PDBsum entry: 1re4

Blood clotting

PDB id: 1re4

Contents

Protein chains

65 a.a. *

306 a.a. *

298 a.a. *

60 a.a. *

Ligands

NAG ×2

Metals

_CA ×6

Waters ×164

* Residue conservation analysis

PDB id:

1re4

Name:

Blood clotting

Title:

Crystal structure of fragment d of bbetad398a fibrinogen

Structure:

Fibrinogen alpha/alpha-e chain. Chain: a, d. Fragment: fragment d of fibrinogen alpha chain. Engineered: yes. Fibrinogen beta chain. Chain: b, e. Fragment: fragment d of bbetad398a fibrinogen beta chain. Engineered: yes. Mutation: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: fga. Expressed in: cricetulus griseus. Expression_system_taxid: 10029. Expression_system_cell_line: cho. Expression_system_organ: ovary. Gene: fgb.

Biol. unit:

Trimer (from PQS)

Resolution:

2.70Å R-factor: 0.220 R-free: 0.271

Authors:

M.S.Kostelansky,L.Betts,O.V.Gorkun,S.T.Lord

Key ref:

M.S.Kostelansky et al. (2004). B beta Glu397 and B beta Asp398 but not B beta Asp432 are required for "B:b" interactions. Biochemistry, 43, 2465-2474. PubMed id: 14992584 DOI: 10.1021/bi035996f

Date:

06-Nov-03 Release date: 25-May-04

Protein chain

P02671  (FIBA_HUMAN) -  Fibrinogen alpha chain

Seq: 866 a.a.

Struc: 65 a.a.

Protein chains

P02675  (FIBB_HUMAN) -  Fibrinogen beta chain

Seq: 491 a.a.

Struc: 306 a.a.*

Protein chains

P02679  (FIBG_HUMAN) -  Fibrinogen gamma chain

Seq: 453 a.a.

Struc: 298 a.a.

Protein chain

P02671  (FIBA_HUMAN) -  Fibrinogen alpha chain

Seq: 866 a.a.

Struc: 60 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular space (2 terms)
• Biological process: signal transduction (3 terms)
• Biochemical function: receptor binding (2 terms)

DOI no: 10.1021/bi035996f

Biochemistry 43:2465-2474 (2004)

PubMed id: 14992584

B beta Glu397 and B beta Asp398 but not B beta Asp432 are required for "B:b" interactions.

M.S.Kostelansky, B.Bolliger-Stucki, L.Betts, O.V.Gorkun, S.T.Lord.

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.