3.4.21.5: thrombin

This is an abbreviated version, for detailed information about thrombin, go to the full flat file.

Reaction

selective cleavage of Arg-/-Gly bonds in fibrinogen to form fibrin and release fibrinopeptides A and B =

Synonyms

activated factor II, alpha-thrombin, alphaTh, beta-thrombin, blood-coagulation factor II, activated, blood-coagulation factor IIa, clotting factor IIa, EC 3.4.4.13, factor IIa, fibrinogenase, thrombase, thrombin, E, thrombin-C, thrombofort, topical, tropostasin

ECTree

     3 Hydrolases
         3.4 Acting on peptide bonds (peptidases)
             3.4.21 Serine endopeptidases
                3.4.21.5 thrombin

Crystallization

Crystallization on EC 3.4.21.5 - thrombin

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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
enzyme complex formed with the benzamidine and Arg-based thrombin inhibitors Nalpha-(2-naphthalenesulfonyl)-glycyl-D-3-aminophenyl-alanyl-piperidine, N-alpha-tosyl-(3-amidinophenyl)alanine piperidine and (2R,4R)-4-methyl-1-[Nalpha-(3-methyl-1,2,3,4-tetrahydro-8-quinolinesulfonyl)-L-arginyl]-2-piperidine carboxylic acid
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purified enzyme, hanging drop vapour diffusion metod, 20C, 0.002 ml of protein in 10 mM Tris-HCl, pH 8.0, and 50 mM NaCl, is mixed with 0.002 ml of reservoir solution containing 0.1 M sodium citrate, pH 5.6, 14-16% w/v PEG 4000, and 20% w/v 2-propanol, and equilibration against 0.1 ml reservoir solution, X-ray diffraction structure determination and analysis at 2.8 A resolution, molecular replacement method
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8 mg/ml purified enzyme in complex with factor XIII(28-37) peptide as a chloromethylketone derivative, hanging drop vapor diffusion method, room temperature, 24% PEG 8000, 200 mM sodium chloride, 50 mM sodium citrate, pH 5.5, 2 weeks for full size crystals, X-ray diffraction structure determination and analysis at 1.6 A
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about 6 mg/ml alpha-thrombin in ternary complex with hirugen and inhibitor RWJ-51438, in 50 mM phosphate buffer, pH 7.3, room temperature, hanging drop method, equal volume of 0.003 mL of protein complex and reservoir solution, the latter containing 0.1 M sodium cacodylate, pH 6.5, 0.75 M sodium acetate, 0.01% w/v sodium azide, 20% w/v PEG 4000, equilibration against 1 ml reservoir solution, 5 days, X-ray diffraction structure determination and analysis at 1.7 A resolution with 25% glycerol as cryoprotectant
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alpha-thrombin complexed with synthetic variegin, hanging drop vapor diffusion method, 0.001 ml of protein solution, containing 20 mg/ml protein, 3 mg/ml variegin inhibitor, 50 mM HEPES, pH 7.5, and 375 mM NaCl, is mixed with 0.001 ml of precipitant solution, containing 100 mM HEPES, pH 7.4, and 20-25% PEG 8000, and equilibrated against 1 ml of the precipitant solution, 4C, X-ray diffraction structure determination and analysis at 2.4 A resolution, modeling
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alpha-thrombin is crystallized at 4C in a complex with sulfated hirudin 53-65, sitting drop vapor diffusion method
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bound to a heparin fragment of eight monosaccharide units in length
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crystal growth of enzyme complexed with acyl (alpha-aminoalkyl)phosphonate inhibitor within 1 week, formation of 2 different complexes, pentacoordinated complex I and tetracoordinated complex II, X-ray diffraction structure determination and analysis at 1.4-1.75 A
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crystal structure of thrombin complexed to a novel series of synthetic inhibitors containing a 5,5'-trans-lactone template
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crystallographic studies of thrombin with Ac-D-Phe-Pro-boroArg-OH and its Lys, amidine, homolysine, and Orn analogs
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D120N mutant thrombin slow enzyme form in a self-inhibited conformation, X-ray diffraction structure determination and analysis at 1.87 A resolution
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enzyme complexed with hirugen, 5.5 mg/ml in 24-30% PEG 4000, 0.1 M sodium phosphate, pH 7.3, 20C, vapour diffusion method, single crystals are soaked overnight in 30% PEG 4000, 0.1 M sodium phosphate, pH 7.3, and 0.5 mg/ml inhibitor, X-ray diffraction structure determination and analysis
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free enzyme mutant R77aA in presence of K+, two molecules in the asymmetric unit, one with the cation site bound to K+ and the other with the site free, X-ray diffraction structure determination and analysis at 1.9 A resolution
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gamma thrombin
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hanging drop vapor diffusion method, using 100 mM MES, 30% (w/v) polyethylene glycol 400, pH 6.5
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hanging drop vapor diffusion method, using 28% (w/v) PEG 8000 and 100 mM sodium phosphate buffer (pH 7.5)
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mutant D221A/D222K bound with a fragment of hirudin, slight collapse of the 186 and 220 loops into the Na+ bindung site. Crucial role of D221/D187 ion pair in stabilizing the fast form of enzyme
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mutant E217K, shows repositioned E192 and destructed oxyanion hole
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mutant enzyme N143P is crystallized by the hanging drop vapor diffusion method, using 0.2 M NaNO3 and 20% (w/v) PEG3350
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mutant W215A/E217A, free and in complex with inhibitor D-Phe-Pro-Arg-chloromethylketone
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Na+-free form, Na+-binding site is in a highly ordered position slightly removed from that seen in the Na+-bound state
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prethrombin 2 bound to a fully active fragment of residues 1-325 from Staphylococcus aureus staphylocoagluase. Complex forms dimers
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purified alpha-thrombin complexed with a modified 15-mer thrombin-binding aptamer, sitting drop vapour diffusion method, 8 mg/ml protein in 50 mM potassium phosphate, pH 7.1, and 0.1 M KCl, is mixed in a 1:1 ratio of 0.001 ml each with crystallization solution, containing 20% v/v PEG 20 000, 0.2 M ammonium sulfate, 3% v/v n-propanol, 100 mM sodium acetate, pH 5.8, 20C, a few days, X-ray diffraction structure determination and analysis at 2.15 A resolution
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purified hirudin-alpha-thrombin in complex with inhibitors RA-1008, RA-1014, aeruginosin 98-B, and aeruginosin 298-A, hanging-drop vapour diffusion method, the protein solution contains 4-5 mg/ml protein, 50 mg/ml hirudin, and 2-3 mM inhibitor and is mixed with reservoir solution containing 22-27% polyethylene glycol 8000 and 0.1 M sodium phosphate buffer, pH 7.5, a few days to microcrystals, macroseeding to obtain laregr crystals, X-ray diffraction structure determination and analysis at 1.85 A resolution, modeling
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thrombin in complex with fibrinogen gamma' peptide, X-ray diffraction structure determination and analysis at 2.4 A resolution
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thrombin in complex with hirudin, hanging drop vapor diffusion method, using 0.05 M sodium phosphate buffer pH 7.3, 28% (w/v) PEG8000
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thrombin mutant S195A in complex with a 30-residue long uncleaved extracellular fragment of protease-activated receptor 1, hanging drop vapor diffusion method, using 0.2 M potassium/sodium tartrate, 20%,(w/v) PEG 3350, at 22C
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thrombin-suramin complex refined at 2.4 A resolution,. hanging drop vapor diffusion method, using 400 mM NaCl, 20 mM MES pH 6.0, 25% (v/v) tert-butanol, 100 mM Tris pH 8.5
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hanging drop vapor diffusion method, using either 0.2 M NH4Cl, 20% (w/v) polyethylene glycol 3350, pH 6.3, or 0.2 M NH4Cl, 14% (w/v) polyethylene glycol 3350, pH 4.6, or 0.2 M Na2SO4, 20% (w/v) polyethylene glycol 3350, pH 6.6
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wild-type and mutant S195A thrombins in complex with the extracellular fragments of murine protease-activated receptors PAR-3 and PAR-4, X-ray diffraction structure determination and anaylsis at 2.0-3.5 A resolution
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