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PDBsum entry 2cbb
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Lyase(oxo-acid)
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PDB id
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2cbb
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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 native and apo carbonic anhydrase ii and structure of some of its anion-Ligand complexes.
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Authors
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K.Håkansson,
M.Carlsson,
L.A.Svensson,
A.Liljas.
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Ref.
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J Mol Biol, 1992,
227,
1192-1204.
[DOI no: ]
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PubMed id
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Abstract
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In order to obtain a better structural framework for understanding the catalytic
mechanism of carbonic anhydrase, a number of inhibitor complexes of the enzyme
were investigated crystallographically. The three-dimensional structure of free
human carbonic anhydrase II was refined at pH 7.8 (1.54 A resolution) and at pH
6.0 (1.67 A resolution). The structure around the zinc ion was identical at both
pH values. The structure of the zinc-free enzyme was virtually identical with
that of the native enzyme, apart from a water molecule that had moved 0.9 A to
fill the space that would be occupied by the zinc ion. The complexes with the
anionic inhibitors bisulfite and formate were also studied at neutral pH.
Bisulfite binds with one of its oxygen atoms, presumably protonized, to the zinc
ion and replaces the zinc water. Formate, lacking a hydroxyl group, is bound
with its oxygen atoms not far away from the position of the non-protonized
oxygen atoms of the bisulfite complex, i.e. at hydrogen bond distance from
Thr199 N and at a position between the zinc ion and the hydrophobic part of the
active site. The result of these and other studies have implications for our
view of the catalytic function of the enzyme, since virtually all inhibitors
share some features with substrate, product or expected transition states. A
reaction scheme where electrophilic activation of carbon dioxide plays an
important role in the hydration reaction is presented. In the reverse direction,
the protonized oxygen of the bicarbonate is forced upon the zinc ion, thereby
facilitating cleavage of the carbon-oxygen bond. This is achieved by the
combined action of the anionic binding site, which binds carboxyl groups, the
side-chain of threonine 199, which discriminates between hydrogen bond donors
and acceptors, and hydrophobic interaction between substrate and the active site
cavity. The required proton transfer between the zinc water and His64 can take
place through water molecules 292 and 318.
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Figure 1.
Figure 1. The molecules involved in he hydrogen bond chain between His64 an the zinc water molecule in native
carbnic anhydrase at pH 7%. Distances and angles are; 64Nd' -2920HH-3180HH: (322 A. 196.7''. 2.73 A) and
2920HH-3180HH-2630HH: (2.7 A, lOS.l'', 2.79 A).
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Figure 3.
Figure 3. A larger view than in Fig. 2 of the active site. Note the ydrophobic nature of the right hand sde of the cleft
ith valins 121, 143 and 207, leucines 141 and 198 and tryptophan 209.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1992,
227,
1192-1204)
copyright 1992.
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Secondary reference #1
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Title
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Structure of cobalt carbonic anhydrase complexed with bicarbonate.
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Authors
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K.Håkansson,
A.Wehnert.
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Ref.
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J Mol Biol, 1992,
228,
1212-1218.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. The Co(II)carbonic anhydrasebicarbnate complex. Difference electron maps were calculated after
refinement of native co-ordinates without waters molecules 263 and 338 and with Co(H) instead of Zn(II). Positive
(continuous lines) and negative (broken lines) IF,/ IF,1 contours were rawn at +3a. The broken thinner molecular
drawings renresent the bindinn sites for formate in native CA11 (Hbkansson et a.Z., 1992) and for bicarbonate in mant
T200HUCAIi (Xue t al., 1992y.
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Figure 2.
Figure 2. The carbonic anhydrase mechanism of Hakansson et ai. (1992) in stereo. The `-states'' refer to Fig. 8 in that
paper. (a) (State 1) Native carbonic anhydrase II: with a zinc hydroxyl (23) at the 4th (tetrahedral) co-ordination site.
b) (State 2,3) A carbon dioxide molecule (500) is bound to the enzyme and is electrophilically activated. This is the
crystal structure of carbonic anhydrase complexed with cyanate (Lindahl et aZ., 19923). The broken lines represent the
binding of the sulfonamide group in the carbonic anhydrseDiamo complex; which may be analogous to an early tage
of nucleophilic attack on the carbon dioxide. (c) (State 4) This state s hypotheticl. The zinc hydroxyl is now a part of
the bicarbonate product and is bound at the zin water position wit,h the tetrahedral geometry o t,he native enzyme. The
oxygen atom itself is also tetrahedrally surrounded by water molecule 318, Thr1990Y, the zinc ion and the bicarbonate
arbon atom. The position of bicaronate is similar to what is found in th mutant T200H-bicarbonate complex,
although the solvent structures are different in the 2 cases (Xue et al.; 1992) (d) (State 5) Water molecule 318 is leaving
its normal position and makes a long co-ordination contact with te zinc ion and is now called 263. The bicarbonate
group is pushed away to a longer co-ordination distance. This is the crysta structure rported in this paper. The
bicarbonate molecule is now free to leave. The zinc water then takes its tetrahedral postin and a solution molecule takes
the vacant 318 osition. This step is co-ordinated with the proton shuttle (Liang & Lipscomb, 1989), where 1 of the zinc
water protons is shuttled through water molecules 31%292.Hi64 and released to a nearby buffer molecule in order to
omplete the cycle and regenerate the zinc hydroxide.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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