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PDBsum entry 2cbe

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Lyase(oxo-acid) PDB id
2cbe
Jmol
Contents
Protein chain
258 a.a.
Waters ×218

References listed in PDB file
Key reference
Title Structure of native and apo carbonic anhydrase ii and structure of some of its anion-Ligand complexes.
Authors K.Håkansson, M.Carlsson, L.A.Svensson, A.Liljas.
Ref. J Mol Biol, 1992, 227, 1192-1204. [DOI no: 10.1016/0022-2836(92)90531-N]
PubMed id 1433293
Abstract
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.
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).
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.
The above figures are reprinted by permission from Elsevier: J Mol Biol (1992, 227, 1192-1204) copyright 1992.
Secondary reference #1
Title Structure of cobalt carbonic anhydrase complexed with bicarbonate.
Authors K.Håkansson, A.Wehnert.
Ref. J Mol Biol, 1992, 228, 1212-1218. [DOI no: 10.1016/0022-2836(92)90327-G]
PubMed id 1474587
Full text Abstract
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.
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.
The above figures are reproduced from the cited reference with permission from Elsevier
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