PDBsum entry 1nn6

Hydrolase

PDB id: 1nn6

Contents

Protein chain

222 a.a. *

Ligands

NAG-NAG

NAG

Waters ×153

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structure of human pro-Chymase: a model for the activating transition of granule-Associated proteases.

Authors

K.K.Reiling, J.Krucinski, L.J.Miercke, W.W.Raymond, G.H.Caughey, R.M.Stroud.

Ref.

Biochemistry, 2003, 42, 2616-2624. [DOI no: 10.1021/bi020594d]

PubMed id

12614156

Abstract

Human chymase is a protease involved in physiological processes ranging from inflammation to hypertension. As are all proteases of the trypsin fold, chymase is synthesized as an inactive "zymogen" with an N-terminal pro region that prevents the transition of the zymogen to an activated conformation. The 1.8 A structure of pro-chymase, reported here, is the first zymogen with a dipeptide pro region (glycine-glutamate) to be characterized at atomic resolution. Three segments of the pro-chymase structure differ from that of the activated enzyme: the N-terminus (Gly14-Gly19), the autolysis loop (Gly142-Thr154), and the 180s loop (Pro185A-Asp194). The four N-terminal residues (Gly14-Glu15-Ile16-Ile17) are disordered. The autolysis loop occupies a position up to 10 A closer to the active site than is seen in the activated enzyme, thereby forming a hydrogen bond with the catalytic residue Ser195 and occluding the S1' binding pocket. Nevertheless, the catalytic triad (Asp102-His57-Ser195) is arrayed in a geometry close to that seen in activated chymase (all atom rmsd of 0.52 A). The 180s loop of pro-chymase is, on average, 4 A removed from its conformation in the activated enzyme. This conformation disconnects the oxyanion hole (the amides of Gly193 and Ser195) from the active site and positions only approximately 35% of the S1-S3 binding pockets in the active conformation. The backbone of residue Asp194 is rotated 180 degrees when compared to its conformation in the activated enzyme, allowing a hydrogen bond between the main-chain amide of residue Trp141 and the carboxylate of Asp194. The side chains of residues Phe191 and Lys192 of pro-chymase fill the Ile16 binding pocket and the base of the S1 binding pocket, respectively. The zymogen positioning of both the 180s and autolysis loops are synergistic structural elements that appear to prevent premature proteolysis by chymase and, quite possibly, by other dipeptide zymogens.

Secondary reference #1

Title

Crystal structure of phenylmethanesulfonyl fluoride-Treated human chymase at 1.9 a.

Authors

M.E.Mcgrath, T.Mirzadegan, B.F.Schmidt.

Ref.

Biochemistry, 1997, 36, 14318-14324. [DOI no: 10.1021/bi971403n]

PubMed id

9400368

Secondary reference #2

Title

The 2.2 a crystal structure of human chymase in complex with succinyl-Ala-Ala-Pro-Phe-Chloromethylketone: structural explanation for its dipeptidyl carboxypeptidase specificity.

Authors

P.J.Pereira, Z.M.Wang, H.Rubin, R.Huber, W.Bode, N.M.Schechter, S.Strobl.

Ref.

J Mol Biol, 1999, 286, 163-173. [DOI no: 10.1006/jmbi.1998.2462]

PubMed id

9931257

Figure 3.
Figure 3. Solid surface representation of chymase, tryptase, and cathepsin G. The colors indicate positive (blue) and negative (red) electrostatic potential at the molecular surface. The Figure was produced with the GRASP program [Nicholls et al 1993]. HC and CAT-G are shown from the "backside", turned by 180° as compared with that shown in Figure 1 and Figure 2. The tryptase C-D dimer [Pereira et al 1998] is shown edge-on, in the same orientation.

Figure 4.
Figure 4. Structural basis of substrate recognition. The proteinase is represented as a yellow stick model, superimposed with its Connolly dot surface. The inhibitor or the modeled substrates are shown as green stick figures. The orientation of HC is the same as that shown in Figure 1(a). Figure prepared with Insight II (Biosym/MSI, SanDiego). (a) Close view of the active centre of HC, with bound inhibitor (Suc-Ala-Ala-Pro-Phe-CMK). (b) Modeled interaction between HC and angiotensin I (same view as shown in (a)). (c) Modeled interaction between HC and angiotensin II (same view as shown in (a)).

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

Secondary reference #3

Title

Structure of bovine trypsinogen at 1.9 a resolution.

Authors

A.A.Kossiakoff, J.L.Chambers, L.M.Kay, R.M.Stroud.

Ref.

Biochemistry, 1977, 16, 654-664. [DOI no: 10.1021/bi00623a016]

PubMed id

556951

Secondary reference #4

Title

Structure, Chromosomal assignment, And deduced amino acid sequence of a human gene for mast cell chymase.

Authors

G.H.Caughey, E.H.Zerweck, P.Vanderslice.

Ref.

J Biol Chem, 1991, 266, 12956-12963.

PubMed id

2071582