PDBsum entry 4cha

Hydrolase (serine proteinase)

PDB id: 4cha

Contents

Protein chains

11 a.a. *

131 a.a. *

97 a.a. *

Ligands

CYS-GLY-VAL-PRO-ALA-ILE-GLN-PRO-VAL-LEU

Waters ×85

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structure of alpha-Chymotrypsin refined at 1.68 a resolution.

Authors

H.Tsukada, D.M.Blow.

Ref.

J Mol Biol, 1985, 184, 703-711. [DOI no: 10.1016/0022-2836(85)90314-6]

PubMed id

4046030

Abstract

Diffraction data for alpha-chymotrypsin crystals at -10 degrees C were measured at 1.68 A resolution and refined by restrained structure-factor least-squares refinement. The two independent chymotrypsin molecules in the crystallographic asymmetric unit were refined independently. The overall structure of alpha-chymotrypsin is little changed from published co-ordinates. The root-mean-square shift of C alpha co-ordinates is 0.42 A, co-ordinates for the two molecules showing a root-mean-square difference of 0.19 A. Certain regions with high disorder (residues 9 to 14, 73 to 79) remain difficult to interpret and several side-chains are disordered. Some water molecule positions have been changed. The absence of the tosyl group has made a significant difference to the refined structure at the active site. This now agrees closely with other enzymes of the trypsin family that have been refined at high resolution. There is a strong hydrogen bond between N epsilon 2 (His57) and O gamma (Ser195) in the free enzyme, in line with the published description of the charge relay system.

Figure 2.
Figur 2. An example of the non-reciprocal interactions between molecles related by non-crystallographic dyad with a small screw component. The carbonyls of (a) Ser92 nd b) Tyr94 in molecule 1 form hydrogen bonds ys93 N'' in molecule 343). The side-chain f Lys93 molecule ) is free in the solvent (Table C). The broken ines show contours in the (2F,,--F,) density.

Figure 3.
Figure 3. Electron densty 2F,-FF,) for the charge relay system. Density nd ydrogen bonds nvolving Ser214 nd Tyr146' 396) of he molecule related by 2-fold local ymmetry are shown.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1985, 184, 703-711) copyright 1985.

Secondary reference #1

Title

Structure and mechanism of chymotrypsin

Author

D.M.Blow.

Ref.

acc chem res, 1976, 9, 145.

Secondary reference #2

Title

The active centers of serine proteinases.

Author

B.S.Hartley.

Ref.

Ann N Y Acad Sci, 1974, 227, 438-445.

PubMed id

4597310

Secondary reference #3

Title

Comparison of the crystal structures of chymotrypsinogen-A and alpha-Chymotrypsin.

Author

H.T.Wright.

Ref.

J Mol Biol, 1973, 79, 1. [DOI no: 10.1016/0022-2836(73)90265-9]

PubMed id

4745847

Figure 3.
FIG. 3. Computer drawn ribbon diagram of chymotrypsinoge backbone (program written by Andrew McLachlan).

Figure 5.
FIU. 5. Schematic diagram of the most important intramolecular contacts which propagate onformational changes in the actiation of chymotrypsinogen. Segments denoted by Roman umerals and sequence numbers are in ellipses. Large arrows between ellipses are hypothetical directions of movements. Amino acids in boxes next to large arrows are those which make either van der Waals or hydrogen bond contact between segment. They are proposed to be responsibl for the propagation of intersegmental movement idicated by large arrows between boxes.

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #4

Title

Structure of crystalline -Chymotrypsin. V. The atomic structure of tosyl- -Chymotrypsin at 2 a resolution.

Authors

J.J.Birktoft, D.M.Blow.

Ref.

J Mol Biol, 1972, 68, 187-240. [DOI no: 10.1016/0022-2836(72)90210-0]

PubMed id

5069789

Figure 16.
FIG. 16. The environments of buried water molecules W6 and Wi', showing their hydrogen bonds with the csrbonyl groups of Thr139, GlylQ3 end Asp194, with the amido groups of Trpl41 and Gln30. 8nd with Naa of Hi&O Viewpoint (-6.0, 30.0, -40.0); centre of projection plane (10.4, -a.$ 11.4).

Figure 17.
Fro. 17. The hydrogen-bond network involving WlO and Wll. The hydogen bonde with water involve the cerbonyl groups of Lys79 and IleQQ, the amid0 group of AenlOl, and the side chains of Am100 and Ser214. Also shown m the presumed hydroge bonds between the side chains of Ser214, Asp102, His67. As~umingN~(Asn100) to be hydrogen-bonded to Wll, and the two water moleoulee to be electrioally neutral, the hydrogen-bond network can be drawn in a sstisectory manner (see sketch). The X-ray diffraction results do not distinguish Nd and O6 in aaparagine. Viewpoint {30*0, 20.0, 0.0); centre of projection plane (23.2, 4.6, 12.0).

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #5

Title

Structure of crystalline methyl-Chymotrypsin.

Authors

C.S.Wright, G.P.Hess, D.M.Blow.

Ref.

J Mol Biol, 1972, 63, 295-303. [DOI no: 10.1016/0022-2836(72)90376-2]

PubMed id

4634509

Figure 3.
FIG. 3. Stereoscopic. drawing, showing formyl-L-tryptophan bond to crystalline methyl- chymtrypsin in an identical fashion to that found for the formyl-L-tryptophan : n-chymotrypsin complex (Steitz, et al. 1969). Impossibly short contacts occur between the carboxylate oxygens of the substrate, H,-N@ (His-57) and OV (Ser-95).

Figure 4.
FIU. 4. Hypothetical drawing, showing how acylsted methyl-chymotrypsin miht be deacylated in a ``productive'' mode. The conformation of methyl-His-57 shown here is impossible in crystals due to obstruction by an adjacent molecul.

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #6

Title

-Chymotrypsin: what can we learn about catalysis from X-Ray diffraction?

Authors

R.Henderson, C.S.Wright, G.P.Hess, D.M.Blow.

Ref.

Cold Spring Harb Symp Quant Biol, 1972, 36, 63-70.

PubMed id

4508173

Secondary reference #7

Title

Chymotrypsin-Chemical properties and catalysis

Author

G.P.Hess.

Ref.

the enzymes,third edition, 1971, 3, 213.

Secondary reference #8

Title

The structure of chymotrypsin

Author

D.M.Blow.

Ref.

the enzymes,third edition, 1971, 3, 185.

Secondary reference #9

Title

Structure of crystalline alpha-Chymotrypsin. Iv. The structure of indoleacryloyl-Alpha-Chyotrypsin and its relevance to the hydrolytic mechanism of the enzyme.

Author

R.Henderson.

Ref.

J Mol Biol, 1970, 54, 341-354. [DOI no: 10.1016/0022-2836(70)90434-1]

PubMed id

5494034

Figure 4.
FIG. 4. The differenc in electron density between tosyl-a-ohymotrypsin and native chymotrypsin at 2.6 A resolution. The largest feature is the sulphoyl group.

Figure 6.
FIG. 6. A detailed view of the geometry of the ester link to Ser-196 in indoleacryloyl-a-chymo- trysin.

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #10

Title

I. Serine proteinases. The structure of alpha-Chymotrypsin.

Authors

J.J.Birktoft, D.M.Blow, R.Henderson, T.A.Steitz.

Ref.

Philos Trans R Soc Lond B Biol Sci, 1970, 257, 67-76.

PubMed id

4399050

Secondary reference #11

Title

The study of alpha-Chymotrypsin by X-Ray diffraction. The third ciba medal lecture.

Author

D.M.Blow.

Ref.

Biochem J, 1969, 112, 261-268.

PubMed id

5801300

Secondary reference #12

Title

Structure of crystalline alpha-Chymotrypsin. 3. Crystallographic studies of substrates and inhibitors bound to the active site of alpha-Chymotrypsin.

Authors

T.A.Steitz, R.Henderson, D.M.Blow.

Ref.

J Mol Biol, 1969, 46, 337-348. [DOI no: 10.1016/0022-2836(69)90426-4]

PubMed id

5360043

Secondary reference #13

Title

Structure of crystalline -Chymotrypsin. Ii. A preliminary report including a hypothesis for the activation mechanism.

Authors

P.B.Sigler, D.M.Blow, B.W.Matthews, R.Henderson.

Ref.

J Mol Biol, 1968, 35, 143-164. [DOI no: 10.1016/S0022-2836(68)80043-9]

PubMed id

5760561

Secondary reference #14

Title

Three-Dimensional structure of tosyl-Alpha-Chymotrypsin.

Authors

B.W.Matthews, P.B.Sigler, R.Henderson, D.M.Blow.

Ref.

Nature, 1967, 214, 652-656.

PubMed id

6049071