PDBsum entry 1xvm

Hydrolase

PDB id: 1xvm

Contents

Protein chain

224 a.a. *

Ligands

GLY-ALA-ARG

Waters ×131

* Residue conservation analysis

PDB id:

1xvm

Name:

Hydrolase

Title:

Trypsin from fusarium oxysporum- room temperature to atomic resolution

Structure:

Trypsin. Chain: a. Substrate tripeptide gly-ala-arg. Chain: b. Engineered: yes

Source:

Fusarium oxysporum. Organism_taxid: 5507. Synthetic: yes. Other_details: the peptide is chemically synthesized.

Biol. unit:

Dimer (from PQS)

Resolution:

1.10Å R-factor: 0.144

Authors:

A.Schmidt,V.S.Lamzin

Key ref:

A.Schmidt and V.S.Lamzin (2005). Extraction of functional motion in trypsin crystal structures. Acta Crystallogr D Biol Crystallogr, 61, 1132-1139. PubMed id: 16041079 DOI: 10.1107/S0907444905016732

Date:

28-Oct-04 Release date: 26-Jul-05

Protein chain

P35049  (TRYP_FUSOX) -  Trypsin from Fusarium oxysporum

Seq: 248 a.a.

Struc: 224 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.21.4 - trypsin.
• Reaction: Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.

DOI no: 10.1107/S0907444905016732

Acta Crystallogr D Biol Crystallogr 61:1132-1139 (2005)

PubMed id: 16041079

Extraction of functional motion in trypsin crystal structures.

A.Schmidt, V.S.Lamzin.

ABSTRACT

The analysis of anisotropic atomic displacement parameters for the direct extraction of functionally relevant motion from X-ray crystal structures of Fusarium oxysporum trypsin is presented. Several atomic resolution structures complexed with inhibitors or substrates and determined at different pH values and temperatures were investigated. The analysis revealed a breathing-like molecular motion conserved across trypsin structures from two organisms and three different crystal forms. Directional motion was observed suggesting a change of the width of the substrate-binding cleft and a change in the length of the specificity pocket. The differences in direction of motion across the structures are dependent on the mode of substrate or inhibitor binding and the chemical environment around the active-site residues. Together with the occurrence of multiple-residue conformers, they reflect spatial rearrangement throughout the deacylation pathway.

Selected figure(s)

Figure 1.
Figure 1 Active site in F. oxysporum trypsin. The top row shows the change in the interaction between the substrate and the catalytic serine and histidine, as well as Asp189 in the specificity pocket in the ROOM, PH4 and PH5 structures. The distances of interest around the substrate carbonyl group and in the specificity pocket are shown by dotted lines with their lengths given in angstroms. W1 and W2 are two water molecules located in the active site: W1 acts as the nucleophile and W2 as an activator by forming a strong hydrogen bond to the substrate carbonyl O atom. In the bottom row, the same arrangement of residues is shown. The protein atoms and coordinate axes are represented and coloured following the same scheme as in Fig. 3[107] [link]-[108][turqarr.gif] to indicate their directional motion. The orientation is the same as in Fig. 3[109] [link]-[110][turqarr.gif] . The figure was created with MOLSCRIPT/RASTER3D (Kraulis, 1991[111] [Kraulis, P. J. (1991). J. Appl. Cryst. 24, 946-950.]-[112][bluearr.gif] ; Merritt & Murphy, 1994[113] [Merritt, E. A. & Murphy, M. E. (1994). Acta Cryst. D50, 869-873.]-[114][bluearr.gif] ).

Figure 2.
Figure 2 Trypsin structures with the degree of anisotropy (average per residue) mapped onto the C^ [137][alpha] trace. The figure was produced with GRASP (Nicholls et al., 1991[138] [Nicholls, A., Sharp, K. A. & Honig, B. (1991). Proteins, 11, 281-296.]-[139][bluearr.gif] ). The deacylation pathway is depicted on the right-hand side of the figure.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 1132-1139) copyright 2005.

Figures were selected by an automated process.