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- PDB-3nek: Crystal structure of a nitrogen repressor-like protein MJ0159 fro... -

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Basic information

Entry
Database: PDB / ID: 3nek
TitleCrystal structure of a nitrogen repressor-like protein MJ0159 from Methanococcus jannaschii
Componentsnitrogen repressor-like protein MJ0159
Keywordsstructural genomics / unknown function / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


mj0159-like / NrpR domain superfamily / NrpR repressor / NrpR regulatory domains NRD1 and 2 / Ribonuclease R winged-helix domain / Ribonuclease R winged-helix domain / NrpR regulatory domain / Winged helix DNA-binding domain superfamily / Alpha-Beta Plaits / Winged helix-like DNA-binding domain superfamily ...mj0159-like / NrpR domain superfamily / NrpR repressor / NrpR regulatory domains NRD1 and 2 / Ribonuclease R winged-helix domain / Ribonuclease R winged-helix domain / NrpR regulatory domain / Winged helix DNA-binding domain superfamily / Alpha-Beta Plaits / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Global nitrogen regulator NrpR
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsBonanno, J.B. / Patskovsky, Y. / Malashkevich, V. / Ozyurt, S. / Dickey, M. / Wu, B. / Maletic, M. / Rodgers, L. / Koss, J. / Sauder, J.M. ...Bonanno, J.B. / Patskovsky, Y. / Malashkevich, V. / Ozyurt, S. / Dickey, M. / Wu, B. / Maletic, M. / Rodgers, L. / Koss, J. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Structure / Year: 2010
Title: Structural underpinnings of nitrogen regulation by the prototypical nitrogen-responsive transcriptional factor NrpR.
Authors: Goragot Wisedchaisri / David M Dranow / Thomas J Lie / Jeffrey B Bonanno / Yury Patskovsky / Sinem A Ozyurt / J Michael Sauder / Steven C Almo / Stephen R Wasserman / Stephen K Burley / John ...Authors: Goragot Wisedchaisri / David M Dranow / Thomas J Lie / Jeffrey B Bonanno / Yury Patskovsky / Sinem A Ozyurt / J Michael Sauder / Steven C Almo / Stephen R Wasserman / Stephen K Burley / John A Leigh / Tamir Gonen /
Abstract: Plants and microorganisms reduce environmental inorganic nitrogen to ammonium, which then enters various metabolic pathways solely via conversion of 2-oxoglutarate (2OG) to glutamate and glutamine. ...Plants and microorganisms reduce environmental inorganic nitrogen to ammonium, which then enters various metabolic pathways solely via conversion of 2-oxoglutarate (2OG) to glutamate and glutamine. Cellular 2OG concentrations increase during nitrogen starvation. We recently identified a family of 2OG-sensing proteins--the nitrogen regulatory protein NrpR--that bind DNA and repress transcription of nitrogen assimilation genes. We used X-ray crystallography to determine the structure of NrpR regulatory domain. We identified the NrpR 2OG-binding cleft and show that residues predicted to interact directly with 2OG are conserved among diverse classes of 2OG-binding proteins. We show that high levels of 2OG inhibit NrpRs ability to bind DNA. Electron microscopy analyses document that NrpR adopts different quaternary structures in its inhibited 2OG-bound state compared with its active apo state. Our results indicate that upon 2OG release, NrpR repositions its DNA-binding domains correctly for optimal interaction with DNA thereby enabling gene repression.
History
DepositionJun 9, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionJun 23, 2010ID: 2QYX
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _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: nitrogen repressor-like protein MJ0159
B: nitrogen repressor-like protein MJ0159
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6905
Polymers54,4132
Non-polymers2763
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-6 kcal/mol
Surface area20490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.009, 80.009, 116.421
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A321 - 539
2116B321 - 539
Detailsprobable dimer

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Components

#1: Protein nitrogen repressor-like protein MJ0159


Mass: 27206.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0159 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q57623
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 1.98 Å3/Da / Density % sol: 37.78 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: 100mM sodium MES pH 7.0, 40% MPD, vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 25, 2007
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 15446 / Num. obs: 15322 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 51.47 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 7.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1 / Rsym value: 0.59 / % possible all: 98.8

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345CCDdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXCDphasing
SHELXEmodel building
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→33.15 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.259 / WRfactor Rwork: 0.233 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.909 / SU B: 27.562 / SU ML: 0.278 / SU R Cruickshank DPI: 1.955 / SU Rfree: 0.348 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.348
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 785 5.1 %RANDOM
Rwork0.246 ---
obs0.247 15303 99.3 %-
all-15411 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 98.77 Å2 / Biso mean: 55.556 Å2 / Biso min: 19.78 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å20.75 Å20 Å2
2--1.49 Å20 Å2
3----2.24 Å2
Refinement stepCycle: LAST / Resolution: 2.5→33.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3507 0 18 14 3539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223580
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.9794814
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0075439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.91925.03165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.78715677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5861518
X-RAY DIFFRACTIONr_chiral_restr0.0750.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212634
X-RAY DIFFRACTIONr_mcbond_it0.4881.52181
X-RAY DIFFRACTIONr_mcangle_it0.95523529
X-RAY DIFFRACTIONr_scbond_it1.34331399
X-RAY DIFFRACTIONr_scangle_it2.2474.51285
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1741 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.55
LOOSE THERMAL1.9510
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 60 -
Rwork0.312 1053 -
all-1113 -
obs-1053 98.9 %
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)
12.6418-0.4923-1.19411.6964-0.18813.3975-0.0746-0.14280.03440.01360.09370.140.15340.1517-0.01910.00330.0339-0.05320.0263-0.00110.2191-18.709-19.558-13.408
23.21630.1227-0.00542.7040.56812.0329-0.09760.2161-0.1822-0.1367-0.0018-0.1553-0.01490.03640.0993-0.0218-0.02360.0180.04790.02810.2294-6.178-28.46-44.811
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A321 - 540
2X-RAY DIFFRACTION2B319 - 539

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