6GT6

Crystal structure of recombinant coagulation factor beta-XIIa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


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Literature

Crystal structures of the recombinant beta-factor XIIa protease with bound Thr-Arg and Pro-Arg substrate mimetics.

Pathak, M.Manna, R.Li, C.Kaira, B.G.Hamad, B.K.Belviso, B.D.Bonturi, C.R.Dreveny, I.Fischer, P.M.Dekker, L.V.Oliva, M.L.V.Emsley, J.

(2019) Acta Crystallogr D Struct Biol 75: 578-591

  • DOI: 10.1107/S2059798319006910
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Coagulation factor XII (FXII) is a key initiator of the contact pathway, which contributes to inflammatory pathways. FXII circulates as a zymogen, which when auto-activated forms factor XIIa (FXIIa). Here, the production of the recombinant FXIIa prot ...

    Coagulation factor XII (FXII) is a key initiator of the contact pathway, which contributes to inflammatory pathways. FXII circulates as a zymogen, which when auto-activated forms factor XIIa (FXIIa). Here, the production of the recombinant FXIIa protease domain (βFXIIa His ) with yields of ∼1-2 mg per litre of insect-cell culture is reported. A second construct utilized an N-terminal maltose-binding protein (MBP) fusion (MBP-βFXIIa His ). Crystal structures were determined of MBP-βFXIIa His in complex with the inhibitor D-Phe-Pro-Arg chloromethyl ketone (PPACK) and of βFXIIa His in isolation. The βFXIIa His structure revealed that the S2 and S1 pockets were occupied by Thr and Arg residues, respectively, from an adjacent molecule in the crystal. The Thr-Arg sequence mimics the P2-P1 FXIIa cleavage-site residues present in the natural substrates prekallikrein and FXII, and Pro-Arg (from PPACK) mimics the factor XI cleavage site. A comparison of the βFXIIa His structure with the available crystal structure of the zymogen-like FXII protease revealed large conformational changes centred around the S1 pocket and an alternate conformation for the 99-loop, Tyr99 and the S2 pocket. Further comparison with activated protease structures of factors IXa and Xa, which also have the Tyr99 residue, reveals that a more open form of the S2 pocket only occurs in the presence of a substrate mimetic. The FXIIa inhibitors EcTI and infestin-4 have Pro-Arg and Phe-Arg P2-P1 sequences, respectively, and the interactions that these inhibitors make with βFXIIa are also described. These structural studies of βFXIIa provide insight into substrate and inhibitor recognition and establish a scaffold for the structure-guided drug design of novel antithrombotic and anti-inflammatory agents.


    Organizational Affiliation

    Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, England.,Biochemistry Department, Federal University of São Paulo, 04044-020 São Paulo-SP, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor XII
B
253Homo sapiensMutation(s): 0 
Gene Names: F12
EC: 3.4.21.38
Find proteins for P00748 (Homo sapiens)
Go to Gene View: F12
Go to UniProtKB:  P00748
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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

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Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CYS
Query on CYS

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Download CCD File 
B
CYSTEINE
C3 H7 N O2 S
XUJNEKJLAYXESH-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.211 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 106.932α = 90.00
b = 106.932β = 90.00
c = 65.962γ = 90.00
Software Package:
Software NamePurpose
xia2data reduction
REFMACrefinement
xia2data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-06-15 
  • Released Date: 2019-07-17 
  • Deposition Author(s): Pathak, M., Emsley, J.

Funding OrganizationLocationGrant Number
British Heart FoundationUnited Kingdom--

Revision History 

  • Version 1.0: 2019-07-17
    Type: Initial release