Three-dimensional structure of human ornithine aminotransferase: charge distribution at the active site explains the selectivity for W-group of dibasic amino acids

Up to now the three-dimensional structure of t-PA or parts of this enzyme is unknown. Using computer graphical methods the spatial structure of the enzymatic part of t-PA is predicted on the hypothesis, the three-dimensional backbone structure of t-PA being similar to that of other serine proteases. The t-PA model was built up in three steps:1) Alignment of the t-PA sequence with other serine proteases. Comparison of enzyme structures available from Brookhaven Protein Data Bank proved elastase as a basis for modeling.2) Exchange of amino acids of elastase differing from the t-PA sequence. The replacement of amino acids was performed such that backbone atoms overlapp completely and side chains superpose as far as possible.3) Modeling of insertions and deletions. To determine the spatial arrangement of insertions and deletions parts of related enzymes such as chymotrypsin or trypsin were used whenever possible. Otherwise additional amino acid sequences were folded to a B-turn at the surface of the proteine, where all insertions or deletions are located. Finally the side chain torsion angles of amino acids were optimised to prevent close contacts of neigh bouring atoms and to improve hydrogen bonds and salt bridges.The resulting model was used to explain binding of arginine 560 of plasminogen to the active site of t-PA. Arginine 560 interacts with Asp 189, Gly 19 3, Ser 19 5 and Ser 214 of t-PA (chymotrypsin numbering). Furthermore interaction of chromo-genic substrate S 2288 with the active site of t-PA was studied. The need for D-configuration of the hydrophobic amino acid at the N-terminus of this tripeptide derivative could be easily explained.

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An attempt to evaluate the influence of neighboring amino acids (n − 1) and (n + 1) on the backbone conformation of amino acid (n) in proteins. Use in predicting the three-dimensional structure of the polypeptide backbone of other proteins

Journal of Molecular Biology ◽

10.1016/0022-2836(73)90526-3 ◽

1973 ◽

Vol 75 (1) ◽

pp. 13-31 ◽

Cited By ~ 48

Author(s):

Tai Te Wu ◽

Elvin A. Kabat

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Three Dimensional ◽

Dimensional Structure ◽

Three Dimensional Structure ◽

Backbone Conformation ◽

Polypeptide Backbone

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Three-dimensional structure of β-momorcharin at 2.55 Å resolution

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s0907444999003297 ◽

1999 ◽

Vol 55 (6) ◽

pp. 1144-1151 ◽

Cited By ~ 19

Author(s):

Yu-Ren Yuan ◽

Yong-Ning He ◽

Jian-Ping Xiong ◽

Zong-Xiang Xia

Keyword(s):

Active Site ◽

Structural Model ◽

Three Dimensional ◽

Dimensional Structure ◽

Molecular Replacement ◽

Ribosome Inactivating Protein ◽

Three Dimensional Structure ◽

Replacement Method ◽

Enzymatic Function ◽

Molecular Replacement Method

β-Momorcharin (Mr ≃ 29 kDa) is a single-chained ribosome-inactivating protein (RIP) with a branched hexasaccharide bound to Asn51. The crystal structure of β-momorcharin has been determined using the molecular-replacement method and refined to 2.55 Å resolution. The final structural model gave an R factor of 17.2% and root-mean-square deviations of 0.016 Å and 1.76° from ideal bond lengths and bond angles, respectively. β-Momorcharin contains nine α-helices, two 310 helices and three β-sheets, and its overall structure is similar to those of other single-chained RIPs. Residues Tyr70, Tyr109, Glu158 and Arg161 are expected to define the active site of β-momorcharin as an rRNA N-glycosidase. The oligosaccharide is linked to the protein through an N-glycosidic bond, β-GlcNAc–(1-N)-Asn51, and stretches from the surface of the N-terminal domain far from the active site, which suggests that it should not play a role in enzymatic function. The oligosaccharide of each β-momorcharin molecule interacts with the protein through hydrogen bonds, although in the crystals most of these are intermolecular interactions with the protein atoms in an adjacent unit cell. This is the first example of an RIP structure which provides information about the three-dimensional structure and binding site of the oligosaccharide in the active chains of RIPs.

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