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PDBsum entry 1nug

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Transferase PDB id
1nug
Jmol
Contents
Protein chain
675 a.a. *
Metals
_MG ×2
_CL ×4
_CA ×4
Waters ×809
* Residue conservation analysis

References listed in PDB file
Key reference
Title Roles of calcium ions in the activation and activity of the transglutaminase 3 enzyme.
Authors B.Ahvazi, K.M.Boeshans, W.Idler, U.Baxa, P.M.Steinert.
Ref. J Biol Chem, 2003, 278, 23834-23841. [DOI no: 10.1074/jbc.M301162200]
PubMed id 12679341
Abstract
The transglutaminase 3 enzyme is widely expressed in many tissues including epithelia. We have shown previously that it can bind three Ca2+ ions, which in site one is constitutively bound, while those in sites two and three are acquired during activation and are required for activity. In particular, binding at site three opens a channel through the enzyme and exposes two tryptophan residues near the active site that are thought to be important for enzyme reaction. In this study, we have solved the structures of three more forms of this enzyme by x-ray crystallography in the presence of Ca2+ and/or Mg2+, which provide new insights on the precise contribution of each Ca2+ ion to activation and activity. First, we found that Ca2+ ion in site one can be exchanged with difficulty, and it has a binding affinity of Kd = 0.3 microm (DeltaH = -6.70 +/- 0.52 kcal/mol), which suggests it is important for the stabilization of the enzyme. Site two can be occupied by some lanthanides but only Ca2+ of the Group 2 family of alkali earth metals, and its occupancy are required for activity. Site three can be occupied by some lanthanides, Ca2+,or Mg2+; however, when Mg2+ is present, the enzyme is inactive, and the channel is closed. Thus Ca2+ binding in both sites two and three cooperate in opening the channel. We speculate that manipulation of the channel opening could be controlled by intracellular cation levels. Together, these data have important implications for reaction mechanism of the enzyme: the opening of a channel perhaps controls access to and manipulation of substrates at the active site.
Figure 1.
FIG. 1. Conformations of the forms I (a and b), II (c and d), and III (e and g) solved in this study. The upper row shows the solved structures of the three forms. This is nominally the front side of the enzyme. The amino-terminal -sandwich (red), catalytic core (blue), -barrel 1 (magenta), and -barrel 2 (orange) domains are shown. The Ca^2^+ ions are shown in yellow, the sole Mg2^+ ion in cyan. Below are shown the electrostatic surface potential images. The acidic and basic residues are colored red and blue, respectively. The electrostatic potentials, including Ca^2^+ and Mg2^+ ions, have been mapped onto the surface plan from -15 kT (deep red) to +15 kT (deep blue). The open channel is clearly evident in b. In g, the back side of the enzyme has a deep cavity; the front side (f) remains closed.
Figure 2.
FIG. 2. Identification of key residues involved in the coordination with metal ions in sites one, two, and three in forms I-III. The details of these interactions and the bond lengths are summarized in Table III.
The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 23834-23841) copyright 2003.
Secondary reference #1
Title Three-Dimensional structure of the human transglutaminase 3 enzyme: binding of calcium ions changes structure for activation.
Authors B.Ahvazi, H.C.Kim, S.H.Kee, Z.Nemes, P.M.Steinert.
Ref. EMBO J, 2002, 21, 2055-2067. [DOI no: 10.1093/emboj/21.9.2055]
PubMed id 11980702
Full text Abstract
Figure 5.
Figure 5 Structural comparison of the zymogen and activated form. The upper and lower rows represent images rotated 180° with respect to each other, to show the channel in the active form. The electrostatic surface potential maps are shown in the center. The acidic and basic regions are colored red and blue, respectively. The arrow denotes a channel that opens on binding of a Ca^2+ ion in site 3. On the left and right are secondary structure images of the zymogen and the activated TGase 3 in the same orientations. The electrostatic potential, including calcium ions, has been mapped onto the surface plan from -15.0 kT (deep red) to +15.0 kT (deep blue).
Figure 6.
Figure 6 Stereo view images of the novel channel opened by Ca^2+ ion binding in site 3. Protein domains are colored as in Figure 3. (A) On one side, the electrostatic surface potential (black transparent) shows that the active site triad residues Cys272, His330 and Asp353 are buried and inaccessible. The movement of the loop bearing residues Asp320−Ser325 opens the channel in the activated TGase 3, and exposes the side chains of the Trp236 and Trp327 residues. (B) On the opposite side, the guanidinium group of Arg396 has moved to form a salt bridge with Glu586, allowing the hole to extend through the protein.
The above figures are reproduced from the cited reference which is an Open Access publication published by Macmillan Publishers Ltd
Secondary reference #2
Title Crystallization and preliminary X-Ray analysis of human transglutaminase 3 from zymogen to active form.
Authors H.C.Kim, Z.Nemes, W.W.Idler, C.C.Hyde, P.M.Steinert, B.Ahvazi.
Ref. J Struct Biol, 2001, 135, 73-77. [DOI no: 10.1006/jsbi.2001.4384]
PubMed id 11562168
Full text Abstract
PROCHECK
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