PDBsum entry 1m0h

Hydrolase

PDB id: 1m0h

Contents

Protein chain

340 a.a.

Theoretical model

PDB id:

1m0h

Name:

Hydrolase

Title:

Theoretical model of cathepsin s precursor

Structure:

Cathepsin s precursor. Chain: a. Ec: 3.4.22.27

Source:

Mus musculus. Mouse

Authors:

K.Beesetti,K.Yadugiri

Key ref:

Y.J.Leu et al. (2003). Residues involved in the catalysis, base specificity, and cytotoxicity of ribonuclease from Rana catesbeiana based upon mutagenesis and X-ray crystallography. J Biol Chem, 278, 7300-7309. PubMed id: 12499382 DOI: 10.1074/jbc.M206701200

Date:

13-Jun-02 Release date: 26-Jun-02

Protein chain

O70370  (CATS_MOUSE) -  Cathepsin S

Seq: 340 a.a.

Struc: 340 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DOI no: 10.1074/jbc.M206701200

J Biol Chem 278:7300-7309 (2003)

PubMed id: 12499382

Residues involved in the catalysis, base specificity, and cytotoxicity of ribonuclease from Rana catesbeiana based upon mutagenesis and X-ray crystallography.

Y.J.Leu, S.S.Chern, S.C.Wang, Y.Y.Hsiao, I.Amiraslanov, Y.C.Liaw, Y.D.Liao.

ABSTRACT

The Rana catesbeiana (bullfrog) ribonucleases, which belong to the RNase A superfamily, exert cytotoxicity toward tumor cells. RC-RNase, the most active among frog ribonucleases, has a unique base preference for pyrimidine-guanine rather than pyrimidine-adenine in RNase A. Residues of RC-RNase involved in base specificity and catalytic activity were determined by site-directed mutagenesis, k(cat)/K(m) analysis toward dinucleotides, and cleavage site analysis of RNA substrate. The results show that Pyr-1 (N-terminal pyroglutamate), Lys-9, and Asn-38 along with His-10, Lys-35, and His-103 are involved in catalytic activity, whereas Pyr-1, Thr-39, Thr-70, Lys-95, and Glu-97 are involved in base specificity. The cytotoxicity of RC-RNase is correlated, but not proportional to, its catalytic activity. The crystal structure of the RC-RNase.d(ACGA) complex was determined at 1.80 A resolution. Residues Lys-9, His-10, Lys-35, and His-103 interacted directly with catalytic phosphate at the P(1) site, and Lys-9 was stabilized by hydrogen bonds contributed by Pyr-1, Tyr-28, and Asn-38. Thr-70 acts as a hydrogen bond donor for cytosine through Thr-39 and determines B(1) base specificity. Interestingly, Pyr-1 along with Lys-95 and Glu-97 form four hydrogen bonds with guanine at B(2) site and determine B(2) base specificity.

Selected figure(s)

Figure 5.
Fig. 5. Ribbon diagram of the three-dimensional structure of two RC-RNase·d(ACGA) complex molecules. Two d(ACGA) molecules are shown by liquorice representation viewing down along the noncrystallographic 2-fold axis. The -helix and -sheet strand are colored green and blue, respectively. The base stacking and continuity of the phosphate backbone are clearly seen in the central area of the diagram.

Figure 7.
Fig. 7. Stereo diagrams of RC-RNase and oligonucleotide complex. A, ribbon diagram of RC-RNase with d(CG), the -helix, -sheet, and d(CG) are shown in green, blue, and red, respectively. The relevant residues in the B[1], B[2], and P[1] sites are numbered. B, C, and D show the hydrogen bonds between respective residues and substrates in B[1], B[2], and P[1] sites, respectively. The hydrogen bonds are shown as blue dashed lines. The substrate in red was shown within the electronic density omit map (contoured at 1.5 ). The image was generated by SwissPDBviewer (50), Turbo-Frodo, and Photoshop (Adobe Systems, Inc.).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 7300-7309) copyright 2003.

Figures were selected by an automated process.