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- PDB-2rd5: Structural basis for the regulation of N-acetylglutamate kinase b... -

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Basic information

Entry
Database: PDB / ID: 2rd5
TitleStructural basis for the regulation of N-acetylglutamate kinase by PII in Arabidopsis thaliana
Components
  • Acetylglutamate kinase-like protein
  • PII protein
KeywordsPROTEIN BINDING / protein-protein complex / regulation of arginine biosynthesis / nitrogen metabolism / Kinase / Transferase / Transcription / Transcription regulation
Function / homology
Function and homology information


regulation of arginine biosynthetic process via ornithine / acetylglutamate kinase regulator activity / anthocyanin-containing compound biosynthetic process / regulation of fatty acid biosynthetic process / acetylglutamate kinase activity / acetylglutamate kinase / chloroplast thylakoid / response to sucrose / arginine biosynthetic process via ornithine / regulation of nitrogen utilization ...regulation of arginine biosynthetic process via ornithine / acetylglutamate kinase regulator activity / anthocyanin-containing compound biosynthetic process / regulation of fatty acid biosynthetic process / acetylglutamate kinase activity / acetylglutamate kinase / chloroplast thylakoid / response to sucrose / arginine biosynthetic process via ornithine / regulation of nitrogen utilization / arginine biosynthetic process / arginine binding / plastid / chloroplast stroma / nitrogen compound metabolic process / response to light stimulus / enzyme regulator activity / chloroplast / phosphorylation / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
N-Acetyl-L-glutamate kinase, cyclic / Acetylglutamate kinase ArgB / Acetylglutamate kinase family / Glutamate/acetylglutamate kinase / Nitrogen regulatory protein P-II / Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / P-II protein family profile. / Nitrogen regulatory protein PII / Nitrogen regulatory protein P-II ...N-Acetyl-L-glutamate kinase, cyclic / Acetylglutamate kinase ArgB / Acetylglutamate kinase family / Glutamate/acetylglutamate kinase / Nitrogen regulatory protein P-II / Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / P-II protein family profile. / Nitrogen regulatory protein PII / Nitrogen regulatory protein P-II / Acetylglutamate kinase-like / Carbamate kinase / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acetylglutamate kinase, chloroplastic / ADENOSINE-5'-DIPHOSPHATE / ARGININE / N-ACETYL-L-GLUTAMATE / ADENOSINE-5'-TRIPHOSPHATE / Nitrogen regulatory protein P-II homolog
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsMizuno, Y. / Moorhead, G.B.G. / Ng, K.K.S.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural Basis for the Regulation of N-Acetylglutamate Kinase by PII in Arabidopsis thaliana.
Authors: Mizuno, Y. / Moorhead, G.B. / Ng, K.K.
History
DepositionSep 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylglutamate kinase-like protein
B: Acetylglutamate kinase-like protein
C: PII protein
D: PII protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,73915
Polymers92,0684
Non-polymers2,67011
Water1,15364
1
A: Acetylglutamate kinase-like protein
B: Acetylglutamate kinase-like protein
C: PII protein
D: PII protein
hetero molecules

A: Acetylglutamate kinase-like protein
B: Acetylglutamate kinase-like protein
C: PII protein
D: PII protein
hetero molecules

A: Acetylglutamate kinase-like protein
B: Acetylglutamate kinase-like protein
C: PII protein
D: PII protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,21645
Polymers276,20512
Non-polymers8,01133
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
MethodPISA
Unit cell
Length a, b, c (Å)171.133, 171.133, 171.133
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11D-1003-

HOH

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Acetylglutamate kinase-like protein


Mass: 31254.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: T8H10.160 / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-Gami pLysRARE / References: UniProt: Q9SCL7, acetylglutamate kinase
#2: Protein PII protein / P II nitrogen sensing protein GLB I / At4g01900


Mass: 14779.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT4g01900, T7B11.16 / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-Gami pLysRARE / References: UniProt: Q9ZST4

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Non-polymers , 6 types, 75 molecules

#3: Chemical ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#4: 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
#5: Chemical ChemComp-NLG / N-ACETYL-L-GLUTAMATE / N-Acetylglutamic acid


Mass: 189.166 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11NO5
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 4.54 Å3/Da / Density % sol: 72.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 8.5% PEG 8000, 8.5% PEG 1000, 0.1 M Na-HEPES, 0.4 M TMAO, 50 mM L-aginine, 2 mM DTT, 12% (w/v) glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.3361 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 24, 2007 / Details: vertically focusing mirror
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3361 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 57349 / Num. obs: 57349 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 17.7 % / Biso Wilson estimate: 61.9 Å2 / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 38
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 3.2 / Num. unique all: 5692 / Rsym value: 0.95 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MxDCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 2BUF, 2O66
Resolution: 2.51→40 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / SU B: 12.315 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.239 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22928 2907 5.1 %RANDOM
Rwork0.20116 ---
all0.20261 54380 --
obs0.20261 54380 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 67.497 Å2
Refinement stepCycle: LAST / Resolution: 2.51→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6095 0 169 64 6328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226348
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2912.0138572
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4415811
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95524.052232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.505151136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7131546
X-RAY DIFFRACTIONr_chiral_restr0.080.21007
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024560
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.190.22527
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.24328
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2185
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.2144
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.80224158
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.6682.56491
X-RAY DIFFRACTIONr_scbond_it4.23.52445
X-RAY DIFFRACTIONr_scangle_it5.7594.52081
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.51→2.572 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 221 -
Rwork0.262 3987 -
obs-4206 99.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.8031-0.2990.06181.87850.00240.4131-0.0130.25990.0368-0.31760.02760.0449-0.02740.0224-0.0146-0.04410.0903-0.0378-0.039-0.0915-0.130886.650748.250545.387
21.0816-0.3490.18431.8145-0.33420.9519-0.01770.11830.0083-0.02160.0182-0.18120.06250.175-0.0005-0.1331-0.03-0.0693-0.11240.0985-0.168779.710693.325148.3085
32.0039-0.44020.6741.1982-0.43012.0778-0.00540.04890.29610.00140.004-0.2775-0.12850.32840.0014-0.1439-0.0923-0.0442-0.1059-0.0105-0.078395.649992.183180.7885
42.5274-0.26270.80881.4496-0.2851.75850.00950.415-0.0705-0.27930.00220.07270.25660.0343-0.0117-0.0064-0.0583-0.1055-0.0217-0.1294-0.119151.840845.307136.2927
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA17 - 29618 - 297
2X-RAY DIFFRACTION2BB15 - 29616 - 297
3X-RAY DIFFRACTION3CC5 - 1296 - 130
4X-RAY DIFFRACTION4DD5 - 1306 - 131

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