
(2000).
Movement of the biotin carboxylase B-domain as a result of ATP binding.
|
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J Biol Chem,
275,
16183-16190.
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PDB codes:
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J.B.Thoden,
S.Firestine,
A.Nixon,
S.J.Benkovic,
and
H.M.Holden
(2000).
Molecular structure of Escherichia coli PurT-encoded glycinamide ribonucleotide transformylase.
|
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Biochemistry,
39,
8791-8802.
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PDB codes:
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K.A.Denessiouk,
and
M.S.Johnson
(2000).
When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families.
|
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Proteins,
38,
310-326.
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K.L.Levert,
R.B.Lloyd,
and
G.L.Waldrop
(2000).
Do cysteine 230 and lysine 238 of biotin carboxylase play a role in the activation of biotin?
|
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Biochemistry,
39,
4122-4128.
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S.Karlin,
and
J.Mrázek
(2000).
Predicted highly expressed genes of diverse prokaryotic genomes.
|
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J Bacteriol,
182,
5238-5250.
|
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A.Marina,
P.M.Alzari,
J.Bravo,
M.Uriarte,
B.Barcelona,
I.Fita,
and
V.Rubio
(1999).
Carbamate kinase: New structural machinery for making carbamoyl phosphate, the common precursor of pyrimidines and arginine.
|
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Protein Sci,
8,
934-940.
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PDB code:
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C.H.Weber,
Y.S.Park,
S.Sanker,
C.Kent,
and
M.L.Ludwig
(1999).
A prototypical cytidylyltransferase: CTP:glycerol-3-phosphate cytidylyltransferase from bacillus subtilis.
|
| |
Structure,
7,
1113-1124.
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PDB code:
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C.Li,
T.J.Kappock,
J.Stubbe,
T.M.Weaver,
and
S.E.Ealick
(1999).
X-ray crystal structure of aminoimidazole ribonucleotide synthetase (PurM), from the Escherichia coli purine biosynthetic pathway at 2.5 A resolution.
|
| |
Structure,
7,
1155-1166.
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PDB code:
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C.Z.Blanchard,
Y.M.Lee,
P.A.Frantom,
and
G.L.Waldrop
(1999).
Mutations at four active site residues of biotin carboxylase abolish substrate-induced synergism by biotin.
|
| |
Biochemistry,
38,
3393-3400.
|
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E.Meyer,
T.J.Kappock,
C.Osuji,
and
J.Stubbe
(1999).
Evidence for the direct transfer of the carboxylate of N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) to generate 4-carboxy-5-aminoimidazole ribonucleotide catalyzed by Escherichia coli PurE, an N5-CAIR mutase.
|
| |
Biochemistry,
38,
3012-3018.
|
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F.M.Raushel,
J.B.Thoden,
and
H.M.Holden
(1999).
The amidotransferase family of enzymes: molecular machines for the production and delivery of ammonia.
|
| |
Biochemistry,
38,
7891-7899.
|
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G.Polekhina,
P.G.Board,
R.R.Gali,
J.Rossjohn,
and
M.W.Parker
(1999).
Molecular basis of glutathione synthetase deficiency and a rare gene permutation event.
|
| |
EMBO J,
18,
3204-3213.
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PDB code:
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I.I.Mathews,
T.J.Kappock,
J.Stubbe,
and
S.E.Ealick
(1999).
Crystal structure of Escherichia coli PurE, an unusual mutase in the purine biosynthetic pathway.
|
| |
Structure,
7,
1395-1406.
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PDB codes:
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J.B.Thoden,
F.M.Raushel,
M.M.Benning,
I.Rayment,
and
H.M.Holden
(1999).
The structure of carbamoyl phosphate synthetase determined to 2.1 A resolution.
|
| |
Acta Crystallogr D Biol Crystallogr,
55,
8.
|
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PDB code:
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J.B.Thoden,
G.Wesenberg,
F.M.Raushel,
and
H.M.Holden
(1999).
Carbamoyl phosphate synthetase: closure of the B-domain as a result of nucleotide binding.
|
| |
Biochemistry,
38,
2347-2357.
|
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PDB code:
|
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|
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M.Kobayashi,
and
S.Shimizu
(1999).
Cobalt proteins.
|
| |
Eur J Biochem,
261,
1-9.
|
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|
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|
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M.Uriarte,
A.Marina,
S.Ramón-Maiques,
I.Fita,
and
V.Rubio
(1999).
The carbamoyl-phosphate synthetase of Pyrococcus furiosus is enzymologically and structurally a carbamate kinase.
|
| |
J Biol Chem,
274,
16295-16303.
|
 |
|
|
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|
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T.M.Weaver,
W.Wang,
and
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}
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