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PDBsum entry 2rb5
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Unknown function
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PDB id
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2rb5
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References listed in PDB file
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Key reference
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Title
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The catalytic scaffold of the haloalkanoic acid dehalogenase enzyme superfamily acts as a mold for the trigonal bipyramidal transition state.
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Authors
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Z.Lu,
D.Dunaway-Mariano,
K.N.Allen.
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Ref.
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Proc Natl Acad Sci U S A, 2008,
105,
5687-5692.
[DOI no: ]
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PubMed id
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Abstract
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The evolution of new catalytic activities and specificities within an enzyme
superfamily requires the exploration of sequence space for adaptation to a new
substrate with retention of those elements required to stabilize key
intermediates/transition states. Here, we propose that core residues in the
large enzyme family, the haloalkanoic acid dehalogenase enzyme superfamily
(HADSF) form a "mold" in which the trigonal bipyramidal transition states formed
during phosphoryl transfer are stabilized by electrostatic forces. The vanadate
complex of the hexose phosphate phosphatase BT4131 from Bacteroides
thetaiotaomicron VPI-5482 (HPP) determined at 1.00 A resolution via X-ray
crystallography assumes a trigonal bipyramidal coordination geometry with the
nucleophilic Asp-8 and one oxygen ligand at the apical position. Remarkably, the
tungstate in the complex determined to 1.03 A resolution assumes the same
coordination geometry. The contribution of the general acid/base residue Asp-10
in the stabilization of the trigonal bipyramidal species via hydrogen-bond
formation with the apical oxygen atom is evidenced by the 1.52 A structure of
the D10A mutant bound to vanadate. This structure shows a collapse of the
trigonal bipyramidal geometry with displacement of the water molecule formerly
occupying the apical position. Furthermore, the 1.07 A resolution structure of
the D10A mutant complexed with tungstate shows the tungstate to be in a typical
"phosphate-like" tetrahedral configuration. The analysis of 12 liganded HADSF
structures deposited in the protein data bank (PDB) identified stringently
conserved elements that stabilize the trigonal bipyramidal transition states by
engaging in favorable electrostatic interactions with the axial and equatorial
atoms of the transferring phosphoryl group.
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Figure 1.
The general catalytic mechanism for phosphohydrolase members
of the HAD superfamily. Catalysis proceeds through an
aspartylphosphate intermediate.
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Figure 4.
The HPP-D10A active site in the presence of phosphate mimics
and the cofactor Mg^2+ (magenta sphere). The 2Fo-Fc
composite-omit electron density maps (gray cages) are contoured
at 1.5σ. (A) The 1.52 Å resolution structure of HPP-D10A
complexed with vanadate. Bond angles are O1-V-O2, 111.6°;
O2-V-O3, 122.9°; O1-V-O3, 117.7°; O1-V-OAsp8, 95.2°;
O2-V-OAsp8, 100.1°; O3-V-OAsp8, 102.3°. (B) The 1.07
Å resolution structure of HPP-D10A complexed with
tungstate. Bond angles are O1-W-O2, 112.8°; O2-W-O3,
118.8°; O1-W-O3, 112.3°; O1-W-O4, 103.8°; O2-W-O4,
104.1°; O3-W-O4, 102.9°{ideal bond angles tungstate [PDB
accession code 1FR3 (32)] O1-W-O2, 111.1°; O2-W-O3,
111.1°; O1-W-O3, 108.2°; O1-W-O4, 107.7°; O2-W-O4,
111.3°; O3-W-O4, 107.6°}. The water molecules are
depicted as red spheres.
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