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- PDB-5jui: domain-swapped dimer of the the KRT10-binding region (BR) of PsrP -

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Basic information

Entry
Database: PDB / ID: 5jui
Titledomain-swapped dimer of the the KRT10-binding region (BR) of PsrP
ComponentsCell wall surface anchor family protein
KeywordsSTRUCTURAL PROTEIN / Streptococcus pneumoniae / Pneumococcal Serine Rich Repeat Protein / Oligomerisation / Bacterial aggregation / Biofilm formation / DNA
Function / homology
Function and homology information


Gram-positive-bacterium-type cell wall / symbiont-mediated perturbation of host defense response / single-species biofilm formation / cell adhesion / cell surface / DNA binding / extracellular region
Similarity search - Function
Serine-rich repeat adhesion glycoprotein / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
Pneumococcal serine-rich repeat protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSchulte, T. / Mikaelsson, C. / Achour, A.
Funding support Sweden, 4items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Knut and Alice Wallenberg Foundation Sweden
Wenner-Gren Foundation Sweden
European UnionFP7/2007-2013 Sweden
Citation
Journal: Sci Rep / Year: 2016
Title: The BR domain of PsrP interacts with extracellular DNA to promote bacterial aggregation; structural insights into pneumococcal biofilm formation.
Authors: Tim Schulte / Cecilia Mikaelsson / Audrey Beaussart / Alexey Kikhney / Maya Deshmukh / Sebastian Wolniak / Anuj Pathak / Christine Ebel / Jonas Löfling / Federico Fogolari / Birgitta ...Authors: Tim Schulte / Cecilia Mikaelsson / Audrey Beaussart / Alexey Kikhney / Maya Deshmukh / Sebastian Wolniak / Anuj Pathak / Christine Ebel / Jonas Löfling / Federico Fogolari / Birgitta Henriques-Normark / Yves F Dufrêne / Dmitri Svergun / Per-Åke Nygren / Adnane Achour /
Abstract: The major human pathogen Streptococcus pneumoniae is a leading cause of disease and death worldwide. Pneumococcal biofilm formation within the nasopharynx leads to long-term colonization and ...The major human pathogen Streptococcus pneumoniae is a leading cause of disease and death worldwide. Pneumococcal biofilm formation within the nasopharynx leads to long-term colonization and persistence within the host. We have previously demonstrated that the capsular surface-associated pneumococcal serine rich repeat protein (PsrP), key factor for biofilm formation, binds to keratin-10 (KRT10) through its microbial surface component recognizing adhesive matrix molecule (MSCRAMM)-related globular binding region domain (BR187-385). Here, we show that BR187-385 also binds to DNA, as demonstrated by electrophoretic mobility shift assays and size exclusion chromatography. Further, heterologous expression of BR187-378 or the longer BR120-378 construct on the surface of a Gram-positive model host bacterium resulted in the formation of cellular aggregates that was significantly enhanced in the presence of DNA. Crystal structure analyses revealed the formation of BR187-385 homo-dimers via an intermolecular β-sheet, resulting in a positively charged concave surface, shaped to accommodate the acidic helical DNA structure. Furthermore, small angle X-ray scattering and circular dichroism studies indicate that the aggregate-enhancing N-terminal region of BR120-166 adopts an extended, non-globular structure. Altogether, our results suggest that PsrP adheres to extracellular DNA in the biofilm matrix and thus promotes pneumococcal biofilm formation.
#1: Journal: Open Biol / Year: 2014
Title: The basic keratin 10-binding domain of the virulence-associated pneumococcal serine-rich protein PsrP adopts a novel MSCRAMM fold.
Authors: Tim Schulte / Jonas Löfling / Cecilia Mikaelsson / Alexey Kikhney / Karina Hentrich / Aurora Diamante / Christine Ebel / Staffan Normark / Dmitri Svergun / Birgitta Henriques-Normark / Adnane Achour /
Abstract: Streptococcus pneumoniae is a major human pathogen, and a leading cause of disease and death worldwide. Pneumococcal invasive disease is triggered by initial asymptomatic colonization of the human ...Streptococcus pneumoniae is a major human pathogen, and a leading cause of disease and death worldwide. Pneumococcal invasive disease is triggered by initial asymptomatic colonization of the human upper respiratory tract. The pneumococcal serine-rich repeat protein (PsrP) is a lung-specific virulence factor whose functional binding region (BR) binds to keratin-10 (KRT10) and promotes pneumococcal biofilm formation through self-oligomerization. We present the crystal structure of the KRT10-binding domain of PsrP (BR187-385) determined to 2.0 Å resolution. BR187-385 adopts a novel variant of the DEv-IgG fold, typical for microbial surface components recognizing adhesive matrix molecules adhesins, despite very low sequence identity. An extended β-sheet on one side of the compressed, two-sided barrel presents a basic groove that possibly binds to the acidic helical rod domain of KRT10. Our study also demonstrates the importance of the other side of the barrel, formed by extensive well-ordered loops and stabilized by short β-strands, for interaction with KRT10.
History
DepositionMay 10, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell wall surface anchor family protein
B: Cell wall surface anchor family protein
C: Cell wall surface anchor family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3385
Polymers64,2233
Non-polymers1152
Water3,729207
1
A: Cell wall surface anchor family protein
hetero molecules

A: Cell wall surface anchor family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0456
Polymers42,8152
Non-polymers2304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area13790 Å2
ΔGint-96 kcal/mol
Surface area17960 Å2
MethodPISA
2
B: Cell wall surface anchor family protein
C: Cell wall surface anchor family protein


Theoretical massNumber of molelcules
Total (without water)42,8152
Polymers42,8152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13260 Å2
ΔGint-80 kcal/mol
Surface area17600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.827, 162.367, 102.092
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

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Components

#1: Protein Cell wall surface anchor family protein


Mass: 21407.662 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: SP_1772 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2URK1
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

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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: 3.54 Å3/Da / Density % sol: 65.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: The BR187-378 dimer was concentrated to 20 mg/mL in 20 mM Na-Citrate, 500 mM NaCl, 10% (V/V) glycerol, pH 5.5. Well-diffracting crystals were obtained in 100 mM Trisodiumcitrate dihydrate pH ...Details: The BR187-378 dimer was concentrated to 20 mg/mL in 20 mM Na-Citrate, 500 mM NaCl, 10% (V/V) glycerol, pH 5.5. Well-diffracting crystals were obtained in 100 mM Trisodiumcitrate dihydrate pH 5.6; 34-44% 2-methyl-4-pentanediole using the sitting drop vapor-diffusion method.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.95376 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95376 Å / Relative weight: 1
ReflectionResolution: 2.1→48.4 Å / Num. obs: 53483 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 49.1 Å2 / CC1/2: 1 / Rsym value: 0.059 / Net I/σ(I): 16.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZGH

3zgh


Resolution: 2.1→48.361 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.97
Details: A molecular replacement search performed using Phaser revealed three molecules of the BR187-385 monomer (PDB: 3ZGH) within the asymmetric unit. Initial rigid body and restrained refinement ...Details: A molecular replacement search performed using Phaser revealed three molecules of the BR187-385 monomer (PDB: 3ZGH) within the asymmetric unit. Initial rigid body and restrained refinement rounds were performed in CCP4 refmac, and Coot was used for manual model rebuilding. The mFo-DFc electron density difference map clearly indicated that residues Q312-G315 had to be re-built such that residues L202-G315 of chain A were linked to residues Y316-S377 of the symmetry mate [X, -Y, -Z + (1 0 0) & {-1 0 0}), symmetry operation in Coot], and vice versa. The same procedure was applied to swap the corresponding regions between chains B and C. The model was thereafter refined using Phenix with individual isotropic ADP factors, TLS refinement and NCS torsion restraints. The final model was refined to R and Rfree values of 21.1 and 24.4, respectively, and comprised residues L202-S377, residues N203-S377 and residues N203-S376 for chains A, B and C, respectively. The electron density for the structural model of chain A was of higher quality compared to the density for both chains B and C, which was corroborated by higher values for real-space correlation coefficients. This difference in the quality of the electron density map was also true for the crucial loop region around residue S314.
RfactorNum. reflection% reflectionSelection details
Rfree0.2436 2716 5.08 %Random selection
Rwork0.2113 ---
obs0.213 53477 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→48.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4013 0 7 207 4227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034116
X-RAY DIFFRACTIONf_angle_d0.8485589
X-RAY DIFFRACTIONf_dihedral_angle_d11.4761462
X-RAY DIFFRACTIONf_chiral_restr0.054625
X-RAY DIFFRACTIONf_plane_restr0.004705
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13820.34041430.30012662X-RAY DIFFRACTION100
2.1382-2.17930.31971530.29242636X-RAY DIFFRACTION100
2.1793-2.22380.2971350.2712631X-RAY DIFFRACTION100
2.2238-2.27220.27891180.25512657X-RAY DIFFRACTION100
2.2722-2.3250.3071390.25182670X-RAY DIFFRACTION100
2.325-2.38320.29931300.25312643X-RAY DIFFRACTION100
2.3832-2.44760.28031480.25992649X-RAY DIFFRACTION100
2.4476-2.51960.28951620.24792628X-RAY DIFFRACTION100
2.5196-2.60090.29191340.24322652X-RAY DIFFRACTION100
2.6009-2.69390.2871570.24532640X-RAY DIFFRACTION100
2.6939-2.80170.28341270.2342678X-RAY DIFFRACTION100
2.8017-2.92920.25841350.2372655X-RAY DIFFRACTION100
2.9292-3.08360.25471470.23372670X-RAY DIFFRACTION100
3.0836-3.27680.26361520.22332677X-RAY DIFFRACTION100
3.2768-3.52970.25641470.2052678X-RAY DIFFRACTION100
3.5297-3.88480.24481450.20212666X-RAY DIFFRACTION100
3.8848-4.44660.20731410.17952718X-RAY DIFFRACTION100
4.4466-5.60090.19841460.17062721X-RAY DIFFRACTION100
5.6009-48.37420.22531570.20842830X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0026-0.0152-0.0080.05510.01390.00280.04380.0207-0.04430.0508-0.0252-0.04170.29950.0918-00.31060.0046-0.01790.3284-0.08150.2672-51.29617.008722.6434
20.1408-0.0979-0.11260.3854-0.12810.27870.0220.0669-0.1806-0.1841-0.0355-0.15730.0970.0752-0.00760.3373-0.0659-0.00640.3636-0.07040.2525-43.03515.081713.871
30.0153-0.0138-0.00180.01020.004-0.0010.17180.01950.04910.13240.12920.115-0.0652-0.0290.00070.4016-0.0224-0.02210.3644-0.05490.2704-51.402321.259115.4708
40.00180.01740.00680.01590.0286-0.0006-0.01610.2551-0.0382-0.19380.0420.1153-0.01240.006700.5170.0028-0.04320.397-0.09220.3363-51.573110.70243.1139
50.07650.06-0.030.0459-0.03020.1461-0.0311-0.2202-0.00970.20550.0254-0.0005-0.0330.12390.00010.38170.04530.01540.3032-0.07630.2845-45.93-16.1798-10.1427
6-0.00070.0019-0.00020.0090.00360.00160.1818-0.02050.02730.05760.109-0.0919-0.1510.1118-00.5442-0.0898-0.01290.28330.01030.4944-39.9064-6.2541-11.256
70.18420.0725-0.19460.0297-0.08320.2367-0.25680.0042-0.1311-0.1262-0.2321-0.13180.2119-0.1251-0.06290.8184-0.0962-0.04290.5905-0.15010.5225-70.225-42.71231.1452
80.01870.0246-0.00850.0211-0.00250.0372-0.0282-0.0191-0.25710.0397-0.056-0.15090.2304-0.3653-00.7452-0.02810.07780.54780.08230.6072-63.8029-44.7408-5.4191
90.0313-0.0119-0.040.0226-0.01070.109-0.32210.1101-0.21780.07890.0819-0.09680.6174-0.18-00.7663-0.09-0.00260.7610.14190.6428-59.775-46.6513-10.2524
100.0013-0.0024-0.00240.0010.00280.0020.0592-0.10070.00970.24730.0202-0.13230.13470.006900.5109-0.1026-0.07560.7090.23980.5132-59.2674-35.8281-5.7634
110.0732-0.142-0.07480.26950.15770.0860.10130.13120.10720.02430.20210.0073-0.0048-0.3140.08380.3437-0.181-0.10440.68870.20090.5015-70.2761-38.7714-16.696
120.06930.04850.07890.07060.10190.5057-0.2446-0.3222-0.76420.1428-0.1021-0.11780.00170.6987-0.22830.0438-0.28710.22240.30810.50920.9384-94.6094-56.4001-26.922
130.00090.00240.00480.0009-0.00010.0064-0.0303-0.0052-0.12970.01180.1483-0.0116-0.00270.1674-00.3569-0.02210.07670.9410.39081.181-83.3873-58.8105-28.8435
140.67660.0480.01760.30780.15881.2447-0.571-0.56-1.1009-0.211-0.179-0.37680.18390.6406-1.16270.4434-0.08020.35540.49340.29130.9614-92.4908-57.4468-32.2286
150.0467-0.1026-0.0370.56850.22760.0749-0.2657-0.3786-0.39-0.035-0.09410.0548-0.06940.4255-0.09620.35-0.15750.02560.58410.1490.5103-95.7707-50.3619-25.2981
160.0250.0262-0.01280.04020.0050.0474-0.14440.3221-0.13570.0338-0.1134-0.19730.5281-0.4428-0.00050.615-0.14520.03830.64360.01770.6185-63.4687-44.8842-11.2711
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 203 through 219 )
2X-RAY DIFFRACTION2chain 'A' and (resid 220 through 286 )
3X-RAY DIFFRACTION3chain 'A' and (resid 287 through 300 )
4X-RAY DIFFRACTION4chain 'A' and (resid 301 through 319 )
5X-RAY DIFFRACTION5chain 'A' and (resid 320 through 363 )
6X-RAY DIFFRACTION6chain 'A' and (resid 364 through 378 )
7X-RAY DIFFRACTION7chain 'B' and (resid 204 through 219 )
8X-RAY DIFFRACTION8chain 'B' and (resid 220 through 246 )
9X-RAY DIFFRACTION9chain 'B' and (resid 247 through 286 )
10X-RAY DIFFRACTION10chain 'B' and (resid 287 through 300 )
11X-RAY DIFFRACTION11chain 'B' and (resid 301 through 319 )
12X-RAY DIFFRACTION12chain 'B' and (resid 320 through 363 )
13X-RAY DIFFRACTION13chain 'B' and (resid 364 through 378 )
14X-RAY DIFFRACTION14chain 'C' and (resid 204 through 286 )
15X-RAY DIFFRACTION15chain 'C' and (resid 287 through 319 )
16X-RAY DIFFRACTION16chain 'C' and (resid 320 through 377 )

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