PDBsum entry 1op0

Hydrolase

PDB id: 1op0

Contents

Protein chain

234 a.a. *

Ligands

NAG-NAG-FUC

SO4 ×2

Waters ×142

* Residue conservation analysis

PDB id:

1op0

Name:

Hydrolase

Title:

Crystal structure of aav-sp-i, a glycosylated snake venom serine proteinase from agkistrodon acutus

Structure:

Venom serine proteinase. Chain: a. Synonym: snake venom serine proteinase, aav-sp-i. Ec: 3.4.21.-

Source:

Deinagkistrodon acutus. Chinese moccasin. Organism_taxid: 36307. Secretion: venom gland

Resolution:

2.00Å R-factor: 0.181 R-free: 0.208

Authors:

Z.Zhu,M.Teng,L.Niu

Key ref:

Z.Zhu et al. (2005). Crystal structures and amidolytic activities of two glycosylated snake venom serine proteinases. J Biol Chem, 280, 10524-10529. PubMed id: 15632114 DOI: 10.1074/jbc.M412900200

Date:

04-Mar-03 Release date: 25-May-04

Protein chain

Q9I8X1  (VSPP_DEIAC) -  Snake venom serine protease Dav-PA from Deinagkistrodon acutus

Seq: 258 a.a.

Struc: 234 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.21.- - ?????

DOI no: 10.1074/jbc.M412900200

J Biol Chem 280:10524-10529 (2005)

PubMed id: 15632114

Crystal structures and amidolytic activities of two glycosylated snake venom serine proteinases.

Z.Zhu, Z.Liang, T.Zhang, Z.Zhu, W.Xu, M.Teng, L.Niu.

ABSTRACT

We deduced that Agkistrodon actus venom serine proteinases I and II, previously isolated from the venom of A. acutus (Zhu, Z., Gong, P., Teng, M., and Niu, L. (2003) Acta Crystallogr. Sect. D Biol. Crystallogr. 59, 547-550), are encoded by two almost identical genes, with only the single substitution Asp for Asn at residue 62. Amidolytic assays indicated that they possess slightly different enzymatic properties. Crystal structures of A. actus venom serine proteinases I and II were determined at resolution of 2.0 and 2.1 A with the identification of trisaccharide (NAG(301)-FUC(302)-NAG(303)) and monosaccharide (NAG(301)) residues in them, respectively. The substrate binding sites S3 of the two proteinases appear much shallower than that of Trimeresurus stejnegeri venom plasminogen activator despite the overall structural similarity. Based on structural analysis, we showed that these Asn(35)-linked oligosaccharides collide spatially with some inhibitors, such as soybean trypsin inhibitor, and would therefore hinder their inhibitory binding. Difference of the carbohydrates in both the proteinases might also lead to their altered catalytic activities.

Selected figure(s)

Figure 3.
FIG. 3. The saccharides of AaV-SP-I and -II. A and B, the electron density (2Fo-Fc) maps of NAG301-FUC^302-NAG303 and NAG301 of AaV-SP-I and AaV-SP-II are contoured at the 1.0 level. C, superimposed C atoms of segments formed by residues 30-70 for comparing the saccharide residues between AaV-SP-I (cyan) and -II (yellow). The His57 and the Asp59 of AaV-SP-I as well as saccharides of the two AaV-SPs are shown with a stick model. The two hydrogen bonds in AaV-SP-I, one between FUC^302 and His57 and the other between FUC^302 and Asp59, are labeled.

Figure 5.
FIG. 5. Comparison of the 174 loop and 99 loop in AaV-SP-I (cyan) AaV-SP-II (yellow), and TSV-PA (silver-gray) shows the architectural features of substrate binding sites S2 S4 of the three proteins. The key residues (215, 178, 173, 174, 97, 98, 99) for substrate-binding are shown with stick model. The hydrogen bonds between Tyr215 and Glu173 of the two AaV-SPs and the hydrogen bond between Glu97 and Tyr178 of AaV-SP-I are shown. The amino acid residues of AaV-SPs and TSV-PA are displayed in black and blue. The schematic substrate-binding sites 2, 3, and 4 are indicated with a light green ellipse.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 10524-10529) copyright 2005.

Figures were selected by an automated process.