title: Crystal structure of fragment D from lamprey fibrinogen complexed with the peptide Gly-His-Arg-Pro-amide.
abstract: The crystal structure of fragment D from lamprey fibrinogen has been determined at 2.8 A resolution. The 89 kDa protein was cocrystallized with the peptide Gly-His-Arg-Pro-amide, which in many fibrinogens-but not lamprey-corresponds to the B knob exposed by thrombin. Because lamprey fragment D is more than 50% identical in sequence with human fragment D, the structure of which has been reported previously, it was possible to use the method of molecular replacement. The space group of the lamprey crystals is P1; there are four molecules in the unit cell. Although the fragments are packed head to head by the same D:D interface as is observed in other related preparations containing fragments D, the tails are uniquely joined by an unnatural association of the terminal sections of the residual coiled coils from adjacent molecules. Some features of the lamprey structure are clearer than have been observed in previous fragment D structures, including the beta-chain carbohydrate cluster, for one, and the important gamma-chain carboxyl-terminal segment, for another. The most significant differences between the lamprey and human structures occur in connecting loops at the entryways to the beta-chain and gamma-chain binding pockets.
authors.affiliation: Center for Molecular Genetics, University of California, San Diego, La Jolla, California 92093-0634, USA.
authors.forename: Zhe
authors.initials: Z
authors.lastname: Yang
authors.forename: Glen
authors.initials: G
authors.lastname: Spraggon
authors.forename: Leela
authors.initials: L
authors.lastname: Pandi
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Everse
authors.forename: Marcia
authors.initials: M
authors.lastname: Riley
authors.forename: Russell F
authors.initials: RF
authors.lastname: Doolittle
mesh_terms: D000818:Animals; D001665:Binding Sites; D002118:Calcium / Q000737:chemistry; D002241:Carbohydrates / Q000737:chemistry; D003460:Crystallization; D018360:Crystallography, X-Ray; D005338:Fibrin Fibrinogen Degradation Products / Q000737:chemistry*; D006801:Humans; D007798:Lampreys; D008958:Models, Molecular; D009842:Oligopeptides / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary
chemical_list: D002241:Carbohydrates; D005338:Fibrin Fibrinogen Degradation Products; D009842:Oligopeptides; D010446:Peptide Fragments; C015214:fibrinogen D fragment; C048770:glycyl-histidyl-arginyl-proline; D002118:Calcium