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PDBsum entry 2j2c
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References listed in PDB file
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Key reference
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Title
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Crystal structure of human cytosolic 5'-Nucleotidase ii: insights into allosteric regulation and substrate recognition.
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Authors
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K.Walldén,
P.Stenmark,
T.Nyman,
S.Flodin,
S.Gräslund,
P.Loppnau,
V.Bianchi,
P.Nordlund.
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Ref.
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J Biol Chem, 2007,
282,
17828-17836.
[DOI no: ]
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PubMed id
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Abstract
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Cytosolic 5'-nucleotidase II catalyzes the dephosphorylation of 6-hydroxypurine
nucleoside 5'-monophosphates and regulates the IMP and GMP pools within the
cell. It possesses phosphotransferase activity and thereby also catalyzes the
reverse reaction. Both reactions are allosterically activated by adenine-based
nucleotides and 2,3-bisphosphoglycerate. We have solved structures of cytosolic
5'-nucleotidase II as native protein (2.2 Angstrom) and in complex with
adenosine (1.5 Angstrom) and beryllium trifluoride (2.15 Angstrom) The
tetrameric enzyme is structurally similar to enzymes of the haloacid
dehalogenase (HAD) superfamily, including mitochondrial
5'(3')-deoxyribonucleotidase and cytosolic 5'-nucleotidase III but possesses
additional regulatory regions that contain two allosteric effector sites. At
effector site 1 located near a subunit interface we modeled diadenosine
tetraphosphate with one adenosine moiety in each subunit. This efficiently glues
the tetramer subunits together in pairs. The model shows why diadenosine
tetraphosphate but not diadenosine triphosphate activates the enzyme and
supports a role for cN-II during apoptosis when the level of diadenosine
tetraphosphate increases. We have also modeled 2,3-bisphosphoglycerate in
effector site 1 using one phosphate site from each subunit. By comparing the
structure of cytosolic 5'-nucleotidase II with that of mitochondrial
5'(3')-deoxyribonucleotidase in complex with dGMP, we identified residues
involved in substrate recognition.
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Figure 5.
FIGURE 5. Effector sites 1 and 2 of cN-II with bound
adenosine and sulfate. Omit F[o] - F[c] maps are covering
adenosine with  level of 4.5 in
effector site 1 and level of 3 in effector
site 2. A, stereo image of adenosine bound in effector site 1,
with adenosine and amino acid residues colored in turquoise. B,
stereo image of effector site 1 from two adjacent subunits
connected through interface A. Salt bridges are indicated by the
dotted lines. Nitrogens are shown in blue, oxygens in red, and
sulfur in yellow. C, stereo image of adenosine bound in effector
site 2. Note that the ribose moiety is disordered so that the
electron density cannot confirm its location. Waters are colored
in red. Polar atoms are color-coded as following: nitrogen in
blue, oxygens in red, and sulfur in yellow.
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Figure 7.
FIGURE 7. Two subunits of the tetrameric cN-II with three
positively charged regions (K(25)KYRR), (K(359)SKKRQ), and
(Q(420)RRIKK) shown in orange. Adenosines (white), sulfates
(yellow and red), and magnesium (yellow) are also shown.
Nitrogens are shown in blue and oxygens in red. The C-terminal
end of the structure (residue 488) is marked C.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2007,
282,
17828-17836)
copyright 2007.
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