PDBsum entry 1hj8

Hydrolase

PDB id: 1hj8

Contents

Protein chain

222 a.a. *

Ligands

BEN ×2

SO4

Metals

_CA

Waters ×228

* Residue conservation analysis

PDB id:

1hj8

Name:

Hydrolase

Title:

1.00 aa trypsin from atlantic salmon

Structure:

Trypsin i. Chain: a. Fragment: residues 21-242. Ec: 3.4.21.4

Source:

Salmo salar. Atlantic salmon. Organism_taxid: 8030

Biol. unit:

Monomer (from PDB file)

Resolution:

1.00Å R-factor: 0.119 R-free: 0.149

Authors:

H.-K.S.Leiros,S.M.Mcsweeney,A.O.Smalas

Key ref:

H.K.Leiros et al. (2001). Atomic resolution structures of trypsin provide insight into structural radiation damage. Acta Crystallogr D Biol Crystallogr, 57, 488-497. PubMed id: 11264577 DOI: 10.1107/S0907444901000646

Date:

09-Jan-01 Release date: 04-Jan-02

Protein chain

P35031  (TRY1_SALSA) -  Trypsin-1 from Salmo salar

Seq: 242 a.a.

Struc: 222 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

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

DOI no: 10.1107/S0907444901000646

Acta Crystallogr D Biol Crystallogr 57:488-497 (2001)

PubMed id: 11264577

Atomic resolution structures of trypsin provide insight into structural radiation damage.

H.K.Leiros, S.M.McSweeney, A.O.Smalås.

ABSTRACT

Radiation damage is an inherent problem in protein X-ray crystallography and the process has recently been shown to be highly specific, exhibiting features such as cleavage of disulfide bonds, decarboxylation of acidic residues, increase in atomic B factors and increase in unit-cell volume. Reported here are two trypsin structures at atomic resolution (1.00 and 0.95 A), the data for which were collected at a third-generation synchrotron (ESRF) at two different beamlines. Both trypsin structures exhibit broken disulfide bonds; in particular, the bond from Cys191 to Cys220 is very sensitive to synchrotron radiation. The data set collected at the most intense beamline (ID14-EH4) shows increased structural radiation damage in terms of lower occupancies for cysteine residues, more breakage in the six disulfide bonds and more alternate conformations. It appears that high intensity and not only the total X-ray dose is most harmful to protein crystals.

Selected figure(s)

Figure 2.
Figure 2 The catalytic hydrogen bond from His57 N 1 to Asp102 O 2 in anionic salmon trypsin (AST). The 2mF[o] - DF[c] map is contoured at 2.0 (blue) and 4.0 (red), while the mF[o] - DF[c] map around the His57 side chain is contoured at +2.5 (green). Ser195 and Ser214 are also included in the figure, which was created with Bobscript (Esnouf, 1997[Esnouf, R. M. (1997). J. Mol. Graph. 15, 132-134.]).

Figure 3.
Figure 3 (a) Stereoview of the salt-bridge interactions that involve residues uniquely conserved in all cold-adapted trypsins (Leiros et al., 1999[Leiros, H.-K. S., Willassen, N. P. & Smalås, A. O. (1999). Extremophiles, 3, 205-219.], 2000[Leiros, H.-K. S., Willassen, N. P. & Smalås, A. O. (2000). Eur. J. Biochem. 267, 1039-1049.]). The 2mF[o] - DF[c] map of the side chains only is contoured at 1.8 . (b) Location of the ion-pair network relative to the N-terminal (red), the calcium-binding loop (blue) and the autolysis loop (yellow).

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 488-497) copyright 2001.

Figures were selected by an automated process.