1DE7

INTERACTION OF FACTOR XIII ACTIVATION PEPTIDE WITH ALPHA-THROMBIN: CRYSTAL STRUCTURE OF THE ENZYME-SUBSTRATE COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Interaction of the factor XIII activation peptide with alpha -thrombin. Crystal structure of its enzyme-substrate analog complex.

Sadasivan, C.Yee, V.C.

(2000) J.Biol.Chem. 275: 36942-36948

  • DOI: 10.1074/jbc.M006076200

  • PubMed Abstract: 
  • The serine protease thrombin proteolytically activates blood coagulation factor XIII by cleavage at residue Arg(37); factor XIII in turn cross-links fibrin molecules and gives mechanical stability to the blood clot. The 2.0-A resolution x-ray crystal ...

    The serine protease thrombin proteolytically activates blood coagulation factor XIII by cleavage at residue Arg(37); factor XIII in turn cross-links fibrin molecules and gives mechanical stability to the blood clot. The 2.0-A resolution x-ray crystal structure of human alpha-thrombin bound to the factor XIII-(28-37) decapeptide has been determined. This structure reveals the detailed atomic level interactions between the factor XIII activation peptide and thrombin and provides the first high resolution view of this functionally important part of the factor XIII molecule. A comparison of this structure with the crystal structure of fibrinopeptide A complexed with thrombin highlights several important determinants of thrombin substrate interaction. First, the P1 and P2 residues must be compatible with the geometry and chemistry of the S1 and S2 specificity sites in thrombin. Second, a glycine in the P5 position is necessary for the conserved substrate conformation seen in both factor XIII-(28-37) and fibrinopeptide A. Finally, the hydrophobic residues, which occupy the aryl binding site of thrombin determine the substrate conformation further away from the catalytic residues. In the case of factor XIII-(28-37), the aryl binding site is shared by hydrophobic residues P4 (Val(34)) and P9 (Val(29)). A bulkier residue in either of these sites may alter the substrate peptide conformation.


    Related Citations: 
    • The Refined 1.9 Angstroms X-Ray Crystal Structure of D-Phe-Pro-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin: Structure Analysis, Overall Structure, Electrostatic Properties, Detailed Active-Site Geometry, and Structure-Function Relationships
      Bode, W.,Turk, D.,Karshikov, A.
      (1992) Protein Sci. 1: 426
    • Three-Dimensional Structure of a Transglutaminase: Human Blood Coagulation Factor Xiii
      Yee, V.C.,Pedersen, L.C.,Trong, I.L.,Bishop, P.D.,Stenkamp, R.E.,Teller, D.C.
      (1994) Proc.Natl.Acad.Sci.USA 91: 7296
    • The Interaction of Thrombin with Fibrinogen: A Structural Basis for its Specificity
      Stubbs, M.T.,Oschkinat, H.,Mayer, I.,Huber, R.,Angliker, H.,Stoner, S.R.,Bode, W.
      (1992) Eur.J.Biochem. 206: 187


    Organizational Affiliation

    Department of Molecular Cardiology and Structural Biology Center, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALPHA-THROMBIN (LIGHT CHAIN)
L, J
36Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ALPHA-THROMBIN (HEAVY CHAIN)
H, K
259Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
FACTOR XIII ACTIVATION PEPTIDE (28-37)
A, B
11N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
H, K
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
0QE
Query on 0QE
A, B
NON-POLYMERC H3 Cl

--

AR7
Query on AR7
A, B
peptide-likeC6 H17 N4 O2ARG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.070α = 90.00
b = 81.260β = 101.62
c = 85.460γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
X-PLORrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-12-13
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance