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- PDB-8b4a: Nativ complex of PqsE and RhlR with autoinducer C4-HSL -

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Basic information

Entry
Database: PDB / ID: 8b4a
TitleNativ complex of PqsE and RhlR with autoinducer C4-HSL
Components
  • 2-aminobenzoylacetyl-CoA thioesterase
  • Regulatory protein RhlR
KeywordsSIGNALING PROTEIN / QUORUM SENSING / LuxR-type TRANSCRIPTIONAL REGULATOR / PSEUDOMONAS / DNA BINDING PROTEIN / GENE REGULATION / C4-HSL / rhamnolipid / PQS / TRANSCRIPTION
Function / homology
Function and homology information


positive regulation of pyocyanine biosynthetic process / positive regulation of secondary metabolite biosynthetic process / 2-aminobenzoylacetyl-CoA thioesterase / quorum sensing / secondary metabolite biosynthetic process / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / positive regulation of proteolysis / positive regulation of lipid biosynthetic process / protein-DNA complex ...positive regulation of pyocyanine biosynthetic process / positive regulation of secondary metabolite biosynthetic process / 2-aminobenzoylacetyl-CoA thioesterase / quorum sensing / secondary metabolite biosynthetic process / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / positive regulation of proteolysis / positive regulation of lipid biosynthetic process / protein-DNA complex / signaling receptor activity / gene expression / transcription cis-regulatory region binding / hydrolase activity / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / metal ion binding / cytoplasm
Similarity search - Function
Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain superfamily / Autoinducer binding domain / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / : ...Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain superfamily / Autoinducer binding domain / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / N-[(3S)-2-oxotetrahydrofuran-3-yl]butanamide / 2-aminobenzoylacetyl-CoA thioesterase / HTH-type quorum-sensing regulator RhlR
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.06 Å
AuthorsBorgert, S.R. / Blankenfeldt, W.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)281361126/GRK2223 Germany
CitationJournal: Nat Commun / Year: 2022
Title: Moonlighting chaperone activity of the enzyme PqsE contributes to RhlR-controlled virulence of Pseudomonas aeruginosa.
Authors: Borgert, S.R. / Henke, S. / Witzgall, F. / Schmelz, S. / Zur Lage, S. / Hotop, S.K. / Stephen, S. / Lubken, D. / Kruger, J. / Gomez, N.O. / van Ham, M. / Jansch, L. / Kalesse, M. / Pich, A. ...Authors: Borgert, S.R. / Henke, S. / Witzgall, F. / Schmelz, S. / Zur Lage, S. / Hotop, S.K. / Stephen, S. / Lubken, D. / Kruger, J. / Gomez, N.O. / van Ham, M. / Jansch, L. / Kalesse, M. / Pich, A. / Bronstrup, M. / Haussler, S. / Blankenfeldt, W.
History
DepositionSep 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-aminobenzoylacetyl-CoA thioesterase
B: 2-aminobenzoylacetyl-CoA thioesterase
C: Regulatory protein RhlR
D: Regulatory protein RhlR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,64610
Polymers128,0804
Non-polymers5666
Water25214
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.875, 159.875, 285.731
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 1 and (name N or name...
d_2ens_1(chain "B" and (resid 1 through 266 or (resid 267...
d_1ens_2(chain "C" and ((resid 3 through 4 and (name N...
d_2ens_2chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METASPA4 - 304
d_12ens_1FEFEB
d_21ens_1METASPE1 - 301
d_22ens_1FEFEF
d_11ens_2ASNILEI3 - 241
d_12ens_2HL4HL4J
d_21ens_2ASNILEK1 - 239
d_22ens_2HL4HL4L

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.987375288856, -0.0816261361468, 0.135746870516), (-0.080065267812, -0.482265593607, -0.872358555935), (0.136673303345, -0.872213890695, 0.469641711342)-55.9373169087, -109.288743298, -59.5763151342
2given(-0.986303251433, -0.0829622243441, 0.142559340432), (-0.128989012291, -0.150716631843, -0.980125671327), (0.102799469458, -0.985089724958, 0.137951088657)-64.8029457044, -88.3209200313, -69.8373383046

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Components

#1: Protein 2-aminobenzoylacetyl-CoA thioesterase


Mass: 36428.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: pqsE, PA1000 / Production host: Escherichia coli (E. coli)
References: UniProt: P20581, 2-aminobenzoylacetyl-CoA thioesterase
#2: Protein Regulatory protein RhlR / Elastase modulator


Mass: 27611.596 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: rhlR, lasM, vsmR, PA3477 / Production host: Escherichia coli (E. coli) / References: UniProt: P54292
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-HL4 / N-[(3S)-2-oxotetrahydrofuran-3-yl]butanamide / N-butyryl-L-homoserine lactone


Mass: 171.194 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.56 Å3/Da / Density % sol: 65.49 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.1 M (NH4)2HPO4, 10 mM THPP (pH 7), 100 uM C4-HSL, Dropsize: 1 ul + 1 ul in 48-well MRC plates Cryoprotectant: 30% (w/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.032849 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.032849 Å / Relative weight: 1
ReflectionResolution: 3.06→142.87 Å / Num. obs: 26958 / % possible obs: 94.9 % / Redundancy: 10.7 % / Biso Wilson estimate: 105.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.037 / Net I/σ(I): 12.8
Reflection shellResolution: 3.06→3.37 Å / Redundancy: 11.2 % / Rmerge(I) obs: 1.59 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2450 / CC1/2: 0.63 / Rpim(I) all: 0.497 / % possible all: 70.7

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
PHENIX1.20_4459refinement
XDSdata reduction
STARANISOdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.06→56.52 Å / SU ML: 0.4758 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.1948
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2782 1319 4.9 %
Rwork0.2582 25617 -
obs0.2592 26936 76.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 121.77 Å2
Refinement stepCycle: LAST / Resolution: 3.06→56.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8598 0 28 14 8640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00248824
X-RAY DIFFRACTIONf_angle_d0.508911988
X-RAY DIFFRACTIONf_chiral_restr0.03851308
X-RAY DIFFRACTIONf_plane_restr0.00391561
X-RAY DIFFRACTIONf_dihedral_angle_d13.18643228
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.10028194131
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS1.57298615312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.06-3.180.4253310.4144467X-RAY DIFFRACTION12.92
3.18-3.330.4057670.38441390X-RAY DIFFRACTION37.83
3.33-3.50.42591150.38322086X-RAY DIFFRACTION57.05
3.5-3.720.38661420.35222919X-RAY DIFFRACTION78.53
3.72-4.010.34971890.31443610X-RAY DIFFRACTION98.55
4.01-4.410.31772000.26423690X-RAY DIFFRACTION99.97
4.41-5.050.27881710.24053753X-RAY DIFFRACTION99.95
5.05-6.360.24752050.26413765X-RAY DIFFRACTION100
6.36-56.520.21631990.20673937X-RAY DIFFRACTION99.61
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)
17.15829598267-2.72494641568-0.2089475370572.43101282801-0.851144801787.91482311452-0.373262218660.315018835480.278119073649-0.09857284943340.6703405225280.790113787705-0.469013032013-0.949574122085-0.01991160224810.608880325690.1234097599360.05754399972190.5519609569590.1117160077391.45017129819-52.3511416547-25.6411365131-44.298873748
27.64738457714-4.10024350594-2.701478563518.383170796091.471045829145.21825844662-0.6163715212430.143717765581-0.1204861896870.8965171597180.3966377594321.045696101020.0278936771362-0.196479858099-0.04351069284840.5876505657750.0150694264378-0.1241799828060.4426251545850.09747275802610.888070251167-46.9049256602-30.8412714268-39.0335446243
32.813322618271.58119765267-2.048990416011.68389319991-2.304087734083.12675668779-0.2333805561350.446943629552-1.35354513924-1.10708629472-0.2267587894570.4531053065360.472275488611-1.170460290830.02277627904281.292502056160.00174592351138-0.5066596102591.20336271367-0.6545634239941.24321103913-38.7003675158-30.068244391-68.5349099971
42.441052923471.030361326020.7271357795791.28929496688-0.6089548905471.195395453610.06932620772620.993957441671-0.497416041946-1.30802892922-0.13275408440.2014258412630.781187622637-0.214863039141-0.5012599519821.659532428740.0359645358658-0.5555464448151.243196404-0.5144895577150.520031610749-35.2304272908-19.9419455427-75.856544322
56.51338326038-0.861682604072-1.108518072896.462339747280.05888883145495.10427266752-0.526320564512-0.433151094433-0.6179623572470.919878725357-0.260966285001-0.921196485359-0.4264932023910.5263862998380.7208213633790.555673923213-0.0116202660709-0.2755102165150.5338643484980.1076982143090.9525144557855.01913305785-64.9844961218-24.8979459742
61.82953333136-0.440038571066-1.208998730273.07746825276-0.18737441092.66934087197-0.81171330333-1.211514958260.5846319053481.46415537125-0.176538107197-0.538162857-1.17206350506-0.009986334713960.9507676685831.66301036350.0927639194408-0.8137132339881.79628794221-0.1352859654811.478782549688.12533290655-58.9969695588-8.02609209128
78.50262182536-0.80324314758-1.622996673754.953647772390.3363206726753.71936673684-0.2820296905680.05633686029680.1182549594690.398445221028-0.112565034969-1.05077132119-0.4594262571810.4420740801080.2819907573390.564990942991-0.0307460671758-0.2971519254980.3200741631540.08812306499510.557875960012-2.66809887087-56.613556533-29.5114865761
88.28358959527-1.13147120264-1.934935122815.844289069480.127747485673.64162312153-0.24188757919-0.211413120648-0.1875269143120.8744532809410.01998439577290.330879226607-0.995207037819-0.2587314687110.1946061809720.7978019189620.172585413686-0.06340632682650.378559472909-0.0004779075674390.481473256115-17.915773586-56.8284044392-23.4871013256
96.50504001646-0.940601416944-0.5777779444962.19240290228-0.5674642163562.19295034844-0.208069980474-1.50697236431-0.01973991482431.799105537480.3213086902530.319654348511-0.110300880170.170653487806-0.377431526942.410733594120.6655758642410.2622868691151.339741244830.05789302648310.915027151148-20.1941684523-58.7072420087-5.65398122236
105.71094726638-1.457946113060.8443177420544.61119061724-1.353828242162.93954627009-1.23840447144-1.19094020849-0.1528031201841.478148579451.23121592968-0.366669255565-0.604210342023-0.298691426832-0.1081196896251.930668456550.393916693180.06730183667811.186252926460.06813391813720.722684921956-15.3490772906-52.6796553016-10.075536092
111.51568654237-0.5942316786380.4623404421591.46992894130.2465098408410.279748394191-0.199478812336-0.628211519695-0.2200633371530.8532022146550.1989897488091.23268256275-0.153086134906-0.1454968530940.06393911092411.638860667041.001116263661.167291560831.267043252640.7406400716212.03072440411-56.9224309456-53.0553615615-10.0728063753
120.576310460207-0.177652403867-0.1933964328520.199473470283-0.2341006255010.660867394688-0.35630623488-0.589317090482-1.136286913580.861081996120.7534920063391.74433210270.314544693536-0.9158291747580.2107426165110.830405496490.7321774395591.112626150560.9271669738350.6209439344792.86205425714-57.6643810811-61.2259041611-19.8119503721
133.28967641312-0.903121973515-0.2417069734552.714773377620.4059026304040.963610028888-0.481851975514-0.348403793941-1.406683789881.163631276870.6004667808651.424421699620.120485671407-0.000726464811913-0.08909221922171.005468989790.3444206325130.5780890778090.7843126442210.2097845341651.69969746573-36.026472133-65.835233605-20.9152405207
142.86460496163-0.343786944194-0.780847686814.62944570863-0.2498769931973.096339920830.08587396532580.0721063518377-0.1504955454680.3049768967190.00190861208605-0.117621174653-0.6924056427690.5869575534530.03405186411820.739332745628-0.0196121115401-0.1587572065580.762812853441-0.1449368314620.414979263676-21.7755569217-32.9770366185-40.2062387927
154.41699169006-1.8821428121-2.043880261923.41671945712-0.365066356624.33950540142-0.01739970893740.554929933095-0.241123222027-0.658345283340.1747896448290.47175807350.02050073146480.210450894546-0.04214273138650.786294302987-0.0177487087408-0.2360953391760.708122170242-0.2259339268980.409471114216-20.5371312795-38.6357419471-51.9497369965
162.72307186962-2.943146875232.420353077313.2566106225-2.67807112632.19555002157-0.262943283301-0.4193807338320.201929661779-0.3838263363440.0417207600361-0.0733044763425-0.181749051324-0.5260287419890.0845742871151.12295317275-0.0758626979572-0.24492075070.915667210155-0.1532949857420.5801485956-33.8941015208-11.9735221823-53.9135526307
170.676384346197-0.176232811705-0.8278014742882.285011373481.3656306781.771549830720.344802432310.548903346052-0.192592876796-0.44676538534-0.1120874670630.371076058597-0.5026909551010.361544792461-0.131996167441.375644764820.028976647174-0.5789357720370.9517517266580.011238806630.530095555739-38.0028870597-6.71734659078-63.2019140356
183.458742225340.2683403656611.105527955156.5006228545-1.849795459994.63264563111-0.04649810815070.205517422303-1.11717190537-0.9521435332140.4422912125721.232188813180.543023209569-0.386572898662-0.3423920973530.4655178779578.95616801353E-5-0.1841901966490.656637518871-0.129027119841.20594972403-46.3945666607-40.8675769842-44.9946160625
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(( chain 'D' and (resid 58 through 97 )) or ( chain 'D' and resid 301 ))DK - L58 - 30156
22chain 'D' and (resid 98 through 168 )DK98 - 16896 - 166
33chain 'D' and (resid 169 through 193 )DK169 - 193167 - 191
44chain 'D' and (resid 194 through 241 )DK194 - 241192 - 239
55(( chain 'A' and (resid -2 through 101 )) or ( chain 'A' and resid 603 ) or ( chain 'E' and resid 1 ) or ( chain 'E' and resid 2 ) or ( chain 'E' and resid 3 ))A - EA - M-2 - 31
66chain 'A' and (resid 102 through 128 )AA102 - 128105 - 131
77(( chain 'A' and (resid 129 through 187 )) or ( chain 'A' and resid 601 ) or ( chain 'A' and resid 602 ) or ( chain 'E' and resid 4 ) or ( chain 'E' and resid 6 ))A - EA - M129 - 6132
88(( chain 'A' and (resid 188 through 253 )) or ( chain 'E' and resid 5 ) or ( chain 'E' and resid 7 ) or ( chain 'E' and resid 8 ) or ( chain 'E' and resid 9 ))A - EA - M188 - 9191
99chain 'A' and (resid 254 through 273 )AA254 - 273257 - 276
1010chain 'A' and (resid 274 through 301 )AA274 - 301277 - 304
1111chain 'B' and (resid 1 through 54 )BE1 - 541 - 54
1212(( chain 'B' and (resid 55 through 187 )) or ( chain 'B' and resid 601 ) or ( chain 'B' and resid 602 ) or ( chain 'B' and resid 603 ))BE - H55 - 60355
1313(( chain 'B' and (resid 188 through 301 )) or ( chain 'E' and resid 10 ))B - EE - M188 - 10188
1414chain 'C' and (resid 1 through 57 )CI1 - 571 - 57
1515(( chain 'C' and (resid 58 through 169 )) or ( chain 'C' and resid 301 ))CI - J58 - 30158
1616chain 'C' and (resid 170 through 193 )CI170 - 193170 - 193
1717(( chain 'C' and (resid 194 through 241 )) or ( chain 'E' and resid 11 ))C - EI - M194 - 11194
1818chain 'D' and (resid 3 through 57 )DK3 - 571 - 55

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