3PMH

Mechanism of Sulfotyrosine-Mediated Glycoprotein Ib Interaction with Two Distinct alpha-Thrombin Sites


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Binding of alpha-thrombin to surface-anchored platelet glycoprotein Ib(alpha) sulfotyrosines through a two-site mechanism involving exosite I.

Zarpellon, A.Celikel, R.Roberts, J.R.McClintock, R.A.Mendolicchio, G.L.Moore, K.L.Jing, H.Varughese, K.I.Ruggeri, Z.M.

(2011) Proc.Natl.Acad.Sci.USA 108: 8628-8633

  • DOI: 10.1073/pnas.1017042108

  • PubMed Abstract: 
  • The involvement of exosite I in α-thrombin (FIIa) binding to platelet glycoprotein Ibα (GPIbα), which could influence interactions with other substrates, remains undefined. To address the problem, we generated the GPIbα amino terminal domain (GPIbα-N ...

    The involvement of exosite I in α-thrombin (FIIa) binding to platelet glycoprotein Ibα (GPIbα), which could influence interactions with other substrates, remains undefined. To address the problem, we generated the GPIbα amino terminal domain (GPIbα-N) fully sulfated on three tyrosine residues and solved the structure of its complex with FIIa. We found that sulfotyrosine (Tys) 278 enhances the interaction mainly by establishing contacts with exosite I. We then evaluated how substituting tyrosine with phenylalanine, which cannot be sulfated, affects FIIa binding to soluble or surface-immobilized GPIbα-N. Mutating Tyr(276), which mostly contacts exosite II residues, markedly reduced FIIa interaction with both soluble and immobilized GPIbα-N; mutating Tyr(278) or Tyr(279), which mostly contact exosite I residues, reduced FIIa complexing in solution by 0-20% but affinity for immobilized GPIbα-N 2 to 6-fold, respectively. Moreover, three exosite I ligands--aptamer HD1, hirugen, and lepirudin--did not interfere with soluble FIIa complexing to GPIbα-N, excluding that their binding caused allosteric effects influencing the interaction; nonetheless, all impaired FIIa binding to immobilized GPIbα-N and platelet GPIb nearly as much as aptamer HD22 and heparin, both exosite II ligands. Bound HD1 and hirugen alter Trp(148) orientation in a loop near exosite I preventing contacts with the sulfate oxygen atoms of Tys(279). These results support a mechanism in which binding occurs when the two exosites of one FIIa molecule independently interact with two immobilized GPIbα molecules. Through exosite engagement, GPIbα may influence FIIa-dependent processes relevant to hemostasis and thrombosis.


    Organizational Affiliation

    Department of Molecular and Experimental Medicine, Roon Research Center for Arteriosclerosis and Thrombosis, The Scripps Research Institute, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THROMBIN ALPHA-CHAIN
A
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
THROMBIN BETA-CHAIN
B
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
Platelet glycoprotein Ib alpha chain
G
290Homo sapiensMutation(s): 1 
Gene Names: GP1BA
Find proteins for P07359 (Homo sapiens)
Go to Gene View: GP1BA
Go to UniProtKB:  P07359
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0G7
Query on 0G7

Download SDF File 
Download CCD File 
B
D-phenylalanyl-N-[(3S)-6-carbamimidamido-1-chloro-2-oxohexan-3-yl]-L-prolinamide
d-Phe-Pro-Arg chloromethylketone (PPACK)
C21 H31 Cl N6 O3
KWPACVJPAFGBEQ-IKGGRYGDSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
B, G
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000021 (0G7)
Query on PRD_000021
BD-Phe-Pro-Arg chloromethylketone (PPACK)Peptide-like / Inhibitor

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Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
G
L-PEPTIDE LINKINGC9 H11 N O6 STYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.220 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 67.657α = 90.00
b = 67.657β = 90.00
c = 329.730γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSphasing
ADSCdata collection
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-08-10
    Type: Database references
  • Version 1.3: 2012-12-12
    Type: Other