Figure 2 - full size

 

Figure 2.
FIG. 2. A, left panels, stereo view of the 2.0-Å resolution 3 F[o] - 2 F[c] electron density map around the GMP contoured at 1.0- level in the. Right panel, view of cleft surface (yellow) and the surrounding residues within 6.5 Å of the GMP nucleotide located at the interface of the core domain (top) and the -barrel 1 domain (bottom). B, a view of the guanine nucleotide-binding site pocket in TGase 3·GMP complex. The hydrogen bonds and ion pair interactions are shown as dashed lines. All the important residues in the guanine nucleotide-binding site pocket and the GMP are shown in ball-and-stick. C, identification of key residues involved in the coordination with metal ions in sites 1, 2, and 3 in TGase 3 complex. In site 1, the Ca^2+ ion in the TGase 3·GMP forms direct contacts with the main chain carbonyl oxygen atoms of Ala^221, Asn224, Asn226, the carboxyl side-chain oxygen of Asn224, Asp 228, and to a water molecule. Site 2 exists near the end of catalytic core domain, next to the -helical segment (residues Asn430-Glu448), leading to the loop connecting the -barrel 1 domain. The Ca^2+ ion forms contacts with the carboxyl side-chain atoms of Asn393, Glu443, and Glu448, the main chain carbonyl oxygen atom of Ser415, and two water molecules. Mg2+ in site 3 binds in the vicinity of the loop segment, leading to the catalytic His330 at the active site. This Mg2+ ion forms contacts with the carboxyl side-chain oxygen atoms of Asp301 and Asp303, the side-chain atoms of Asn305, the main chain carbonyl oxygen atoms of Ser307, and a water molecule. The loop bearing residues 320DKGSDS325 has moved from its position in the native enzyme, closing the channel.

The above figure is reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 26716-26725) copyright 2004.