PDBsum entry 2esc

Signaling protein

PDB id: 2esc

Contents

Protein chain

361 a.a. *

Ligands

NAG-NAG-MAN-MAN-MAN-MAN

Waters ×247

* Residue conservation analysis

PDB id:

2esc

Name:

Signaling protein

Title:

Crystal structure of a 40 kda protective signalling protein from bovine (spc-40) at 2.1 a resolution

Structure:

Chitinase-3-like protein 1. Chain: a. Synonym: signal processing protein, spc-40

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Secretion: mammary gland

Resolution:

2.10Å R-factor: 0.176 R-free: 0.220

Authors:

J.Kumar,A.S.Ethayathulla,D.B.Srivastav,S.Sharma,A.Srinivasan, T.P.Singh

Key ref:

J.Kumar et al. (2006). Structure of a bovine secretory signalling glycoprotein (SPC-40) at 2.1 Angstrom resolution. Acta Crystallogr D Biol Crystallogr, 62, 953-963. PubMed id: 16929095 DOI: 10.1107/S0907444906020427

Date:

26-Oct-05 Release date: 20-Dec-05

Protein chain

P30922  (CH3L1_BOVIN) -  Chitinase-3-like protein 1 from Bos taurus

Seq: 383 a.a.

Struc: 361 a.a.*

* PDB and UniProt seqs differ at 9 residue positions (black crosses)

DOI no: 10.1107/S0907444906020427

Acta Crystallogr D Biol Crystallogr 62:953-963 (2006)

PubMed id: 16929095

Structure of a bovine secretory signalling glycoprotein (SPC-40) at 2.1 Angstrom resolution.

J.Kumar, A.S.Ethayathulla, D.B.Srivastava, S.Sharma, S.B.Singh, A.Srinivasan, M.P.Yadav, T.P.Singh.

ABSTRACT

A recently discovered new class of 40 kDa glycoproteins forms a major component of the secretory proteins in the dry secretions of non-lactating animals. These proteins are implicated as protective signalling factors that determine which cells are to survive during the processes of drastic tissue remodelling. In order to understand its role in the remodelling of mammary glands, the detailed three-dimensional structure of the bovine signalling glycoprotein (SPC-40) has been determined using X-ray crystallography. SPC-40 was purified from bovine dry secretions and crystallized using the hanging-drop vapour-diffusion method. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 62.6, b = 67.4, c = 106.9 Angstrom. The protein was also cloned in order to determine its complete amino-acid sequence. Its three-dimensional structure has been determined using data to 2.1 Angstrom resolution. The amino-acid sequence determination of SPC-40 reveals two potential N-glycosylation sites at Asn39 and Asn345, but electron density for a glycan chain was only present at Asn39. The protein adopts a conformation with the classical (beta/alpha)(8)-barrel fold of triosephosphate isomerase (TIM barrel; residues 1-237 and 310-360) with the insertion of a small alpha+beta domain (residues 240-307) similar to that observed in chitinases. However, the substitution of Leu for Glu in the consensus catalytic sequence in SPC-40 caused a loss of chitinase activity. Furthermore, the chitin-binding groove in SPC-40 is considerably distorted owing to unfavourable conformations of several residues, including Trp78, Tyr120, Asp186 and Arg242. Three surface loops, His188-His197, Phe202-Arg212 and Tyr244-Pro260, have exceptionally high B factors, suggesting large-scale flexibility. Fluorescence studies indicate that various sugars bind to SPC-40 with low affinities.

Selected figure(s)

Figure 5.
Figure 5 Ribbon diagrams (DeLano, 2002[DeLano, W. L. (2002). The PyMOL User's Manual. DeLano Scientific, San Carlos, CA, USA.]) of SPC-40. (a) Top-view orientation showing residues involved in carbohydrate binding (cyan) and some of those assumed to be important in receptor recognition (gold).

Figure 6.
Figure 6 The relative environments near the -barrel and Trp78 are shown for (a) SPC-40 and (b) HCgp-39. The important interactions involving residues Asp186, Tyr120, Leu183 (Met183 in HCgp-39), Arg242, Ile272 (Thr272 in HCgp-39) as well as solvent molecules are indicated.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2006, 62, 953-963) copyright 2006.

Figures were selected by an automated process.