Chemistry Reference
In-Depth Information
MβLs.are.classiied.by.sequence.homology.in.three.subclasses:.B1,.B2,.and.B3.
159-162
.
We.focus.here.on.the.B1.subclass,.which.includes.several.chromosomally.encoded.
enzymes. such. as. the. ones. from.
Bacillus cereus
. (BcII),
163-168
.
Bacteroides fragilis
.
(CcrA)
169,170
.and.
Elizabethkingia meningoseptica
.(BlaB)
171,172
.as.well.as.the.transfer-
able.VIM,.IMP,.SPM,.and.GIM-type.enzymes.
173-179
.Subclass.B1.represents,.to.date,.
the. best. structurally. and. functionally. characterized. MβL. species
161,163,165-170,180-186
.
based.on.its.clinical.relevance.
187
.The.MβL.folding.frame.is.characterized.by.a.com-
pact.αβ/βα.sandwich,.accommodating.an.active.site.that.can.allocate.one.or.two.Zn.
ions.
158,188
.At.the.active.pocket,.the.irst.metal.site.(Zn1).is.tetrahedrally.coordinated.
by.three.histidine.ligands.(His116,.His118,.and.His196).and.the.nucleophilic.hydrox-
ide,.called.the.3H.site.(Figure.1.6)..The.coordination.of.the.second.metal.site.(Zn2).
is. provided. by. the. nucleophile,. one. water. molecule. and. a. ligand. triad. of. protein.
residues.which.includes.Asp120,.His263,.and.Cys221..The.metal.ion.occupancy.in.
B1.enzymes.has.been.also.a.matter.of.debate..The.irst.crystal.structure.of.BcII.(at.
2.5. Å,. PDB. code. 1bmc)
189
. showed. one. zinc. ion. bound. at. the. 3H. site.. Subsequent.
structures.of.BcII.and.CcrA.revealed.a.conserved.dinuclear.metal.center.in.all.B1.
enzymes
163,190,191
.(Figure.1.6)..The.metal.ions.are.essential.for.hydrolysis—fast.mix-
ing.techniques.coupled.to.Trp.luorescence.have.shown.that.apo-BcII,.despite.being.
properly.folded,.is.unable.to.bind.any.substrate.
168
.Unfortunately,.the.characteriza-
tion. of. catalytic. mechanism. in. Zn-enzymes. by. means. of. experimental. techniques.
is.dificult.as.Zn.is.invisible.to.most.spectroscopic.techniques..Thus,.computational.
quantum.mechanical.methods.may.provide.a.full.structural.and.energetics.descrip-
tion.of.the.reactive.mechanism,.providing.a.valuable.instrument.to.dissect.enzymatic.
catalysis.
CEF-BPC-IMI
Lys224
Asn233
WAT
His196
Zn2
His263
OH
-
Zn1
Cys221
His118
Asp120
His116
FIGURE 1.6 (See color insert.)
MD. structural. insights. into. the. binding. mode. of. di-Zn.
MβL.CcrA.in.complex.with.benzylpenicillin,.cefotaxime,.and.imipenem.β-lactam.substrates.
(only.substrate.bi-cyclic.cores.and.residue.heavy.atoms.are.shown.for.sake.of.clarity,.see.also.
Schemes.1.1.and.1.2)..(Adapted.from.Dal.Peraro,.M.,.Vila,.A.J.,.Carloni,.P.,.and.Klein,.M.L.,.
J. Am. Chem. Soc.
,.129,.2808,.2007.)
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