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Review
. 2013 Aug 14;113(8):5871-923.
doi: 10.1021/cr300384w. Epub 2013 Apr 25.

Gates of enzymes

Artur Gora  1 , Jan Brezovsky, Jiri Damborsky
Affiliations
Review

Gates of enzymes

Artur Gora et al. Chem Rev. .
No abstract available

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Figures

Figure 1
Figure 1
Distribution of (A) reviewed proteins and (B) proteins from the PDB database according to EC classes, (C) reviewed proteins and (D) proteins from the PDB database according to SCOP classification, and (E) identity matrix of reviewed enzymes (only the enzymes with sequence identities above 20% are shown for clarity).
Figure 2
Figure 2
Schematic illustration of the molecular functions of protein gates: (A) control of substrate access, (B) control of solvent access, (C) control and synchronization of reactions. Protein is represented by the area colored in gray, active site cavity by the area in white, gating residues by red lines, substrate molecules by green or violet lines, and water molecules by blue lines.
Figure 3
Figure 3
Distribution of gate functions; 71 proteins with 129 different gates were analyzed. Percentages shown in the figure are based on all of the identified functions of each gate; individual gate may perform multiple functions. Detailed description of the analyzed proteins is provided in Table 3.
Figure 4
Figure 4
Relative occurrences of specific amino acid residues in wing and swinging door gates; 71 proteins with 129 gates were analyzed, and 154 residues that form wings or swinging doors were identified. Detailed description of the analyzed proteins is provided in Table 3. Values were normalized against the frequency with which each amino acid appears in all of the protein structures of the UniProtKB/Swiss-Prot database (2012_07).
Figure 5
Figure 5
Frequencies of different gate types based on analysis of 71 proteins with 129 gates. Detailed description of the analyzed proteins is provided in Table 3.
Figure 6
Figure 6
Locations of gates within a protein structure. Schematic representation of an enzyme with two active sites connected by a tunnel (I), a cofactor cavity (II), and multiple access tunnels. Gating residues in red may be located at the entrance to the active site (1), at the entrance or the bottleneck of the tunnel (2), and between the active site cavity and the cofactor cavity (3).
Figure 7
Figure 7
Distribution of gate locations within protein structures based on analysis of 71 proteins with 129 gates. Detailed description of the analyzed proteins is provided in Table 3.
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References

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