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PDBsum entry 7gpb
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Glycogen phosphorylase
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PDB id
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7gpb
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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.2.4.1.1
- glycogen phosphorylase.
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Pathway:
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Glycogen
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Reaction:
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[(1->4)-alpha-D-glucosyl](n) + phosphate = [(1->4)-alpha-D-glucosyl](n-1) + alpha-D-glucose 1-phosphate
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[(1->4)-alpha-D-glucosyl](n)
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+
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phosphate
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=
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[(1->4)-alpha-D-glucosyl](n-1)
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+
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alpha-D-glucose 1-phosphate
Bound ligand (Het Group name = )
matches with 50.00% similarity
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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J Mol Biol
218:233-260
(1991)
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PubMed id:
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Structural mechanism for glycogen phosphorylase control by phosphorylation and AMP.
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D.Barford,
S.H.Hu,
L.N.Johnson.
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ABSTRACT
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The crystal structures of activated R state glycogen phosphorylase a (GPa) and R
and T state glycogen phosphorylase b (GPb) complexed with AMP have been solved
at 2.9 A, 2.9 A and 2.2 A resolution, respectively. The structure of R state GPa
is nearly identical to the structure of sulphate-activated R state GPb, except
in the region of Ser14, where there is a covalently attached phosphate group in
GPa and a non-covalently attached sulphate group in GPb. The contacts made by
the N-terminal tail residues in R state GPa at the subunit interface of the
functionally active dimer are similar to those observed previously for T state
GPa. The quaternary and tertiary structural changes on the T to R transition
allow these interactions to be relayed to the catalytic site in R state GPa. The
transition from the T state GPb structure to the R state GPa structure results
in a change in the N-terminal residues from a poorly ordered extended structure
that makes intrasubunit contacts to an ordered coiled conformation that makes
intersubunit contacts. The distance between Arg10, the first residue to be
located from the N terminus, in R state GPa and T state GPb is 50 A. One of the
important subunit-subunit interactions in the dimer molecule involves contacts
between the helix alpha 2 and the cap' (residues 35' to 45' that form a loop
between the 1st and 2nd alpha helices, alpha 1' and alpha 2' of the other
subunit. The prime denotes residues from the other subunit). The interactions
made by the N-terminal residues induce structural changes at the cap'/alpha 2
helix interface that lead to the creation of a high-affinity AMP site. The
tertiary structural changes at the cap (shifts 1.2 to 2.1 A for residues 35 to
45) are partially compensated by the quaternary structural change so that the
overall shifts in these residues after the combined tertiary and quaternary
changes are between 0.5 and 1.3 A. AMP binds to R state GPb with at least
100-fold greater affinity and exhibits four additional hydrogen bonds, stronger
ionic interactions and more extensive van der Waals' interactions with 116 A2
greater solvent accessible surface area buried compared with AMP bound to T
state GPb.(ABSTRACT TRUNCATED AT 400 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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D.Barford,
and
D.I.Stuart
(2012).
Louise N. Johnson 1940-2012.
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Nat Struct Mol Biol,
19,
1216-1217.
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M.Bouskila,
R.W.Hunter,
A.F.Ibrahim,
L.Delattre,
M.Peggie,
J.A.van Diepen,
P.J.Voshol,
J.Jensen,
and
K.Sakamoto
(2010).
Allosteric regulation of glycogen synthase controls glycogen synthesis in muscle.
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Cell Metab,
12,
456-466.
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X.Liu,
L.Bardwell,
and
Q.Nie
(2010).
A combination of multisite phosphorylation and substrate sequestration produces switchlike responses.
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Biophys J,
98,
1396-1407.
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A.Pautsch,
N.Stadler,
O.Wissdorf,
E.Langkopf,
W.Moreth,
and
R.Streicher
(2008).
Molecular recognition of the protein phosphatase 1 glycogen targeting subunit by glycogen phosphorylase.
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J Biol Chem,
283,
8913-8918.
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PDB code:
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M.D.Daily,
T.J.Upadhyaya,
and
J.J.Gray
(2008).
Contact rearrangements form coupled networks from local motions in allosteric proteins.
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Proteins,
71,
455-466.
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C.Tiraidis,
K.M.Alexacou,
S.E.Zographos,
D.D.Leonidas,
T.Gimisis,
and
N.G.Oikonomakos
(2007).
FR258900, a potential anti-hyperglycemic drug, binds at the allosteric site of glycogen phosphorylase.
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Protein Sci,
16,
1773-1782.
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PDB code:
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J.Kuriyan,
and
D.Eisenberg
(2007).
The origin of protein interactions and allostery in colocalization.
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Nature,
450,
983-990.
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J.L.Jiménez,
B.Hegemann,
J.R.Hutchins,
J.M.Peters,
and
R.Durbin
(2007).
A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database.
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Genome Biol,
8,
R90.
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M.D.Daily,
and
J.J.Gray
(2007).
Local motions in a benchmark of allosteric proteins.
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Proteins,
67,
385-399.
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Z.Serber,
and
J.E.Ferrell
(2007).
Tuning bulk electrostatics to regulate protein function.
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Cell,
128,
441-444.
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C.Cuadri-Tomé,
C.Barón,
V.Jara-Pérez,
A.Parody-Morreale,
J.C.Martinez,
and
A.Cámara-Artigas
(2006).
Kinetic analysis and modelling of the allosteric behaviour of liver and muscle glycogen phosphorylases.
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J Mol Recognit,
19,
451-457.
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C.M.Lukacs,
N.G.Oikonomakos,
R.L.Crowther,
L.N.Hong,
R.U.Kammlott,
W.Levin,
S.Li,
C.M.Liu,
D.Lucas-McGady,
S.Pietranico,
and
L.Reik
(2006).
The crystal structure of human muscle glycogen phosphorylase a with bound glucose and AMP: an intermediate conformation with T-state and R-state features.
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Proteins,
63,
1123-1126.
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PDB code:
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F.Magkos,
and
S.A.Kavouras
(2005).
Caffeine use in sports, pharmacokinetics in man, and cellular mechanisms of action.
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Crit Rev Food Sci Nutr,
45,
535-562.
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N.G.Oikonomakos,
M.N.Kosmopoulou,
E.D.Chrysina,
D.D.Leonidas,
I.D.Kostas,
K.U.Wendt,
T.Klabunde,
and
E.Defossa
(2005).
Crystallographic studies on acyl ureas, a new class of glycogen phosphorylase inhibitors, as potential antidiabetic drugs.
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Protein Sci,
14,
1760-1771.
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PDB codes:
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G.Wu,
and
M.Müller
(2003).
Glycogen phosphorylase sequences from the amitochondriate protists, Trichomonas vaginalis, Mastigamoeba balamuthi, Entamoeba histolytica and Giardia intestinalis.
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J Eukaryot Microbiol,
50,
366-372.
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C.Vénien-Bryan,
E.M.Lowe,
N.Boisset,
K.W.Traxler,
L.N.Johnson,
and
G.M.Carlson
(2002).
Three-dimensional structure of phosphorylase kinase at 22 A resolution and its complex with glycogen phosphorylase b.
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Structure,
10,
33-41.
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H.Kojima,
and
O.Numata
(2002).
Enzymatic form and cytoskeletal form of bifunctional Tetrahymena 49kDa protein is regulated by phosphorylation.
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Zoolog Sci,
19,
37-42.
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N.G.Oikonomakos,
M.Kosmopoulou,
S.E.Zographos,
D.D.Leonidas,
E.D.Chrysina,
L.Somsák,
V.Nagy,
J.P.Praly,
T.Docsa,
B.Tóth,
and
P.Gergely
(2002).
Binding of N-acetyl-N '-beta-D-glucopyranosyl urea and N-benzoyl-N '-beta-D-glucopyranosyl urea to glycogen phosphorylase b: kinetic and crystallographic studies.
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Eur J Biochem,
269,
1684-1696.
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PDB codes:
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J.L.Buchbinder,
V.L.Rath,
and
R.J.Fletterick
(2001).
Structural relationships among regulated and unregulated phosphorylases.
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Annu Rev Biophys Biomol Struct,
30,
191-209.
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N.A.Chebotareva,
S.E.Harding,
and
D.J.Winzor
(2001).
Ultracentrifugal studies of the effect of molecular crowding by trimethylamine N-oxide on the self-association of muscle glycogen phosphorylase b.
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Eur J Biochem,
268,
506-513.
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S.W.Vetter,
and
E.Leclerc
(2001).
Phosphorylation of serine residues affects the conformation of the calmodulin binding domain of human protein 4.1.
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Eur J Biochem,
268,
4292-4299.
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A.C.Biorn,
C.Bartleson,
and
D.J.Graves
(2000).
Site-directed mutants of glycogen phosphorylase are altered in their interaction with phosphorylase kinase.
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Biochemistry,
39,
15887-15894.
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I.Hamachi,
J.I.Watanabe,
R.Eboshi,
T.Hiraoka,
and
S.Shinkai
(2000).
Incorporation of artificial receptors into a protein/peptide surface: a strategy for on/off type of switching of semisynthetic enzymes.
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Biopolymers,
55,
459-468.
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N.G.Oikonomakos,
V.T.Skamnaki,
K.E.Tsitsanou,
N.G.Gavalas,
and
L.N.Johnson
(2000).
A new allosteric site in glycogen phosphorylase b as a target for drug interactions.
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Structure,
8,
575-584.
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PDB code:
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R.Griessler,
S.D'Auria,
F.Tanfani,
and
B.Nidetzky
(2000).
Thermal denaturation pathway of starch phosphorylase from Corynebacterium callunae: oxyanion binding provides the glue that efficiently stabilizes the dimer structure of the protein.
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Protein Sci,
9,
1149-1161.
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A.A.Komissarov,
and
S.L.Deutscher
(1999).
Thermodynamics of Fab-ssDNA interactions: contribution of heavy chain complementarity determining region 3.
|
| |
Biochemistry,
38,
14631-14637.
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A.Tholey,
A.Lindemann,
V.Kinzel,
and
J.Reed
(1999).
Direct effects of phosphorylation on the preferred backbone conformation of peptides: a nuclear magnetic resonance study.
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Biophys J,
76,
76-87.
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D.Graves,
C.Bartleson,
A.Biorn,
and
M.Pete
(1999).
Substrate and inhibitor recognition of protein kinases: what is known about the catalytic subunit of phosphorylase kinase?
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Pharmacol Ther,
82,
143-155.
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G.Kung,
J.A.Runquist,
H.M.Miziorko,
and
D.H.Harrison
(1999).
Identification of the allosteric regulatory site in bacterial phosphoribulokinase.
|
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Biochemistry,
38,
15157-15165.
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K.A.Denessiouk,
A.I.Denesyuk,
J.V.Lehtonen,
T.Korpela,
and
M.S.Johnson
(1999).
Common structural elements in the architecture of the cofactor-binding domains in unrelated families of pyridoxal phosphate-dependent enzymes.
|
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Proteins,
35,
250-261.
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K.A.Watson,
C.McCleverty,
S.Geremia,
S.Cottaz,
H.Driguez,
and
L.N.Johnson
(1999).
Phosphorylase recognition and phosphorolysis of its oligosaccharide substrate: answers to a long outstanding question.
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EMBO J,
18,
4619-4632.
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PDB codes:
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K.E.Tsitsanou,
N.G.Oikonomakos,
S.E.Zographos,
V.T.Skamnaki,
M.Gregoriou,
K.A.Watson,
L.N.Johnson,
and
G.W.Fleet
(1999).
Effects of commonly used cryoprotectants on glycogen phosphorylase activity and structure.
|
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Protein Sci,
8,
741-749.
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PDB codes:
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N.G.Oikonomakos,
K.E.Tsitsanou,
S.E.Zographos,
V.T.Skamnaki,
S.Goldmann,
and
H.Bischoff
(1999).
Allosteric inhibition of glycogen phosphorylase a by the potential antidiabetic drug 3-isopropyl 4-(2-chlorophenyl)-1,4-dihydro-1-ethyl-2-methyl-pyridine-3,5,6-tricarbo xylate.
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Protein Sci,
8,
1930-1945.
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PDB codes:
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Z.X.Wang
(1999).
Kinetic study on the dimer-tetramer interconversion of glycogen phosphorylase a.
|
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Eur J Biochem,
259,
609-617.
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A.Pappas,
W.L.Yang,
T.S.Park,
and
G.M.Carman
(1998).
Nucleotide-dependent tetramerization of CTP synthetase from Saccharomyces cerevisiae.
|
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J Biol Chem,
273,
15954-15960.
|
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M.Gregoriou,
M.E.Noble,
K.A.Watson,
E.F.Garman,
T.M.Krulle,
C.de la Fuente,
G.W.Fleet,
N.G.Oikonomakos,
and
L.N.Johnson
(1998).
The structure of a glycogen phosphorylase glucopyranose spirohydantoin complex at 1.8 A resolution and 100 K: the role of the water structure and its contribution to binding.
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Protein Sci,
7,
915-927.
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PDB codes:
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M.Schutkowski,
A.Bernhardt,
X.Z.Zhou,
M.Shen,
U.Reimer,
J.U.Rahfeld,
K.P.Lu,
and
G.Fischer
(1998).
Role of phosphorylation in determining the backbone dynamics of the serine/threonine-proline motif and Pin1 substrate recognition.
|
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Biochemistry,
37,
5566-5575.
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A.Cámara-Artigas,
A.Parody-Morreale,
and
C.Barón
(1997).
Analogous activation of bovine liver glycogen phosphorylase by AMP and IMP.
|
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Int J Biochem Cell Biol,
29,
849-856.
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A.Nilsson,
D.Stys,
T.Drakenberg,
M.D.Spangfort,
S.Forsén,
and
J.F.Allen
(1997).
Phosphorylation controls the three-dimensional structure of plant light harvesting complex II.
|
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J Biol Chem,
272,
18350-18357.
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B.Kobe,
I.G.Jennings,
C.M.House,
S.C.Feil,
B.J.Michell,
T.Tiganis,
M.W.Parker,
R.G.Cotton,
and
B.E.Kemp
(1997).
Regulation and crystallization of phosphorylated and dephosphorylated forms of truncated dimeric phenylalanine hydroxylase.
|
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Protein Sci,
6,
1352-1357.
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D.G.Hardie,
and
D.Carling
(1997).
The AMP-activated protein kinase--fuel gauge of the mammalian cell?
|
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Eur J Biochem,
246,
259-273.
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E.D.Lowe,
M.E.Noble,
V.T.Skamnaki,
N.G.Oikonomakos,
D.J.Owen,
and
L.N.Johnson
(1997).
The crystal structure of a phosphorylase kinase peptide substrate complex: kinase substrate recognition.
|
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EMBO J,
16,
6646-6658.
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PDB code:
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J.L.Buchbinder,
C.B.Luong,
M.F.Browner,
and
R.J.Fletterick
(1997).
Partial activation of muscle phosphorylase by replacement of serine 14 with acidic residues at the site of regulatory phosphorylation.
|
| |
Biochemistry,
36,
8039-8044.
|
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K.A.Watson,
R.Schinzel,
D.Palm,
and
L.N.Johnson
(1997).
The crystal structure of Escherichia coli maltodextrin phosphorylase provides an explanation for the activity without control in this basic archetype of a phosphorylase.
|
| |
EMBO J,
16,
1.
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K.Lin,
P.K.Hwang,
and
R.J.Fletterick
(1997).
Distinct phosphorylation signals converge at the catalytic center in glycogen phosphorylases.
|
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Structure,
5,
1511-1523.
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M.Chandra,
W.J.Dong,
B.S.Pan,
H.C.Cheung,
and
R.J.Solaro
(1997).
Effects of protein kinase A phosphorylation on signaling between cardiac troponin I and the N-terminal domain of cardiac troponin C.
|
| |
Biochemistry,
36,
13305-13311.
|
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M.O'Reilly,
K.A.Watson,
R.Schinzel,
D.Palm,
and
L.N.Johnson
(1997).
Oligosaccharide substrate binding in Escherichia coli maltodextrin phosphorylase.
|
| |
Nat Struct Biol,
4,
405-412.
|
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PDB code:
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S.E.Zographos,
N.G.Oikonomakos,
K.E.Tsitsanou,
D.D.Leonidas,
E.D.Chrysina,
V.T.Skamnaki,
H.Bischoff,
S.Goldmann,
K.A.Watson,
and
L.N.Johnson
(1997).
The structure of glycogen phosphorylase b with an alkyldihydropyridine-dicarboxylic acid compound, a novel and potent inhibitor.
|
| |
Structure,
5,
1413-1425.
|
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PDB codes:
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D.E.Koshland
(1996).
The structural basis of negative cooperativity: receptors and enzymes.
|
| |
Curr Opin Struct Biol,
6,
757-761.
|
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E.P.Mitchell,
S.G.Withers,
P.Ermert,
A.T.Vasella,
E.F.Garman,
N.G.Oikonomakos,
and
L.N.Johnson
(1996).
Ternary complex crystal structures of glycogen phosphorylase with the transition state analogue nojirimycin tetrazole and phosphate in the T and R states.
|
| |
Biochemistry,
35,
7341-7355.
|
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PDB codes:
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J.L.Buchbinder,
and
R.J.Fletterick
(1996).
Role of the active site gate of glycogen phosphorylase in allosteric inhibition and substrate binding.
|
| |
J Biol Chem,
271,
22305-22309.
|
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|
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J.Stubbe,
and
L.N.Johnson
(1996).
Catalysis and regulation.
|
| |
Curr Opin Struct Biol,
6,
733-735.
|
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|
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L.García-Fuentes,
A.Cámara-Artigas,
O.López-Mayorga,
and
C.Barón
(1996).
Thermodynamic characterization of 5'-AMP binding to bovine liver glycogen phosphorylase a.
|
| |
J Biol Chem,
271,
27569-27574.
|
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|
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L.N.Johnson,
and
M.O'Reilly
(1996).
Control by phosphorylation.
|
| |
Curr Opin Struct Biol,
6,
762-769.
|
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|
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N.G.Oikonomakos,
S.E.Zographos,
K.E.Tsitsanou,
L.N.Johnson,
and
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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
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so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
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}
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