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- PDB-4ly6: Nucleotide-induced asymmetry within ATPase activator ring drives ... -

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Basic information

Entry
Database: PDB / ID: 4ly6
TitleNucleotide-induced asymmetry within ATPase activator ring drives s54-RNAP interaction and ATP hydrolysis
ComponentsTranscriptional regulator (NtrC family)
KeywordsTRANSCRIPTION REGULATOR / AAA+ ATPase / bacterial enhancer binding protein / s54-dependent transcription activator / molecular machine / sigma54 / s54-RNAP
Function / homology
Function and homology information


phosphorelay signal transduction system / sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding
Similarity search - Function
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 / Helicase, Ruva Protein; domain 3 - #60 ...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 / Helicase, Ruva Protein; domain 3 - #60 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Helicase, Ruva Protein; domain 3 / Homeobox-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-08T / ADENOSINE-5'-DIPHOSPHATE / Transcriptional regulator (NtrC family)
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.6 Å
AuthorsSysoeva, T.A. / Chowdhury, S. / Guo, L. / Nixon, B.T.
Citation
Journal: Genes Dev / Year: 2013
Title: Nucleotide-induced asymmetry within ATPase activator ring drives σ54-RNAP interaction and ATP hydrolysis.
Authors: Tatyana A Sysoeva / Saikat Chowdhury / Liang Guo / B Tracy Nixon /
Abstract: It is largely unknown how the typical homomeric ring geometry of ATPases associated with various cellular activities enables them to perform mechanical work. Small-angle solution X-ray scattering, ...It is largely unknown how the typical homomeric ring geometry of ATPases associated with various cellular activities enables them to perform mechanical work. Small-angle solution X-ray scattering, crystallography, and electron microscopy (EM) reconstructions revealed that partial ATP occupancy caused the heptameric closed ring of the bacterial enhancer-binding protein (bEBP) NtrC1 to rearrange into a hexameric split ring of striking asymmetry. The highly conserved and functionally crucial GAFTGA loops responsible for interacting with σ54-RNA polymerase formed a spiral staircase. We propose that splitting of the ensemble directs ATP hydrolysis within the oligomer, and the ring's asymmetry guides interaction between ATPase and the complex of σ54 and promoter DNA. Similarity between the structure of the transcriptional activator NtrC1 and those of distantly related helicases Rho and E1 reveals a general mechanism in homomeric ATPases whereby complex allostery within the ring geometry forms asymmetric functional states that allow these biological motors to exert directional forces on their target macromolecules.
#1: Journal: To Be Published
Title: Crystallization and preliminary X-ray analysis of a sigma54-dependent transcription activator NtrC1 from Aquifex aeolicus bound to ground state ATP analog
Authors: Sysoeva, T.A. / Yennawar, N. / Allaire, M. / Nixon, B.T.
History
DepositionJul 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_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: Transcriptional regulator (NtrC family)
B: Transcriptional regulator (NtrC family)
C: Transcriptional regulator (NtrC family)
D: Transcriptional regulator (NtrC family)
E: Transcriptional regulator (NtrC family)
F: Transcriptional regulator (NtrC family)
G: Transcriptional regulator (NtrC family)
H: Transcriptional regulator (NtrC family)
I: Transcriptional regulator (NtrC family)
J: Transcriptional regulator (NtrC family)
K: Transcriptional regulator (NtrC family)
L: Transcriptional regulator (NtrC family)
M: Transcriptional regulator (NtrC family)
N: Transcriptional regulator (NtrC family)
O: Transcriptional regulator (NtrC family)
P: Transcriptional regulator (NtrC family)
Q: Transcriptional regulator (NtrC family)
R: Transcriptional regulator (NtrC family)
S: Transcriptional regulator (NtrC family)
T: Transcriptional regulator (NtrC family)
U: Transcriptional regulator (NtrC family)
V: Transcriptional regulator (NtrC family)
W: Transcriptional regulator (NtrC family)
X: Transcriptional regulator (NtrC family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)748,74366
Polymers737,55824
Non-polymers11,18542
Water00
1
A: Transcriptional regulator (NtrC family)
B: Transcriptional regulator (NtrC family)
C: Transcriptional regulator (NtrC family)
D: Transcriptional regulator (NtrC family)
E: Transcriptional regulator (NtrC family)
F: Transcriptional regulator (NtrC family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,97216
Polymers184,3906
Non-polymers2,58310
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18210 Å2
ΔGint-95 kcal/mol
Surface area61580 Å2
MethodPISA
2
G: Transcriptional regulator (NtrC family)
H: Transcriptional regulator (NtrC family)
I: Transcriptional regulator (NtrC family)
J: Transcriptional regulator (NtrC family)
K: Transcriptional regulator (NtrC family)
L: Transcriptional regulator (NtrC family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,39917
Polymers184,3906
Non-polymers3,01011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18110 Å2
ΔGint-100 kcal/mol
Surface area62610 Å2
MethodPISA
3
M: Transcriptional regulator (NtrC family)
N: Transcriptional regulator (NtrC family)
O: Transcriptional regulator (NtrC family)
P: Transcriptional regulator (NtrC family)
Q: Transcriptional regulator (NtrC family)
R: Transcriptional regulator (NtrC family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,97216
Polymers184,3906
Non-polymers2,58310
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17770 Å2
ΔGint-100 kcal/mol
Surface area61820 Å2
MethodPISA
4
S: Transcriptional regulator (NtrC family)
T: Transcriptional regulator (NtrC family)
U: Transcriptional regulator (NtrC family)
V: Transcriptional regulator (NtrC family)
W: Transcriptional regulator (NtrC family)
X: Transcriptional regulator (NtrC family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,39917
Polymers184,3906
Non-polymers3,01011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18020 Å2
ΔGint-104 kcal/mol
Surface area62860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.339, 130.037, 206.368
Angle α, β, γ (deg.)90.00, 89.73, 89.90
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain segments: (Selection details: chain 'X')

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Components

#1: Protein ...
Transcriptional regulator (NtrC family)


Mass: 30731.598 Da / Num. of mol.: 24 / Fragment: UNP residues 121-387
Source method: isolated from a genetically manipulated source
Details: Met plus residues 121-387 / Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: aq_1117, ntrC1 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL2 (DE3) Rosetta / References: UniProt: O67198
#2: Chemical
ChemComp-08T / [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium


Mass: 492.201 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C10H14BeF3N5O10P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 4.34 Å3/Da / Density % sol: 71.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 20% ethylene glycol, pH 7.9, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→37.86 Å / Num. all: 143704 / Num. obs: 109790 / % possible obs: 76.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.66 % / Biso Wilson estimate: 102.03 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.6-3.731.50.3631.2144.3
3.73-3.881.630.3181.4177.3
3.88-4.051.590.2341.8154.9
4.05-4.271.670.2042.3180.2
4.27-4.531.670.1323.7180.4
4.53-4.881.690.1084.6181.9
4.88-5.371.670.1034.8184.6
5.37-6.151.660.0935.6186.7
6.15-7.741.710.0697.5189.4
7.74-37.861.660.03813.4184.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREK9.7 W8RSSIdata scaling
d*TREK9.7 W8RSSIdata reduction
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→37.855 Å / Occupancy max: 1 / Occupancy min: 0.36 / SU ML: 0.57 / σ(F): 1.96 / Phase error: 37.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3077 5517 5.04 %
Rwork0.2578 --
obs0.2603 109504 76.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 161.7593 Å2
Refinement stepCycle: LAST / Resolution: 3.6→37.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47496 0 694 0 48190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0149110
X-RAY DIFFRACTIONf_angle_d1.08766063
X-RAY DIFFRACTIONf_dihedral_angle_d14.03918990
X-RAY DIFFRACTIONf_chiral_restr0.0387240
X-RAY DIFFRACTIONf_plane_restr0.0048302
Refine LS restraints NCSNumber: 29753 / Type: POSITIONAL / Rms dev position: 12.501 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5998-3.64070.48311720.423427X-RAY DIFFRACTION76
3.6407-3.68350.4584400.3899864X-RAY DIFFRACTION22
3.6835-3.72840.4199990.40031717X-RAY DIFFRACTION40
3.7284-3.77550.42381920.35813565X-RAY DIFFRACTION79
3.7755-3.82520.44632150.34953612X-RAY DIFFRACTION79
3.8252-3.87750.39191650.34543245X-RAY DIFFRACTION72
3.8775-3.93280.4849300.3449632X-RAY DIFFRACTION14
3.9328-3.99150.41191720.33083129X-RAY DIFFRACTION69
3.9915-4.05380.36792100.29683706X-RAY DIFFRACTION81
4.0538-4.12020.36361820.30743615X-RAY DIFFRACTION79
4.1202-4.19110.37621920.29973663X-RAY DIFFRACTION81
4.1911-4.26720.36991880.2983636X-RAY DIFFRACTION80
4.2672-4.34920.35991910.28933640X-RAY DIFFRACTION81
4.3492-4.43780.32481820.26983687X-RAY DIFFRACTION80
4.4378-4.53420.30871780.26293679X-RAY DIFFRACTION81
4.5342-4.63950.3311850.24243688X-RAY DIFFRACTION81
4.6395-4.75530.32621800.23463749X-RAY DIFFRACTION82
4.7553-4.88360.28471960.24533742X-RAY DIFFRACTION83
4.8836-5.0270.29882000.23263824X-RAY DIFFRACTION83
5.027-5.18890.31422000.2243862X-RAY DIFFRACTION85
5.1889-5.37380.29442180.24363818X-RAY DIFFRACTION86
5.3738-5.58830.28942120.24723916X-RAY DIFFRACTION86
5.5883-5.84180.28932080.24043901X-RAY DIFFRACTION86
5.8418-6.14860.31662440.25653963X-RAY DIFFRACTION88
6.1486-6.5320.31282010.25434042X-RAY DIFFRACTION88
6.532-7.03330.27872180.24654064X-RAY DIFFRACTION90
7.0333-7.73570.25612410.23284101X-RAY DIFFRACTION90
7.7357-8.84260.25911890.22633873X-RAY DIFFRACTION85
8.8426-11.0940.22392180.20873835X-RAY DIFFRACTION85
11.094-37.85720.28021990.23743792X-RAY DIFFRACTION83

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