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

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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Crystallization and structure solution of p53 (residues 326–356) by molecular replacement using an NMR model as template

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s0907444997006550 ◽

1998 ◽

Vol 54 (1) ◽

pp. 86-89 ◽

Cited By ~ 45

Author(s):

Peer R. E. Mittl ◽

Patrick Chène ◽

Markus G. Grütter

Keyword(s):

Crystal Structure ◽

Three Dimensional ◽

Dimensional Structure ◽

Molecular Replacement ◽

Additional Information ◽

Nmr Structures ◽

Replacement Method ◽

Tetramerization Domain ◽

Structure Solution ◽

Molecular Replacement Method

The molecular replacement method is a powerful technique for crystal structure solution but the use of NMR structures as templates often causes problems. In this work the NMR structure of the p53 tetramerization domain has been used to solve the crystal structure by molecular replacement. Since the rotation- and translation-functions were not sufficiently clear, additional information about the symmetry of the crystal and the protein complex was used to identify correct solutions. The three-dimensional structure of residues 326–356 was subsequently refined to a final R factor of 19.1% at 1.5 Å resolution.

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Structure of the histidine-containing phosphotransfer (HPt) domain of the anaerobic sensor protein ArcB complexed with the chemotaxis response regulator CheY

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s0907444999005053 ◽

1999 ◽

Vol 55 (7) ◽

pp. 1257-1263 ◽

Cited By ~ 12

Author(s):

Masato Kato ◽

Toshiyuki Shimizu ◽

Takeshi Mizuno ◽

Toshio Hakoshima

Keyword(s):

Response Regulator ◽

Three Dimensional ◽

Dimensional Structure ◽

Molecular Replacement ◽

Sulfate Ion ◽

Final Model ◽

Replacement Method ◽

Molecular Replacement Method ◽

Solvent Molecules ◽

Significant Conformational Change

The three-dimensional structure of the HPt domain of ArcB complexed with CheY has been determined using the molecular-replacement method. The structure was refined to a crystallographic R factor of 18.3% at 2.68 Å resolution. The final model included 1899 protein atoms (117 residues from the HPt domain and 128 residues from CheY), one sulfate ion and 44 solvent molecules. In the crystal, CheY molecules stacked along the a axis of the cell with no interactions between neighbouring rows and the HPt domain bridged the CheY molecules. The phosphodonor residue His715 was fully exposed to the solvent region, even though the HPt domain was in contact with four molecules of CheY. CheY showed significant conformational change. This indicates that the HPt domain has a rigid structure when complexed with CheY.

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

Acta Crystallographica Section A Foundations of Crystallography ◽

10.1107/s0108767396094640 ◽

1996 ◽

Vol 52 (a1) ◽

pp. C113-C113

Author(s):

B. W. Shen ◽

M. Hennig ◽

E. Hohenester ◽

J. N. Jansonius

Keyword(s):

Amino Acids ◽

Charge Distribution ◽

Active Site ◽

Three Dimensional ◽

Dimensional Structure ◽

Ornithine Aminotransferase ◽

Three Dimensional Structure ◽

Dibasic Amino Acids

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PREDICTION OF THE THREE-DIMENSIONAL STRUCTURE OF THE ENZYMATIC PART OF T-PA

10.1055/s-0038-1644407 ◽

1987 ◽

Author(s):

A Heckel ◽

K M Hasselbach

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Active Site ◽

Serine Proteases ◽

Three Dimensional ◽

Amino Acid Sequences ◽

Dimensional Structure ◽

Salt Bridges ◽

Three Dimensional Structure ◽

Insertions And Deletions

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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