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The crystal structure of fragment double-D from cross-linked lamprey fibrin reveals isopeptide linkages across an unexpected D-D interface

Biochemistry, ISSN: 0006-2960, Vol: 41, Issue: 52, Page: 15610-15617
2002
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Article Description

The crystal structure of fragment double-D from factor XIII-cross-linked lamprey fibrin has been determined at 2.9 Å resolution. The 180 kDa covalent dimer was cocrystallized with the peptide Gly-His-Arg-Pro-amide, which in many fibrinogens, but not that of lamprey, corresponds to the B-knob exposed by thrombin. The structure was determined by molecular replacement, a recently determined structure of lamprey fragment D being used as a search model. GHRPam was found in both the γ- and β-chain holes. Unlike the situation with fragment D, the crystal packing of the cross-linked double-D structure exhibits two different D-D interfaces, each γ- chain facing γ-chains on two other molecules. One of these (interface I) involves the asymmetric interface observed in all other D fragments and related structures. The other (interface II) encompasses a completely different set of residues. The two abutments differ in that interface I results in an "in line" arrangement of abutting molecules and the interface II in a "zigzag" arrangement. So far as can be determined (the electron density could only be traced on one side of the cross-links), it is the γ-chains of the newly observed zigzag units (interface II) that are joined by the reciprocal ε-amino-γ-glutamyl cross-links. Auspiciously, the same novel D-D interface was observed in two lower-resolution crystal structures of human double-D preparations that had been crystallized under unusual circumstances. These observations show that double-D structures are linked in a way that is sufficiently flexible to accommodate different D-D interfaces under different circumstances.

Bibliographic Details

Yang, Zhe; Pandi, Leela; Doolittle, Russell F

American Chemical Society (ACS)

Biochemistry, Genetics and Molecular Biology

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