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PDBsum entry 1ycp

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protein ligands Protein-protein interface(s) links
Hydrolase/hydrolase substrate PDB id
1ycp
Jmol
Contents
Protein chains
29 a.a. *
247 a.a. *
146 a.a. *
101 a.a. *
Ligands
TYR ×2
GLY-VAL-ARG-GLY-
PRO
×2
Waters ×276
* Residue conservation analysis
PDB id:
1ycp
Name: Hydrolase/hydrolase substrate
Title: The crystal structure of fibrinogen-aa peptide 1-23 (f8y) bo bovine thrombin explains why the mutation of phe-8 to tyros strongly inhibits normal cleavage at arginine-16
Structure: Epsilon thrombin. Chain: l, j. Alpha thrombin. Chain: h. Fibrinopeptide a-alpha. Chain: f, n. Fragment: residues 1 - 23. Engineered: yes. Mutation: yes.
Source: Bos taurus. Cattle. Organism_taxid: 9913. Tissue: blood. Tissue: blood
Biol. unit: Tetramer (from PQS)
Resolution:
2.50Å     R-factor:   0.183     R-free:   0.245
Authors: M.G.Malkowski,B.F.P.Edwards
Key ref: M.G.Malkowski et al. (1997). Crystal structure of fibrinogen-Aalpha peptide 1-23 (F8Y) bound to bovine thrombin explains why the mutation of Phe-8 to tyrosine strongly inhibits normal cleavage at Arg-16. Biochem J, 326, 815-822. PubMed id: 9307032
Date:
01-May-97     Release date:   06-May-98    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00735  (THRB_BOVIN) -  Prothrombin
Seq:
Struc:
 
Seq:
Struc:
625 a.a.
29 a.a.
Protein chain
Pfam   ArchSchema ?
P00735  (THRB_BOVIN) -  Prothrombin
Seq:
Struc:
 
Seq:
Struc:
625 a.a.
247 a.a.
Protein chain
Pfam   ArchSchema ?
P00735  (THRB_BOVIN) -  Prothrombin
Seq:
Struc:
 
Seq:
Struc:
625 a.a.
146 a.a.
Protein chain
Pfam   ArchSchema ?
P00735  (THRB_BOVIN) -  Prothrombin
Seq:
Struc:
 
Seq:
Struc:
625 a.a.
101 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains L, H, J, K, M: E.C.3.4.21.5  - Thrombin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Arg-|-Gly; activates fibrinogen to fibrin and releases fibrinopeptide A and B.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     blood coagulation   2 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
Biochem J 326:815-822 (1997)
PubMed id: 9307032  
 
 
Crystal structure of fibrinogen-Aalpha peptide 1-23 (F8Y) bound to bovine thrombin explains why the mutation of Phe-8 to tyrosine strongly inhibits normal cleavage at Arg-16.
M.G.Malkowski, P.D.Martin, S.T.Lord, B.F.Edwards.
 
  ABSTRACT  
 
A peptide containing residues 1-50 of the Aalpha-chain of fibrinogen, expressed as a fusion peptide with beta-galactosidase, is rapidly cleaved by thrombin at Arg-16, similarly to whole fibrinogen. When Phe-8, which is highly conserved, is replaced with tyrosine (F8Y), the cleavage is slowed drastically [Lord, Byrd, Hede, Wei and Colby (1990) J. Biol. Chem. 265, 838-843]. To examine the structural basis for this result, we have determined the crystal structure of bovine thrombin complexed with a synthetic peptide containing residues 1-23 of fibrinogen Aalpha and the F8Y mutation. The crystals are in space group P43212, with unit-cell dimensions of a = 88.3 A (1 A = 0.1 nm), c = 195.5 A and two complexes in the asymmetric unit. The final R factor is 0.183 for 2sigma data from 7.0 to 2.5 A resolution. There is continuous density for the five residues in the P3, P2, P1, P1' and P2' positions of the peptide (Gly-14f to Pro-18f) at the active site of thrombin, and isolated but well-defined density for Tyr-8f at position P9 in the hydrophobic pocket of thrombin. The tyrosine residue is shifted relative to phenylalanine in the native peptide because the phenol side chain is larger and makes a novel, intrapeptide hydrogen bond with Gly-14f. Adjacent peptide residues cannot form the hydrogen bonds that stabilize the secondary structure of the native peptide. Consequently, the 'reaction'geometry at the scissile bond, eight residues from the mutation, is perturbed and the peptide is mostly uncleaved in the crystal structure.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19644995 C.Y.Koh, M.Kazimirova, P.A.Nuttall, and R.M.Kini (2009).
Noncompetitive inhibitor of thrombin.
  Chembiochem, 10, 2155-2158.  
16102053 J.A.Huntington (2005).
Molecular recognition mechanisms of thrombin.
  J Thromb Haemost, 3, 1861-1872.  
15892855 W.Bode (2005).
The structure of thrombin, a chameleon-like proteinase.
  J Thromb Haemost, 3, 2379-2388.  
14567919 K.Ponnuraj, M.G.Bowden, S.Davis, S.Gurusiddappa, D.Moore, D.Choe, Y.Xu, M.Hook, and S.V.Narayana (2003).
A "dock, lock, and latch" structural model for a staphylococcal adhesin binding to fibrinogen.
  Cell, 115, 217-228.
PDB codes: 1r17 1r19
10380350 A.Lombardi, G.De Simone, S.Galdiero, N.Staiano, F.Nastri, and V.Pavone (1999).
From natural to synthetic multisite thrombin inhibitors.
  Biopolymers, 51, 19-39.  
9753458 M.M.Rooney, J.L.Mullin, and S.T.Lord (1998).
Substitution of tyrosine for phenylalanine in fibrinopeptide A results in preferential thrombin cleavage of fibrinopeptide B from fibrinogen.
  Biochemistry, 37, 13704-13709.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.