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PDBsum entry 2aky
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Adenylate kinase
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PDB id
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2aky
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References listed in PDB file
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Key reference
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Title
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High-Resolution structures of adenylate kinase from yeast ligated with inhibitor ap5a, Showing the pathway of phosphoryl transfer.
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Authors
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U.Abele,
G.E.Schulz.
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Ref.
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Protein Sci, 1995,
4,
1262-1271.
[DOI no: ]
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PubMed id
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Abstract
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The structure of adenylate kinase from yeast ligated with the
two-substrate-mimicking inhibitor Ap5A and Mg2+ has been refined to 1.96 A
resolution. In addition, the refined structure of the same complex with a bound
imidazole molecule replacing Mg2+ has been determined at 1.63 A. These
structures indicate that replacing Mg2+ by imidazole disturbs the water
structure and thus the complex. A comparison with the G-proteins shows that Mg2+
is exactly at the same position with respect to the phosphates. However,
although the Mg2+ ligand sphere of the G-proteins is a regular octahedron
containing peptide ligands, the reported adenylate kinase has no such ligands
and an open octahedron leaving space for the Mg2+ to accompany the transferred
phosphoryl group. A superposition of the known crystalline and therefore
perturbed phosphoryl transfer geometries in the adenylate kinases demonstrates
that all of them are close to the start of the forward reaction with bound ATP
and AMP. Averaging all observed perturbed structures gives rise to a close
approximation of the transition state, indicating in general how to establish an
elusive transition state geometry. The average shows that the in-line phosphoryl
transfer is associative, because there is no space for a dissociative
metaphosphate intermediate. As a side result, the secondary dipole interaction
in the alpha-helices of both protein structures has been quantified.
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Figure 4.
Fig. 4. Relationbetweenthelengthsofprimaryandsecondaryhydro-
genbonds in a-helicesasreferredtothedonoramdeatposition . The
plotcontainsalla-helicalH-bonds(Fig. 3) frombothreportedstruc-
tures.Averageangles N,-H,. . .0,-4 and N,-H,. . .0,-3 are 161" and
I1 I, respectively.
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Figure 6.
Fig. 6. BindingofImandMg2+in
AK,,, ligated with Ap,A.Mostresidues
andtwowatermoleulesarelabeled.
Chaincutsaremarked by dots. A: Posi-
tion f Mg2+(dot) in an extendedwater
cluster.Detailedenvronment of Mg2+
is showninFigures8Band9. : Bind-
ing of s suspended between hetird
phosphteandAsp89.Imidazoledis-
turbsappreciablythewateretworkat
theactivecenter.
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The above figures are
reprinted
from an Open Access publication published by the Protein Society:
Protein Sci
(1995,
4,
1262-1271)
copyright 1995.
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Secondary reference #1
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Title
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Stability, Activity and structure of adenylate kinase mutants.
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Authors
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P.Spuergin,
U.Abele,
G.E.Schulz.
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Ref.
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Eur J Biochem, 1995,
231,
405-413.
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PubMed id
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Secondary reference #2
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Title
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The cdna sequence encoding cytosolic adenylate kinase from baker'S yeast (saccharomyces cerevisiae).
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Authors
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K.Proba,
A.G.Tomasselli,
P.Nielsen,
G.E.Schulz.
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Ref.
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Nucleic Acids Res, 1987,
15,
7187.
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PubMed id
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Secondary reference #3
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Title
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Structure of the complex of yeast adenylate kinase with the inhibitor p1,P5-Di(adenosine-5'-)Pentaphosphate at 2.6 a resolution.
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Authors
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U.Egner,
A.G.Tomasselli,
G.E.Schulz.
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Ref.
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J Mol Biol, 1987,
195,
649-658.
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PubMed id
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Secondary reference #4
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Title
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The complete amino acid sequence of adenylate kinase from baker'S yeast.
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Authors
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A.G.Tomasselli,
E.Mast,
W.Janes,
E.Schiltz.
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Ref.
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Eur J Biochem, 1986,
155,
111-119.
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PubMed id
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