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- PDB-4lrz: Crystal Structure of the E.coli DhaR(N)-DhaL complex -

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Basic information

Entry
Database: PDB / ID: 4lrz
TitleCrystal Structure of the E.coli DhaR(N)-DhaL complex
Components
  • PTS-dependent dihydroxyacetone kinase operon regulatory protein
  • PTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL
KeywordsTransferase/Transcription Regulator / coiled-coil / helix rotation / GAF / PAS / transcriptional regulation complex / Transferase-Transcription Regulator complex
Function / homology
Function and homology information


phosphoenolpyruvate-glycerone phosphotransferase / phosphoenolpyruvate-glycerone phosphotransferase activity / glycerone kinase activity / glycerol metabolic process / carbohydrate phosphorylation / transferase complex / glycerol catabolic process / pyruvate metabolic process / ADP binding / sequence-specific DNA binding ...phosphoenolpyruvate-glycerone phosphotransferase / phosphoenolpyruvate-glycerone phosphotransferase activity / glycerone kinase activity / glycerol metabolic process / carbohydrate phosphorylation / transferase complex / glycerol catabolic process / pyruvate metabolic process / ADP binding / sequence-specific DNA binding / DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / ATP hydrolysis activity / ATP binding / cytosol
Similarity search - Function
Dihydroxyacetone kinase, subunit L / DhaL domain / DhaL domain / DhaL domain superfamily / DAK2 domain / DhaL domain profile. / Dak2 / Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. ...Dihydroxyacetone kinase, subunit L / DhaL domain / DhaL domain / DhaL domain superfamily / DAK2 domain / DhaL domain profile. / Dak2 / Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / GAF domain / PAS domain / GAF domain / GAF domain / GAF-like domain superfamily / Beta-Lactamase / PAS fold / PAS fold / PAS domain / PAS domain / PAS domain superfamily / Homeobox-like domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PEP-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL / PTS-dependent dihydroxyacetone kinase operon regulatory protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.32 Å
AuthorsShi, R. / McDonald, L. / Cygler, M. / Ekiel, I.
CitationJournal: Structure / Year: 2014
Title: Coiled-Coil Helix Rotation Selects Repressing or Activating State of Transcriptional Regulator DhaR.
Authors: Shi, R. / McDonald, L. / Cygler, M. / Ekiel, I.
History
DepositionJul 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Data collection
Revision 1.2Mar 26, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL
B: PTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL
C: PTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL
D: PTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL
E: PTS-dependent dihydroxyacetone kinase operon regulatory protein
F: PTS-dependent dihydroxyacetone kinase operon regulatory protein
G: PTS-dependent dihydroxyacetone kinase operon regulatory protein
H: PTS-dependent dihydroxyacetone kinase operon regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,12920
Polymers230,2268
Non-polymers1,90312
Water8,017445
1
A: PTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL
B: PTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL
F: PTS-dependent dihydroxyacetone kinase operon regulatory protein
H: PTS-dependent dihydroxyacetone kinase operon regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,06510
Polymers115,1134
Non-polymers9526
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12610 Å2
ΔGint-100 kcal/mol
Surface area38500 Å2
MethodPISA
2
C: PTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL
D: PTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL
E: PTS-dependent dihydroxyacetone kinase operon regulatory protein
G: PTS-dependent dihydroxyacetone kinase operon regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,06510
Polymers115,1134
Non-polymers9526
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12560 Å2
ΔGint-103 kcal/mol
Surface area38700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.766, 91.500, 93.808
Angle α, β, γ (deg.)84.150, 72.420, 90.010
Int Tables number1
Space group name H-MP1
DetailsThe biological unit is a heterotetramer. There are 2 biological units in the asymmetric unit (chains A & B and chains C & D

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Components

#1: Protein
PTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL


Mass: 22666.660 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b1199, dhaL, dhaR, JW5186, ycgS / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P76014, Transferases; Transferring phosphorus-containing groups
#2: Protein
PTS-dependent dihydroxyacetone kinase operon regulatory protein


Mass: 34889.887 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b1201, dhaL, dhaR, JW5188, ycgU / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P76016
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 3.17 Å3/Da / Density % sol: 61.22 %
Crystal growTemperature: 295 K / Method: microbatch, sitting drop / pH: 6.5
Details: 30% (v/v) 2-ethoxyethanol, pH 6.5, microbatch, sitting drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.32→91 Å / Num. obs: 119216 / % possible obs: 97.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.09 / Χ2: 1.001 / Net I/σ(I): 9.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.32-2.43.40.588113170.999192.1
2.4-2.53.70.491117391.001196.5
2.5-2.613.90.373120161.001197.9
2.61-2.7540.279119821198.2
2.75-2.9240.208120321.001198.3
2.92-3.1540.141120231.001198.6
3.15-3.4740.096120771198.8
3.47-3.9740.075120671.001199
3.97-540.06121421.001199.3
5-503.90.046118211.001196.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→90.91 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.2614 / WRfactor Rwork: 0.2113 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8091 / SU B: 15.31 / SU ML: 0.166 / SU R Cruickshank DPI: 0.2706 / SU Rfree: 0.2214 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2474 6008 5 %RANDOM
Rwork0.1997 ---
obs0.2021 119153 97.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 122.71 Å2 / Biso mean: 45.984 Å2 / Biso min: 13.29 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å2-0.23 Å20.06 Å2
2---0.49 Å20.89 Å2
3---1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.32→90.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15367 0 116 445 15928
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02215769
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.96821414
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.97252018
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.18724.678667
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.016152695
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.541596
X-RAY DIFFRACTIONr_chiral_restr0.1260.22498
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111722
X-RAY DIFFRACTIONr_mcbond_it0.8131.510023
X-RAY DIFFRACTIONr_mcangle_it1.576216051
X-RAY DIFFRACTIONr_scbond_it2.7435746
X-RAY DIFFRACTIONr_scangle_it4.4524.55358
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 401 -
Rwork0.268 7683 -
all-8084 -
obs--88.64 %
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)
11.2325-0.15690.06590.5985-0.10841.32520.12260.06750.00570.0258-0.09060.09520.0408-0.0916-0.03210.0461-0.0191-0.00030.0453-0.04330.1716-73.202116.9407-13.3539
21.3947-0.2157-0.11430.71380.14091.43860.14590.0688-0.02960.032-0.1245-0.0993-0.05880.0805-0.02140.0634-0.0302-0.00260.07020.07060.1584-26.887229.6937-13.5219
31.19530.11290.11430.5918-0.03571.30260.1221-0.07730.0088-0.0146-0.1133-0.10970.0590.0733-0.00880.06520.02590.01930.05620.07030.167217.83862.5707-23.9038
41.35170.23-0.00980.9485-0.15951.53130.1218-0.1178-0.0136-0.0056-0.10580.1191-0.0398-0.0902-0.01590.04620.01930.01970.0563-0.03430.1725-28.303175.4213-23.8171
50.65950.31110.6751.44440.38410.85170.0874-0.06980.07840.0387-0.1368-0.0020.02680.00330.04940.0867-0.08130.0170.0889-0.01880.11381.38683.4316-4.3066
60.7285-0.3205-0.58491.60010.36371.05250.07530.0535-0.078-0.0454-0.13730.00410.0081-0.0070.0620.09030.08320.00420.0903-0.01530.115-43.49238.9108-33.0023
70.7210.3921-0.43631.4831-0.35341.31540.1197-0.1019-0.07080.0327-0.16250.01080.02420.01940.04280.1144-0.0918-0.00080.11140.0420.1042-11.782254.5894-4.3059
80.7725-0.41080.57281.3692-0.35191.16170.09260.07320.0741-0.0345-0.13430.0132-0.00930.01030.04160.09610.08160.02360.09040.04680.1103-56.784637.7542-33.1582
91.91190.424-0.02251.71671.16182.77060.02850.3563-0.2279-0.1358-0.15140.12690.0034-0.07480.12290.09440.07420.00180.1288-0.06290.1316-13.773462.6476-52.3532
102.09410.1550.13981.93661.36943.040.1055-0.41540.19730.1509-0.20110.2278-0.0551-0.04010.09570.1132-0.08330.04740.1237-0.06360.0843-58.676229.969914.9736
112.19530.6246-0.76991.6152-1.28182.75550.06730.30890.2024-0.0971-0.1436-0.1060.0008-0.00240.07630.08580.07610.07860.11720.10430.11583.844876.2258-51.9619
121.7836-0.0564-0.25542.2576-1.49362.90470.0985-0.3635-0.31010.1533-0.2744-0.1753-0.0720.13280.17590.0857-0.0913-0.04660.1670.12930.1344-41.612616.288214.3701
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 302
2X-RAY DIFFRACTION2B0 - 302
3X-RAY DIFFRACTION3C0 - 302
4X-RAY DIFFRACTION4D0 - 302
5X-RAY DIFFRACTION5E13 - 190
6X-RAY DIFFRACTION6F13 - 190
7X-RAY DIFFRACTION7G13 - 190
8X-RAY DIFFRACTION8H13 - 190
9X-RAY DIFFRACTION9E191 - 306
10X-RAY DIFFRACTION10F191 - 306
11X-RAY DIFFRACTION11G191 - 306
12X-RAY DIFFRACTION12H191 - 306

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