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- PDB-5ya0: Crystal structure of LsrK and HPr complex -

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Basic information

Entry
Database: PDB / ID: 5ya0
TitleCrystal structure of LsrK and HPr complex
Components
  • Autoinducer-2 kinase
  • Phosphocarrier protein HPr
KeywordsSTRUCTURAL PROTEIN / quorum sensing
Function / homology
Function and homology information


autoinducer-2 kinase / autoinducer-2 kinase activity / phosphotransferase activity, nitrogenous group as acceptor / regulation of carbon utilization / antisigma factor binding / positive regulation of glycogen catabolic process / quorum sensing / phosphoenolpyruvate-dependent sugar phosphotransferase system / single-species biofilm formation / enzyme inhibitor activity ...autoinducer-2 kinase / autoinducer-2 kinase activity / phosphotransferase activity, nitrogenous group as acceptor / regulation of carbon utilization / antisigma factor binding / positive regulation of glycogen catabolic process / quorum sensing / phosphoenolpyruvate-dependent sugar phosphotransferase system / single-species biofilm formation / enzyme inhibitor activity / enzyme regulator activity / enzyme activator activity / carbohydrate metabolic process / cytosol / cytoplasm
Similarity search - Function
Autoinducer-2 kinase / : / Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / HPr-like / Histidine-containing Protein; Chain: A; / Phosphocarrier protein HPr-like / HPr-like superfamily ...Autoinducer-2 kinase / : / Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / HPr-like / Histidine-containing Protein; Chain: A; / Phosphocarrier protein HPr-like / HPr-like superfamily / : / PTS HPr component phosphorylation site / PTS HPR domain profile. / Carbohydrate kinase, FGGY / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
HEXANE-1,6-DIOL / PHOSPHATE ION / Phosphocarrier protein HPr / Autoinducer-2 kinase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.997 Å
AuthorsRyu, K.S. / Ha, J.H.
CitationJournal: Sci Adv / Year: 2018
Title: Evidence of link between quorum sensing and sugar metabolism inEscherichia colirevealed via cocrystal structures of LsrK and HPr
Authors: Ha, J.H. / Hauk, P. / Cho, K. / Eo, Y. / Ma, X. / Stephens, K. / Cha, S. / Jeong, M. / Suh, J.Y. / Sintim, H.O. / Bentley, W.E. / Ryu, K.S.
History
DepositionAug 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: Autoinducer-2 kinase
B: Autoinducer-2 kinase
C: Phosphocarrier protein HPr
D: Phosphocarrier protein HPr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,77512
Polymers135,9684
Non-polymers8068
Water59433
1
A: Autoinducer-2 kinase
C: Phosphocarrier protein HPr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3876
Polymers67,9842
Non-polymers4034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-14 kcal/mol
Surface area23670 Å2
MethodPISA
2
B: Autoinducer-2 kinase
D: Phosphocarrier protein HPr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3876
Polymers67,9842
Non-polymers4034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-15 kcal/mol
Surface area23620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.156, 101.156, 344.323
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Autoinducer-2 kinase / AI-2 kinase


Mass: 58854.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: lsrK, ydeV, b1511, JW1504 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P77432, autoinducer-2 kinase
#2: Protein Phosphocarrier protein HPr / Histidine-containing protein


Mass: 9129.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: ptsH, hpr, b2415, JW2408 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AA04, Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases
#3: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.73 Å3/Da / Density % sol: 67.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 5~20% (v/v) PEG-400, 0.1 M sodium phosphate-citrate (pH 4.2), and 0.2 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 41480 / % possible obs: 98.3 % / Redundancy: 9.8 % / Net I/σ(I): 22.2
Reflection shellResolution: 2.9972→3.0721 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
HKL-20001.9_1692data scaling
PHENIXphasing
PHENIXrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.997→48.004 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 23.72
RfactorNum. reflection% reflection
Rfree0.2387 1991 4.8 %
Rwork0.1988 --
obs0.2007 41468 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.997→48.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8578 0 46 33 8657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058784
X-RAY DIFFRACTIONf_angle_d0.97311934
X-RAY DIFFRACTIONf_dihedral_angle_d13.9243146
X-RAY DIFFRACTIONf_chiral_restr0.0381366
X-RAY DIFFRACTIONf_plane_restr0.0041538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9972-3.07210.33881390.33012729X-RAY DIFFRACTION96
3.0721-3.15520.34121350.31072729X-RAY DIFFRACTION98
3.1552-3.2480.35371380.27622748X-RAY DIFFRACTION98
3.248-3.35280.2631400.27352756X-RAY DIFFRACTION98
3.3528-3.47260.28581400.24262790X-RAY DIFFRACTION98
3.4726-3.61160.27641440.22592793X-RAY DIFFRACTION99
3.6116-3.77590.25461390.22432772X-RAY DIFFRACTION99
3.7759-3.97490.23121410.18952804X-RAY DIFFRACTION98
3.9749-4.22380.20591460.17022825X-RAY DIFFRACTION99
4.2238-4.54970.19191370.15192828X-RAY DIFFRACTION99
4.5497-5.00710.18941470.15112824X-RAY DIFFRACTION98
5.0071-5.73060.24931400.17962870X-RAY DIFFRACTION99
5.7306-7.2160.20871490.20262942X-RAY DIFFRACTION100
7.216-48.01040.23211560.17953067X-RAY DIFFRACTION99
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)
17.0639-1.4930.91113.79990.37473.2980.12520.33040.8339-0.082-0.02840.4834-1.202-1.1953-0.11460.92790.57140.0981.14280.12670.788621.10323.776736.5211
24.95221.0717-0.83172.01950.46244.45390.24610.15490.3501-0.1301-0.0192-0.1324-0.6501-0.2656-0.26330.76250.3020.03430.49840.10560.542843.883916.628338.6487
31.2895-0.5053-0.4760.9019-0.09142.02590.18150.57530.02-0.2401-0.1516-0.0016-0.2784-0.57350.00130.70570.4752-0.05131.08040.09220.713533.530218.271912.0495
48.80690.7304-6.27633.5624-1.36634.9718-0.40390.9119-0.3873-0.67330.0869-0.09570.8953-1.00490.10360.62330.2128-0.05920.93450.03190.777526.47628.848214.4792
56.8128-0.5374-1.88912.6518-0.83333.45440.1040.3663-0.8656-0.04460.0207-0.50751.38851.3105-0.0460.86180.5965-0.11231.1958-0.14080.824280.0587-23.77336.4674
65.31550.94110.32591.8888-0.77894.18360.22860.1117-0.3353-0.1225-0.04690.08760.65090.3412-0.1680.79930.2915-0.05290.4883-0.11890.525557.2581-16.647938.6565
71.48-0.97810.46550.6304-0.13961.67460.1910.5695-0.0498-0.2397-0.2056-0.05380.30090.4902-0.00240.70730.46380.06691.0782-0.11270.674767.6249-18.29612.0648
83.7780.51913.25684.26732.43533.8164-0.35150.69670.2777-0.69710.22570.1614-0.70440.8512-0.22890.5870.17280.05121.1267-0.00810.78774.6554-8.847814.3912
96.314-2.52651.91587.7086-5.51784.42940.6764-0.26011.47840.498-1.99330.1043-0.82563.39290.87731.0648-0.32980.08871.006-0.02390.711970.936421.954649.7037
107.6029-3.73475.44043.1773-4.54356.5117-0.07640.23740.2013-0.75340.4726-0.39490.61070.4561-0.51370.77520.0151-0.00280.765-0.07720.523864.851413.255246.6531
116.8412-4.50432.90168.9022-0.21396.36960.125-0.33540.06481.41460.05120.3165-1.43780.6776-0.09150.6232-0.16560.10630.63260.01960.505963.087720.080249.9727
123.8742.0189-3.63241.4505-1.99233.90810.41440.4698-0.5785-0.075-1.1119-1.7661-2.19052.69160.64281.1011-0.2010.00861.46660.0140.8773.555113.555850.1632
138.2251-3.5702-3.97294.535.20665.91690.4588-0.1887-1.8730.6367-1.91150.0810.6589-3.1110.99680.8361-0.2628-0.14310.79790.07920.792730.2532-21.956749.7192
146.1337-2.9605-4.36748.19294.04773.6654-0.08540.29130.0056-0.29660.49870.4001-0.8534-0.2989-0.52540.7140.01830.02950.77720.01070.565636.2294-13.25846.6394
159.5292-6.6339-1.69919.3011-1.86473.14520.2576-0.235-0.35291.46780.0524-0.21391.4088-0.7529-0.38470.7263-0.2723-0.08290.6982-0.09930.515638.0824-20.061949.993
163.74632.73843.81821.99272.76273.92250.06531.23180.5711-0.0888-0.83691.77741.7265-2.6620.65481.018-0.1222-0.02741.6251-0.13320.906127.6654-13.53650.2002
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 91 )
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 239 )
3X-RAY DIFFRACTION3chain 'A' and (resid 240 through 455 )
4X-RAY DIFFRACTION4chain 'A' and (resid 456 through 505 )
5X-RAY DIFFRACTION5chain 'B' and (resid 10 through 91 )
6X-RAY DIFFRACTION6chain 'B' and (resid 92 through 239 )
7X-RAY DIFFRACTION7chain 'B' and (resid 240 through 455 )
8X-RAY DIFFRACTION8chain 'B' and (resid 456 through 505 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 15 )
10X-RAY DIFFRACTION10chain 'C' and (resid 16 through 37 )
11X-RAY DIFFRACTION11chain 'C' and (resid 38 through 69 )
12X-RAY DIFFRACTION12chain 'C' and (resid 70 through 85 )
13X-RAY DIFFRACTION13chain 'D' and (resid 1 through 15 )
14X-RAY DIFFRACTION14chain 'D' and (resid 16 through 37 )
15X-RAY DIFFRACTION15chain 'D' and (resid 38 through 69 )
16X-RAY DIFFRACTION16chain 'D' and (resid 70 through 85 )

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