PDBsum entry 1b5f

Hydrolase

PDB id: 1b5f

Contents

Protein chains

239 a.a. *

87 a.a. *

Ligands

NAG-NAG-BMA-MAN-FUC

NAG-NAG-BMA-FUC ×2

NAG-NAG-BMA-MAN-MAN-FUC

Waters ×528

* Residue conservation analysis

PDB id:

1b5f

Name:

Hydrolase

Title:

Native cardosin a from cynara cardunculus l.

Structure:

Protein (cardosin a). Chain: a, c. Other_details: residue names according to pepsin numbering after a.R.Sielecki, a.A.Fedorov, a.Boodhoo, n.S.Andreeva, and m.N.G.James (1990).J.Mol.Biol. 214, 143-170. Native cardosin a sequence differs from that deduced from cdna through excision of the psi domain. Mature cardosin a is found in a two chain form due to a post- translational cleavage event. A first, 35 kd chain comprises residues 0/1 - 238 and the second 15 kd chain comprises residues 243 - 326.

Source:

Cynara cardunculus. Organism_taxid: 4265. Organ: flower.Pistil. Tissue: papillar epidermis of the stigma. Organelle: storage vacuoles. Organelle: storage vacuoles

Biol. unit:

Octamer (from PQS)

Resolution:

1.72Å R-factor: 0.206 R-free: 0.256

Authors:

C.Frazao,I.Bento,M.A.Carrondo

Key ref:

C.Frazão et al. (1999). Crystal structure of cardosin A, a glycosylated and Arg-Gly-Asp-containing aspartic proteinase from the flowers of Cynara cardunculus L. J Biol Chem, 274, 27694-27701. PubMed id: 10488111 DOI: 10.1074/jbc.274.39.27694

Date:

06-Jan-99 Release date: 13-Jan-99

Protein chains

Q9XFX3  (CARDA_CYNCA) -  Procardosin-A from Cynara cardunculus

Seq: 504 a.a.

Struc: 239 a.a.

Protein chains

Q9XFX3  (CARDA_CYNCA) -  Procardosin-A from Cynara cardunculus

Seq: 504 a.a.

Struc: 87 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D: E.C.3.4.23.- - ?????

DOI no: 10.1074/jbc.274.39.27694

J Biol Chem 274:27694-27701 (1999)

PubMed id: 10488111

Crystal structure of cardosin A, a glycosylated and Arg-Gly-Asp-containing aspartic proteinase from the flowers of Cynara cardunculus L.

C.Frazão, I.Bento, J.Costa, C.M.Soares, P.Veríssimo, C.Faro, E.Pires, J.Cooper, M.A.Carrondo.

ABSTRACT

Aspartic proteinases (AP) have been widely studied within the living world, but so far no plant AP have been structurally characterized. The refined cardosin A crystallographic structure includes two molecules, built up by two glycosylated peptide chains (31 and 15 kDa each). The fold of cardosin A is typical within the AP family. The glycosyl content is described by 19 sugar rings attached to Asn-67 and Asn-257. They are localized on the molecular surface away from the conserved active site and show a new glycan of the plant complex type. A hydrogen bond between Gln-126 and Manbeta4 renders the monosaccharide oxygen O-2 sterically inaccessible to accept a xylosyl residue, therefore explaining the new type of the identified plant glycan. The Arg-Gly-Asp sequence, which has been shown to be involved in recognition of a putative cardosin A receptor, was found in a loop between two beta-strands on the molecular surface opposite the active site cleft. Based on the crystal structure, a possible mechanism whereby cardosin A might be orientated at the cell surface of the style to interact with its putative receptor from pollen is proposed. The biological implications of these findings are also discussed.

Selected figure(s)

Figure 1.
Fig. 1. A, cartoon representation (49, 50) of the two cardosin A molecules in the a.u. They face each other through an extensive area, although the actual molecule to molecule contacts are relatively few. The two N-linked glycans are represented as ball-and-sticks with side chains of linking Asn67 and Asn257. The active site aspartate side chains, as well as those from a putative molecular adhesion RGD motif (12) (Arg176, Gly177, and Asp178) are also depicted as ball-and-stick representation. The missing PSI domain is indicated near its chain termini. B, accessible surface representation (51) of the contact regions between the two cardosin molecules in the a.u. Molecule 1 (left) and 2 (right) facing surfaces are represented after a 180° rotation around a vertical axis of one of the molecules. The contacts between the two molecules produce a decrease of the local solvent-accessible area represented in blue with the rest of the surface in white. The contacts are highly delocalized over the intermolecular surfaces and are spread over a wide region.

Figure 3.
Fig. 3. Sub-site specificity mapping of cardosin A. Schematic representation (21) of a -casein chain fragment, with peptide scissile bond Phe^105 Met106, where milk clotting is initiated in cheese production. Cardosin A residues within 4.0 Å of the docked -casein fragment are listed and grouped at their sub-sites (Sn and S'n).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (1999, 274, 27694-27701) copyright 1999.

Figures were selected by an automated process.