spacer
spacer

PDBsum entry 2dt3

Go to PDB code: 
protein ligands links
Signaling protein PDB id
2dt3
Jmol PyMol
Contents
Protein chain
361 a.a. *
Ligands
NAG-NAG-MAN-MAN-
MAN
NAG-NAG-NAG-NAG-
NAG-NAG
Waters ×182
* Residue conservation analysis
PDB id:
2dt3
Name: Signaling protein
Title: Crystal structure of the complex formed between goat signall protein and the hexasaccharide at 2.28 a resolution
Structure: Chitinase-3-like protein 1. Chain: a. Synonym: spg-40, mammary gland protein mgp-40, bp40
Source: Capra hircus. Goat. Organism_taxid: 9925. Secretion: milk mammary gland
Resolution:
2.28Å     R-factor:   0.196     R-free:   0.215
Authors: J.Kumar,A.S.Ethayathulla,D.B.Srivastava,N.Singh,S.Sharma,T.P
Key ref:
J.Kumar et al. (2007). Carbohydrate-binding properties of goat secretory glycoprotein (SPG-40) and its functional implications: structures of the native glycoprotein and its four complexes with chitin-like oligosaccharides. Acta Crystallogr D Biol Crystallogr, 63, 437-446. PubMed id: 17372347 DOI: 10.1107/S0907444907001631
Date:
09-Jul-06     Release date:   01-Aug-06    
Supersedes: 2b2z
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q8SPQ0  (CH3L1_CAPHI) -  Chitinase-3-like protein 1
Seq:
Struc:
383 a.a.
361 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   5 terms 
  Biological process     cellular response to tumor necrosis factor   16 terms 
  Biochemical function     carbohydrate binding     4 terms  

 

 
DOI no: 10.1107/S0907444907001631 Acta Crystallogr D Biol Crystallogr 63:437-446 (2007)
PubMed id: 17372347  
 
 
Carbohydrate-binding properties of goat secretory glycoprotein (SPG-40) and its functional implications: structures of the native glycoprotein and its four complexes with chitin-like oligosaccharides.
J.Kumar, A.S.Ethayathulla, D.B.Srivastava, N.Singh, S.Sharma, P.Kaur, A.Srinivasan, T.P.Singh.
 
  ABSTRACT  
 
A 40 kDa glycoprotein (SPG-40) secreted during involution works as a protective signalling factor through its binding to viable cells. The crystal structure of the native protein has been determined at 2.3 A resolution. This is the first report on the carbohydrate-binding properties of SPG-40; the structure determinations of the complexes of SPG-40 with four oligosaccharides of different lengths at resolutions ranging from 2.2 to 2.8 A are described. Carbohydrate-binding studies with N-acetylglucosamines (GlcNAc(n), n = 3-6) using fluorescence spectroscopy revealed poor binding effects with GlcNAc(3) and GlcNAc(4), while GlcNAc(5) and GlcNAc(6) bound to SPG-40 with considerable strength; the dissociation constants (K(d)) were estimated to be 260 +/- 3 and 18 +/- 4 microM, respectively. SPG-40 was cocrystallized with GlcNAc(3), GlcNAc(4), GlcNAc(5) and GlcNAc(6). The overall structure of native SPG-40 was essentially similar to that reported previously at low resolution. The structures of its complexes with GlcNAc(3), GlcNAc(4), GlcNAc(5) and GlcNAc(6) revealed the positions of these oligosaccharides in the carbohydrate-binding groove and provided insights into the mechanism of binding of oligosaccharides to SPG-40, indicating that the preferred subsites in the carbohydrate-binding groove of SPG-40 were from -4 to -2. The structure of the protein remained unperturbed upon binding of GlcNAc(3) and GlcNAc(4), but the structure changed significantly upon binding of GlcNAc(5) and GlcNAc(6). Significant conformational variations were observed in the sugar-binding groove: Trp78 partially flipped out of the barrel in GlcNAc(5), while in the GlcNAc(6) complex a completely flipped-out Trp78 was observed along with several other conformational changes, including those of Asp186 and Arg242. Such changes upon binding to carbohydrates have not previously been observed in chitin-hydrolyzing chitinases and reflect less favourable binding of carbohydrates to SPG-40. As this appears to essentially be a binding protein, this loss of binding affinity might be compensated by other intermolecular interactions such as protein-protein interactions and also by the binding of its own glycan chain.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 Difference |F[o] - F[c]| electron densities for GlcNAc[n] at 2.0 cutoff: (a) GlcNAc[3], (b) GlcNAc[4], (c) GlcNAc[5], (d) GlcNAc[6].
Figure 5.
Figure 5 |2F[o] - F[c]| electron densities for Trp78, Asp186 and Arg242 with bound (a) GlcNAc[3], (b) GlcNAc[4], (c) GlcNAc[5] and (d) GlcNAc[6]. In (c) partial densities for Trp78 and Asp186 are also observed (blue colour).
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2007, 63, 437-446) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21530272 Y.Sato, S.Suzuki, S.Muraoka, N.Kikuchi, N.Noda, T.Matsumoto, H.Inoue, H.Nagasawa, and S.Sakuda (2011).
Preparation of allosamidin and demethylallosamidin photoaffinity probes and analysis of allosamidin-binding proteins in asthmatic mice.
  Bioorg Med Chem, 19, 3054-3059.  
  19241370 K.A.Mercier, J.R.Cort, M.A.Kennedy, E.E.Lockert, S.Ni, M.D.Shortridge, and R.Powers (2009).
Structure and function of Pseudomonas aeruginosa protein PA1324 (21-170).
  Protein Sci, 18, 606-618.
PDB code: 1xpn
18306418 Y.Li, and D.B.Wilson (2008).
Chitin binding by Thermobifida fusca cellulase catalytic domains.
  Biotechnol Bioeng, 100, 644-652.  
  17401190 A.S.Ethayathulla, D.B.Srivastava, J.Kumar, K.Saravanan, S.Bilgrami, S.Sharma, P.Kaur, A.Srinivasan, and T.P.Singh (2007).
Structure of the buffalo secretory signalling glycoprotein at 2.8 A resolution.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 258-265.
PDB code: 2o9o
17543889 Zaheer-ul-Haq, P.Dalal, N.N.Aronson, and J.D.Madura (2007).
Family 18 chitolectins: comparison of MGP40 and HUMGP39.
  Biochem Biophys Res Commun, 359, 221-226.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

spacer

spacer