2PI6

Crystal structure of the sheep signalling glycoprotein (SPS-40) complex with 2-methyl-2-4-pentanediol at 1.65A resolution reveals specific binding characteristics of SPS-40

Summary for 2PI6

• Entry DOI: 10.2210/pdb2pi6/pdb
• Related: 1ZL1 2DPE
• Descriptor: Chitinase-3-like protein 1, alpha-D-mannopyranose-(1-4)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, (4S)-2-METHYL-2,4-PENTANEDIOL, ... (5 entities in total)
• Functional Keywords: complex, signaling protein
• Biological source: Ovis aries (sheep)
• Total number of polymer chains: 1
• Total formula weight: 42042.40

Authors

Sharma, P.,Singh, N.,Sharma, S.,Kaur, P.,Betzel, C.,Singh, T.P. (deposition date: 2007-04-13, release date: 2007-05-01, Last modification date: 2024-10-16)

Primary citation

Sharma, P.,Singh, N.,Sinha, M.,Sharma, S.,Perbandt, M.,Betzel, C.,Kaur, P.,Srinivasan, A.,Singh, T.P.
Tryptophan as a three-way switch in regulating the function of the secretory signalling glycoprotein (SPS-40) from mammary glands: structure of SPS-40 complexed with 2-methylpentane-2,4-diol at 1.6 A resolution.
Acta Crystallogr.,Sect.D, 65:375-378, 2009

PubMed Abstract: The 40 kDa secretory signalling glycoprotein (SPS-40) is the first example with Trp78 in three functional orientations: (i) a resting state with a pinched conformation, (ii) a stacked conformation when bound to hexasaccharide and (iii) an obstructive conformation when inhibited by 2-methylpentane-2,4-diol (MPD). Trp78 is present in the core of the sugar-binding groove. The hexasaccharide N-acetylglucosamine (GlcNAc(6)) has been shown to bind to SPS-40. As a result of this, the conformation of Trp78 alters from the native pinched conformation (chi(1) = -65.5 degrees , chi(2,1) = -78.8 degrees , chi(2,2) = 97.5 degrees ) to the stacked conformation (chi(1) = -170.0 degrees , chi(2,1) = -114.3 degrees , chi(2,2) = 61.6 degrees ). Further binding experiments showed that saccharide binding does not occur in the presence of 20% MPD. The crystal structure determination of the complex of SPS-40 with MPD revealed the presence of two MPD molecules in the sugar-binding groove. The very tightly bound MPD molecules at subsites -2 and -1 induced an unexpected and a rarely observed conformation of Trp78 (chi(1) = 55.9 degrees , chi(2,1) = 90.2 degrees , chi(2,2) = -88.9 degrees ) which is termed an obstructive conformation. The binding of MPD molecules also twisted the side chains of Glu269 and Ile272 considerably. These residues are also part of the sugar-binding groove. The observed obstructive conformation of the side chain of Trp78 in the present structure is the exact opposite of the stacked conformation. This rarely observed conformation is stabilized by a number of hydrogen bonds between Trp78 and Asn79 through water molecules W49, W229, W269, W547 and W557.

PubMed: 19307719
DOI: 10.1107/S0907444909002327

Experimental method

X-RAY DIFFRACTION (1.65 Å)