The structure of the saccharide-binding site of concanavalin A.
A complex of concanavalin A with methyl alpha-D-mannopyranoside has been crystallized in space group P212121 with a = 123.9 A, b = 129.1 A and c = 67.5 A. X-ray diffraction intensities to 2.9 A resolution have been collected on a Xentronics/Nicolet area detector. The structure has been solved by molecular replacement where the starting model was based on refined coordinates of an I222 crystal of saccharide-free concanavalin A. The structure of the saccharide complex was refined by restrained least-squares methods to an R-factor value of 0.19. In this crystal form, the asymmetric unit contains four protein subunits, to each of which a molecule of mannoside is bound in a shallow crevice near the surface of the protein. The methyl alpha-D-mannopyranoside molecule is bound in the C1 chair conformation 8.7 A from the calcium-binding site and 12.8 A from the transition metal-binding site. A network of seven hydrogen bonds connects oxygen atoms O-3, O-4, O-5 and O-6 of the mannoside to residues Asn14, Leu99, Tyr100, Asp208 and Arg228. O-2 and O-1 of the mannoside extend into the solvent. O-2 is hydrogen-bonded through a water molecule to an adjacent asymmetric unit. O-1 is not involved in any hydrogen bond and there is no fixed position for its methyl substituent.
Derewenda
Z
Z
Department of Chemistry, University of York, Heslington, UK.
Yariv
J
J
Helliwell
J R
JR
Kalb
A J
AJ
Dodson
E J
EJ
Papiz
M Z
MZ
Wan
T
T
Campbell
J
J
D001665:Binding Sites; D055598:Chemical Phenomena; D002621:Chemistry; D003208:Concanavalin A / Q000032:analysis* / Q000378:metabolism; D005960:Glucosides / Q000032:analysis / Q000378:metabolism; D006027:Glycosides / Q000032:analysis*; D006860:Hydrogen Bonding; D008362:Mannosides / Q000032:analysis* / Q000378:metabolism; D008766:Methylmannosides / Q000032:analysis / Q000378:metabolism; D008968:Molecular Conformation; D014961:X-Ray Diffraction
D005960:Glucosides; D006027:Glycosides; D008362:Mannosides; D008766:Methylmannosides; D003208:Concanavalin A; C008466:methylmannoside