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- PDB-5ya2: Crystal structure of LsrK-HPr complex with ADP -

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Basic information

Entry
Database: PDB / ID: 5ya2
TitleCrystal structure of LsrK-HPr complex with ADP
Components
  • Autoinducer-2 kinase
  • Phosphocarrier protein HPr
KeywordsSTRUCTURAL PROTEIN / Quorum sensing / LsrK / HPr / complex / ADP binding
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 activator activity / enzyme regulator activity / carbohydrate metabolic process / phosphorylation / 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 / PTS HPr component phosphorylation site ...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
ADENOSINE-5'-DIPHOSPHATE / HEXANE-1,6-DIOL / PHOSPHATE ION / Phosphocarrier protein HPr / Autoinducer-2 kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 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 30, 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)137,62914
Polymers135,9684
Non-polymers1,66110
Water1,08160
1
A: Autoinducer-2 kinase
C: Phosphocarrier protein HPr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9098
Polymers67,9842
Non-polymers9256
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Autoinducer-2 kinase
D: Phosphocarrier protein HPr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7196
Polymers67,9842
Non-polymers7354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.251, 101.251, 344.149
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 2 types, 4 molecules ABCD

#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 (strain K12) (bacteria)
Strain: K12 / Gene: lsrK, ydeV, b1511, JW1504 / Production host: Escherichia coli (E. coli) / 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 (strain K12) (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

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Non-polymers , 4 types, 70 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL / 1,6-Hexanediol


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


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


Mass: 18.015 Da / Num. of mol.: 60 / 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: 3.75 Å3/Da / Density % sol: 67.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 5~20%(v/v) PEG-400, 0.1M sodium phosphate-citrate (pH 4.2), 0.2M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.701→46.316 Å / Num. obs: 55508 / % possible obs: 96.9 % / Redundancy: 7 % / Net I/σ(I): 25.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
PHENIX1.9_1692data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.701→46.316 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 28.82
RfactorNum. reflection% reflection
Rfree0.2546 1990 3.59 %
Rwork0.2137 --
obs0.2152 55484 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.701→46.316 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8526 0 100 60 8686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058784
X-RAY DIFFRACTIONf_angle_d0.97811942
X-RAY DIFFRACTIONf_dihedral_angle_d15.0193154
X-RAY DIFFRACTIONf_chiral_restr0.0361370
X-RAY DIFFRACTIONf_plane_restr0.0051532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7008-2.76840.40571300.38753482X-RAY DIFFRACTION91
2.7684-2.84320.41751340.37063710X-RAY DIFFRACTION95
2.8432-2.92680.32891360.34333691X-RAY DIFFRACTION95
2.9268-3.02130.38511430.32243732X-RAY DIFFRACTION96
3.0213-3.12930.33761340.29453755X-RAY DIFFRACTION96
3.1293-3.25450.30411410.27473805X-RAY DIFFRACTION96
3.2545-3.40260.29581430.25363779X-RAY DIFFRACTION98
3.4026-3.58190.26371480.22893869X-RAY DIFFRACTION98
3.5819-3.80620.22281420.19963849X-RAY DIFFRACTION99
3.8062-4.10.22421450.18413855X-RAY DIFFRACTION98
4.1-4.51220.25861410.16683886X-RAY DIFFRACTION98
4.5122-5.16440.18041450.1593933X-RAY DIFFRACTION98
5.1644-6.50380.26461480.18384000X-RAY DIFFRACTION99
6.5038-46.32270.20091600.17644148X-RAY DIFFRACTION98
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)
16.1785-1.8636-1.75182.1527-0.07112.52420.21940.3541-1.2076-0.1045-0.0657-0.6041.0030.97420.01620.80510.5325-0.07311.1396-0.11020.75880.0808-23.95336.2956
25.16610.6798-0.46451.8689-0.38032.84670.1419-0.0127-0.34420.0388-0.0273-0.00160.46850.2772-0.12910.57980.2706-0.00940.484-0.11330.358757.2888-16.718838.6738
31.2377-0.65590.14781.46180.61821.81190.15690.53710.0606-0.4889-0.140.09550.10410.7096-0.07960.60670.68140.10761.206-0.13030.446567.8531-18.231211.9479
40.77030.62191.63953.60471.77247.7967-0.20660.36940.4226-0.86030.4840.1346-0.84630.8613-0.45610.56350.14630.08151.27020.04270.604875.517-8.66315.009
54.4705-2.31831.14481.49690.10952.31310.21370.57641.1579-0.1482-0.07110.4301-1.024-1.01770.00090.74160.56910.04641.18570.1430.801421.134123.950936.3443
64.98530.84810.27711.81760.52032.77310.14280.04280.37390.0639-0.02090.0504-0.5235-0.2586-0.10950.59830.27390.01130.47690.11990.363943.955816.733738.6691
71.0759-0.5859-0.21531.3172-0.66661.88680.05230.5983-0.0522-0.4445-0.0737-0.074-0.1445-0.8997-0.1310.60150.6577-0.15151.21690.1510.411433.412418.21911.9564
81.2330.4274-1.64513.6858-1.60962.5261-0.28950.3992-0.3398-0.7690.4076-0.02830.6851-0.4584-0.19650.50740.1112-0.10051.3619-0.02040.586125.68718.69715.0615
95.6853-0.8907-4.12498.45932.20143.27140.40140.105-1.59470.2353-1.46590.0481.3121-2.86560.76180.785-0.3865-0.20511.0517-0.0040.776930.3172-21.945449.7964
107.321-3.3002-6.19647.40950.73536.47520.28070.3105-0.2153-1.07720.03130.3990.0004-0.9353-0.32140.5814-0.06-0.0740.81220.00720.422636.2624-13.356346.6349
118.6991-3.2972-0.96265.6316-0.28134.64430.1955-0.545-0.36171.01110.0983-0.20771.4147-0.5153-0.28520.5853-0.1816-0.0580.5587-0.04940.360338.1053-20.178249.9568
121.90840.34761.49548.72154.32345.20040.07151.240.0718-0.7715-0.90591.53150.1617-1.80770.95060.4406-0.202-0.09871.5271-0.17710.731327.71-13.62849.9003
137.6255-0.67065.86867.0798-1.03874.55220.24280.27321.66180.0184-1.1264-0.0228-1.55493.14270.68210.7854-0.45510.28161.1566-0.09550.770870.973721.934349.7548
144.9493-1.98165.99432.0885-2.62177.77220.13340.24940.2049-1.1608-0.2549-0.5960.07731.62080.09140.63850.00570.15780.84260.01810.487464.986813.335746.7406
158.2324-3.55911.40795.57261.34083.19180.1691-0.45760.4690.9279-0.04170.1007-1.49330.7531-0.21570.6356-0.20790.0960.61030.02540.377263.135320.18549.96
165.2791-0.6789-0.48846.2779-5.52885.75130.25060.6274-0.4251-0.7237-1.2499-1.8974-0.28493.07650.91520.6376-0.17410.05541.44760.11180.683273.558213.703649.9511
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 504 )
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 504 )
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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