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PDBsum entry 1vjj

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Transferase PDB id
1vjj
Jmol
Contents
Protein chains
675 a.a. *
Ligands
GDP ×2
Metals
_CL ×2
_CA ×6
_MG ×2
Waters ×898
* Residue conservation analysis

References listed in PDB file
Key reference
Title Structural basis for the coordinated regulation of transglutaminase 3 by guanine nucleotides and calcium/magnesium.
Authors B.Ahvazi, K.M.Boeshans, W.Idler, U.Baxa, P.M.Steinert, F.Rastinejad.
Ref. J Biol Chem, 2004, 279, 7180-7192. [DOI no: 10.1074/jbc.M312310200]
PubMed id 14645372
Abstract
Transglutaminase 3 (TGase 3) is a member of a family of Ca2+-dependent enzymes that catalyze covalent cross-linking reactions between proteins or peptides. TGase 3 isoform is widely expressed and is important for effective epithelial barrier formation in the assembly of the cell envelope. Among the nine TGase enzyme isoforms known in the human genome, only TGase 2 is known to bind and hydrolyze GTP to GDP; binding GTP inhibits its transamidation activity but allows it to function in signal transduction. Here we present biochemical and crystallographic evidence for the direct binding of GTP/GDP to the active TGase 3 enzyme, and we show that the TGase 3 enzyme undergoes a GTPase cycle. The crystal structures of active TGase 3 with guanosine 5'-O-(thiotriphosphate) (GTPgammaS) and GDP were determined to 2.1 and 1.9 A resolution, respectively. These studies reveal for the first time the reciprocal actions of Ca2+ and GTP with respect to TGase 3 activity. GTPgammaS binding is coordinated with the replacement of a bound Ca2+ with Mg2+ and conformational rearrangements that together close a central channel to the active site. Hydrolysis of GTP to GDP results in two stable conformations, resembling both the GTP state and the non-nucleotide bound state, the latter of which allows substrate access to the active site.
Figure 6.
FIG. 6. The electrostatic surface potential comparison of the TGase 3·GTP S/GDP complexes. The front and back view represent images rotated 180° with respect to each other to show the channel in the active TGase 3 form. The acidic and basic regions 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 when Ca^2+ ion is present at site 3 and closed when Ca^2+ metal is replaced by Mg2+ ion in TGase 3·GDP complex. A, the "back" side of the enzyme has a deep cavity; the "front" side remains closed in TGase 3·GTP S complex.
Figure 8.
FIG. 8. A, the view of modeled interactions of SQQ*VT (from loricrin) for the Gln* substrate and KTKQK* (from small proline-rich protein 1) as the Lys* substrate with GDP molecules that is shown in ball-and-stick. The side chains for the active site residues and Cys272, His330, and Asp353 are shown as ball-and-stick. B, the amino acid sequence alignment of TGases family is shown around the guanine nucleotide-binding site pocket. The amino acids highlighted in red are acidic, blue are basic, yellow are nonpolar, and green are polar residues. Arrows indicate the position of the Arg/Phe residues that stack over the guanine ring in TGase 2 and TGase 3 structures, respectively. The other arrows represent two basic residues that are essential for stabilizing the transition states for GTP hydrolysis.
The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 7180-7192) copyright 2004.
Secondary reference #1
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
Full text Abstract
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 reproduced from the cited reference with permission from the ASBMB
Secondary reference #2
Title A model for the reaction mechanism of the transglutaminase 3 enzyme.
Authors B.Ahvazi, P.M.Steinert.
Ref. Exp Mol Med, 2003, 35, 228-242. [DOI no: 10.1038/emm.2003.31]
PubMed id 14508061
Abstract
Secondary reference #3
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 #4
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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