PDBsum entry: 1nb3

Hydrolase

PDB id: 1nb3

Contents

Protein chains

220 a.a. *

98 a.a. *

Ligands

GLU-PRO-GLN-ASN-CYS-SER-ALA-THR ×4

NAG-NAG-BMA ×4

Waters ×543

* Residue conservation analysis

PDB id:

1nb3

Name:

Hydrolase

Title:

Crystal structure of stefin a in complex with cathepsin h: n residues of inhibitors can adapt to the active sites of end exopeptidases

Structure:

Cathepsin h. Chain: a, b, c, d. Cathepsin h mini chain. Chain: p, r, s, t. Stefin a. Chain: i, j, k, l. Synonym: cystatin as, cystatin a. Engineered: yes

Source:

Sus scrofa. Pig. Organism_taxid: 9823. Other_details: protein was isolated from spleen. Homo sapiens. Human. Organism_taxid: 9606. Gene: csta or stf1. Expressed in: escherichia coli.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.80Å R-factor: 0.227 R-free: 0.246

Authors:

S.Jenko,I.Dolenc,G.Guncar,A.Dobersek,M.Podobnik,D.Turk

Key ref:

S.Jenko et al. (2003). Crystal structure of Stefin A in complex with cathepsin H: N-terminal residues of inhibitors can adapt to the active sites of endo- and exopeptidases. J Mol Biol, 326, 875-885. PubMed id: 12581647 DOI: 10.1016/S0022-2836(02)01432-8

Date:

02-Dec-02 Release date: 18-Feb-03

Protein chains

O46427  (CATH_PIG) -  Pro-cathepsin H

Seq: 335 a.a.

Struc: 220 a.a.

Protein chains

P01040  (CYTA_HUMAN) -  Cystatin-A

Seq: 98 a.a.

Struc: 98 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D: E.C.3.4.22.16 - Cathepsin H.
• Reaction: Hydrolysis of proteins, acting as an aminopeptidase (notably, cleaving Arg-|-Xaa bonds) as well as an endopeptidase.

 Gene Ontology (GO) functional annotation 

• Cellular component: intracellular (4 terms)
• Biological process: cell adhesion (7 terms)
• Biochemical function: structural molecule activity (8 terms)

DOI no: 10.1016/S0022-2836(02)01432-8

J Mol Biol 326:875-885 (2003)

PubMed id: 12581647

Crystal structure of Stefin A in complex with cathepsin H: N-terminal residues of inhibitors can adapt to the active sites of endo- and exopeptidases.

S.Jenko, I.Dolenc, G.Guncar, A.Dobersek, M.Podobnik, D.Turk.

ABSTRACT

Binding of cystatin-type inhibitors to papain-like exopeptidases cannot be explained by the stefin B-papain complex. The crystal structure of human stefin A bound to an aminopeptidase, porcine cathepsin H, has been determined in monoclinic and orthorhombic crystal forms at 2.8A and 2.4A resolutions, respectively. The asymmetric unit of each form contains four complexes. The structures are similar to the stefin B-papain complex, but with a few distinct differences. On binding, the N-terminal residues of stefin A adopt the form of a hook, which pushes away cathepsin H mini-chain residues and distorts the structure of the short four residue insertion (Lys155A-Asp155D) unique to cathepsin H. Comparison with the structure of isolated cathepsin H shows that the rims of the cathepsin H structure are slightly displaced (up to 1A) from their position in the free enzyme. Furthermore, comparison with the stefin B-papain complex showed that molecules of stefin A bind about 0.8A deeper into the active site cleft of cathepsin H than stefin B into papain. The approach of stefin A to cathepsin H induces structural changes along the interaction surface of both molecules, whereas no such changes were observed in the stefin B-papain complex. Carboxymethylation of papain seems to have prevented the formation of the genuine binding geometry between a papain-like enzyme and a cystatin-type inhibitor as we observe it in the structure presented here.

Selected figure(s)

Figure 2.
Figure 2. The complex of cathepsin H (bottom) and stefin A (top). The cathepsin H surface is shown in gray and is colored yellow around the catalytic Cys25 residue. The main-chain of stefin A is shown as a green worm, the cathepsin H mini-chain is shown by red sticks and the cathepsin H sugar residues are shown by blue sticks. The Figure was prepared with the program MAIN[48] and the surface was created with GRASP. [52] The image file was rendered with the Raster3D program. [53]

Figure 5.
Figure 5. (a) Stereo image of interactions within the active site cleft of the stefin A-cathepsin H complex. The N-terminal residues of stefin A (green) cannot bind along the active site cleft, as in stefin B with papain, due to presence of the mini-chain residues (red). The push appears to be transferred to the insertion loop (orange). Active site residues Cys25 and His159 are shown in yellow. (b) Stereo view of the averaged ||F[obs]| -|F[calc]|| kicked omit electron-density map of the cathepsin H mini-chain and stefin A N-terminal trunk contoured at 0.8s. The mini-chain is shown in red sticks, stefin A N-terminal trunk in green sticks, catalytic Cys25 in yellow and all other residues, which are represented only as a main-chain trace, in blue. Both Figures were prepared with the program MAIN,[49] merged and finally rendered with the Raster3D program. [53]

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 326, 875-885) copyright 2003.

Figures were selected by the author.