1RE4

Crystal Structure of Fragment D of BbetaD398A Fibrinogen

Summary for 1RE4

• Entry DOI: 10.2210/pdb1re4/pdb
• Related: 1FZA 1FZC 1FZF 1FZG 1LT9 1LTJ 1RE4 1RF0 1RF1
• Descriptor: Fibrinogen alpha/alpha-E chain, Fibrinogen beta chain, Fibrinogen gamma chain, ... (6 entities in total)
• Functional Keywords: recombinant fibrinogen fragment d, recombinant fibrinogen, mutant fibrinogen, variant fibrinogen, bbetad398a fibrinogen, blood clotting
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 6
• Total formula weight: 158405.34

Authors

Kostelansky, M.S.,Betts, L.,Gorkun, O.V.,Lord, S.T. (deposition date: 2003-11-06, release date: 2004-05-25, Last modification date: 2023-08-23)

Primary citation

Kostelansky, M.S.,Bolliger-Stucki, B.,Betts, L.,Gorkun, O.V.,Lord, S.T.
BbetaGlu397 and BbetaAsp398 but not BbetaAsp432 are required for "B:b" interactions.
Biochemistry, 43:2465-2474, 2004

PubMed Abstract: We synthesized three fibrinogen variants, BbetaE397A, BbetaD398A, and BbetaD432A, with substitutions at positions identified in crystallographic studies as critical for binding the "B" peptide, Gly-His-Arg-Pro-amide (GHRPam), to the "b" polymerization site. We examined thrombin- and batroxobin-catalyzed polymerization by turbidity measurements and found that BbetaE397A and BbetaD398A were impaired while BbetaD432A was normal. Changes in polymerization as a function of calcium were similar for variant and normal fibrinogens. We determined crystal structures of fragment D from the variant BbetaD398A in the absence and presence of GHRPam. In the absence of peptide, the structure showed that the alanine substitution altered only specific local interactions, as alignment of the variant structure with the analogous normal structure resulted in an RMSD of 0.53 A over all atoms. The structure also showed reduced occupancy of the beta2 calcium-binding site that includes the side chain carbonyl of BbetaD398, suggesting that calcium was not bound at this site in our polymerization studies. In the presence of peptide, the structure showed that GHRPam was not bound in the "b" site and the conformational changes associated with peptide binding to normal fragment D did not occur. This structure also showed GHRPam bound in the "a" polymerization site, although in two different conformations. Calcium binding was associated with only one of these conformations, suggesting that calcium binding to the gamma2-site and an alternative peptide conformation were induced by crystal packing. We conclude that BbetaE397 and BbetaD398 are essential for the "B:b" interaction, while BbetaD432 is not.

PubMed: 14992584
DOI: 10.1021/bi035996f

Experimental method

X-RAY DIFFRACTION (2.7 Å)