Sb. Xiang et al., THE STRUCTURE OF THE CYTIDINE DEAMINASE PRODUCT COMPLEX PROVIDES EVIDENCE FOR EFFICIENT PROTON-TRANSFER AND GROUND-STATE DESTABILIZATION, Biochemistry, 36(16), 1997, pp. 4768-4774
Crystal structures of the cytidine deaminase-uridine product complex p
repared either by cocrystallizing enzyme with uridine or by diffusing
cytidine into ligand-free crystals show that the product binds as a 4-
ketopyrimidine. They reveal four additional features of the catalytic
process. (1) A water molecule bound to a site previously observed to b
ind the incoming 4-NH2 group represents the site for the leaving ammon
ia molecule. The conserved Pro 128 accommodates both moieties by orien
ting the carbonyl group of the previous residue. (2) The Glu 104 carbo
xylate group rotates from its hydrogen bond to the O4 hydroxyl group i
n transition-state analog complexes, forming a new hydrogen bond to th
e leaving group moiety. Thus, after stabilizing the hydroxyl group in
the transition state, Glu 104 transfers a proton from that group to th
e leaving amino group, promoting enol-to-keto isomerization of the pro
duct. (3) Difference Fourier comparisons with transition-state complex
es indicate that the pyrimidine ring rotates toward the zinc by simila
r to 10 degrees. The active site thus ''pulls'' the ring and 4-NH2 gro
up in opposite directions during catalysis. To preserve coplanarity of
the 4-keto group with the pyrimidine ring, the Nl-Cl' glycosidic bond
bends by similar to 19 degrees out of the ring plane. This distortion
may ''spring-load'' the product complex and promote dissociation. Fai
lure to recognize a similar distortion could explain an earlier crysta
llographic interpretation of the adenosine deaminase-inosine complex [
Wilson, D. K., & Quiocho, F. A. (1994) Nat. Struct. Biol. 1, 691-694].
(4) The Zn-S(gamma)132 bond, which lengthens in transition-state comp
lexes, shortens as the O4 atom returns to a state of lower negative ch
arge in the planar product, consistent with our previous proposal that
this bond buffers the zinc bond valence, compensating buildup of nega
tive charge on the oxygen nucleophile during catalysis.