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- PDB-1nu9: Staphylocoagulase-Prethrombin-2 complex -

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Basic information

Entry
Database: PDB / ID: 1nu9
TitleStaphylocoagulase-Prethrombin-2 complex
Components
  • Staphylocoagulase
  • Thrombin light and heavy chains
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Thrombin non-proteolytic activator / endocarditis / hydrolase-hydrolase inhibitor complex / protein binding
Function / homology
Function and homology information


positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / ligand-gated ion channel signaling pathway / neutrophil-mediated killing of gram-negative bacterium / Defective F8 cleavage by thrombin ...positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / ligand-gated ion channel signaling pathway / neutrophil-mediated killing of gram-negative bacterium / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / negative regulation of fibrinolysis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / regulation of cytosolic calcium ion concentration / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Regulation of Complement cascade / negative regulation of proteolysis / Cell surface interactions at the vascular wall / lipopolysaccharide binding / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / positive regulation of insulin secretion / platelet activation / response to wounding / Golgi lumen / positive regulation of protein localization to nucleus / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / blood coagulation / antimicrobial humoral immune response mediated by antimicrobial peptide / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Staphylcoagulase, helix bundle domain 1 / Staphylcoagulase, helix bundle, domain 2 / Staphylocoagulase repeat / Staphylocoagulase, N-terminal, subdomain 1 / Staphylcoagulase, N-terminal, subdomain 2 / Staphylcoagulase, N-terminal, subdomain 1 / Staphylocoagulase repeat / Staphylococcus aureus coagulase / Staphylocoagulase repeat signature. / Prothrombin/thrombin ...Staphylcoagulase, helix bundle domain 1 / Staphylcoagulase, helix bundle, domain 2 / Staphylocoagulase repeat / Staphylocoagulase, N-terminal, subdomain 1 / Staphylcoagulase, N-terminal, subdomain 2 / Staphylcoagulase, N-terminal, subdomain 1 / Staphylocoagulase repeat / Staphylococcus aureus coagulase / Staphylocoagulase repeat signature. / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Kringle-like fold / Four Helix Bundle (Hemerythrin (Met), subunit A) / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Up-down Bundle / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
N(alpha)-((acetylthio)acetyl)-phenylalanyl-prolyl-arginine chloromethyl ketone / Chem-0ZJ / : / IMIDAZOLE / Prothrombin / Staphylocoagulase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsFriedrich, R. / Bode, W. / Fuentes-Prior, P. / Panizzi, P. / Bock, P.E.
CitationJournal: NATURE / Year: 2003
Title: Staphylocoagulase is a prototype for the mechanism of cofactor-induced zymogen activation
Authors: Friedrich, R. / Panizzi, P. / Fuentes-Prior, P. / Richter, K. / Verhamme, I. / Anderson, P.J. / Kawabata, S. / Huber, R. / Bode, W. / Bock, P.E.
History
DepositionJan 31, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thrombin light and heavy chains
C: Staphylocoagulase
D: Thrombin light and heavy chains
F: Staphylocoagulase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,63216
Polymers133,3594
Non-polymers2,27312
Water14,286793
1
A: Thrombin light and heavy chains
C: Staphylocoagulase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8168
Polymers66,6802
Non-polymers1,1376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-60 kcal/mol
Surface area27570 Å2
MethodPISA
2
D: Thrombin light and heavy chains
F: Staphylocoagulase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8168
Polymers66,6802
Non-polymers1,1376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-61 kcal/mol
Surface area27390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.160, 102.340, 135.540
Angle α, β, γ (deg.)90.00, 129.91, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 4 molecules ADCF

#1: Protein Thrombin light and heavy chains / Coagulation factor II


Mass: 33466.328 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: blood / References: UniProt: P00734, thrombin
#2: Protein Staphylocoagulase


Mass: 33213.258 Da / Num. of mol.: 2 / Fragment: UNP residues 1-281
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q846V4

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Non-polymers , 4 types, 805 molecules

#3: Chemical ChemComp-0ZJ / N-(sulfanylacetyl)-D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide / ATA-FPR-CH2Cl, ATA-PPACK


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 528.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H36ClN6O4S
References: N(alpha)-((acetylthio)acetyl)-phenylalanyl-prolyl-arginine chloromethyl ketone
#4: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg
#5: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 793 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE INHIBITOR IS BOUND TO THE ACTIVE SITE OF THE ENZYME. THE UNBOUND FORM OF THE INHIBITOR IS MCR-D- ...THE INHIBITOR IS BOUND TO THE ACTIVE SITE OF THE ENZYME. THE UNBOUND FORM OF THE INHIBITOR IS MCR-D-PHE-PRO-ARG-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN IT FORMS TWO COVALENT BONDS: 1) A COVALENT BOND TO SER 195 FORMING A HEMIKETAL AR7 AND 2) A COVALENT BOND TO NE2 OF HIS 57

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.59 Å3/Da / Density % sol: 65.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM imidazole, 200mM sodium formate, 12%(w/v) PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 %(v/v)imidazole1reservoirpH7.5
2200 mMsodium formate1reservoir
312 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.0092, 1.0000, 0.9500
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 1, 2002
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00921
211
30.951
ReflectionBiso Wilson estimate: 19 Å2
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 110836 / % possible obs: 91.1 % / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 83.4 % / Rmerge(I) obs: 0.26

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→19.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 548981.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 4424 5 %RANDOM
Rwork0.21 ---
all0.217 96266 --
obs0.217 87632 91.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.1982 Å2 / ksol: 0.315366 e/Å3
Displacement parametersBiso mean: 39.2 Å2
Baniso -1Baniso -2Baniso -3
1-17.28 Å20 Å214.6 Å2
2---16.23 Å20 Å2
3----1.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9358 0 102 793 10253
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.142
X-RAY DIFFRACTIONc_scbond_it2.152
X-RAY DIFFRACTIONc_scangle_it3.122.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 718 5.2 %
Rwork0.315 13205 -
obs--87.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3P43.PARAMP43.TOP
X-RAY DIFFRACTION4ARM.PARAMARM.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.98

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