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PDBsum entry 2g08
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References listed in PDB file
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Key reference
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Title
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Structure of pyrimidine 5'-Nucleotidase type 1. Insight into mechanism of action and inhibition during lead poisoning.
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Authors
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E.Bitto,
C.A.Bingman,
G.E.Wesenberg,
J.G.Mccoy,
G.N.Phillips.
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Ref.
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J Biol Chem, 2006,
281,
20521-20529.
[DOI no: ]
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PubMed id
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Abstract
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Eukaryotic pyrimidine 5'-nucleotidase type 1 (P5N-1) catalyzes dephosphorylation
of pyrimidine 5'-mononucleotides. Deficiency of P5N-1 activity in red blood
cells results in nonspherocytic hemolytic anemia. The enzyme deficiency is
either familial or can be acquired through lead poisoning. We present the
crystal structure of mouse P5N-1 refined to 2.35 A resolution. The mouse P5N-1
has a 92% sequence identity to its human counterpart. The structure revealed
that P5N-1 adopts a fold similar to enzymes of the haloacid dehydrogenase
superfamily. The active site of this enzyme is structurally highly similar to
those of phosphoserine phosphatases. We propose a catalytic mechanism for P5N-1
that is also similar to that of phosphoserine phosphatases and provide
experimental evidence for the mechanism in the form of structures of several
reaction cycle states, including: 1) P5N-1 with bound Mg(II) at 2.25 A, 2)
phosphoenzyme intermediate analog at 2.30 A, 3) product-transition complex
analog at 2.35 A, and 4) product complex at 2.1A resolution with phosphate bound
in the active site. Furthermore the structure of Pb(II)-inhibited P5N-1 (at 2.35
A) revealed that Pb(II) binds within the active site in a way that compromises
function of the cationic cavity, which is required for the recognition and
binding of the phosphate group of nucleotides.
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Figure 2.
FIGURE 2. Comparison of mP5N-1 and its closest structural
homolog. A, a stereo representation of structural superposition
of mP5N-1 (red; Protein Data Bank code 2bdu) and hPSP (cyan;
Protein Data Bank code 1l8o). Every 10th C[  ]carbon of mP5N-1 is
highlighted by a red sphere, and some are labeled by residue
numbers for better orientation. B, structural superposition of
the active sites of mP5N-1 (red) and hPSP (cyan; Protein Data
Bank code 1nnl).
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Figure 3.
FIGURE 3. The reaction scheme of mP5N-1. A, mP5N-1 has two
enzymatic activities: nucleotidase activity (steps 1 and 2a) and
phosphotransferase activity (steps 1 and 2b). B, the proposed
catalytic mechanism for nucleotidase activity of mP5N-1. "R"
represents ribonucleoside. Individual states of the reaction
mechanism include apoenzyme (I), active enzyme (II), the
substrate complex (III), the substrate-transition complex (IV),
the phosphoenzyme intermediate (V), the product-transition
complex (VI), and the product complex (VII).
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2006,
281,
20521-20529)
copyright 2006.
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