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- PDB-2j5t: Glutamate 5-kinase from Escherichia coli complexed with glutamate -

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Basic information

Entry
Database: PDB / ID: 2j5t
TitleGlutamate 5-kinase from Escherichia coli complexed with glutamate
ComponentsGLUTAMATE 5-KINASE
KeywordsTRANSFERASE / PROLINE BIOSYNTHESIS / FEEDBACK REGULATION
Function / homology
Function and homology information


proline binding / glutamate 5-kinase / glutamate 5-kinase activity / proline biosynthetic process / L-proline biosynthetic process / phosphorylation / magnesium ion binding / protein homodimerization activity / RNA binding / ATP binding ...proline binding / glutamate 5-kinase / glutamate 5-kinase activity / proline biosynthetic process / L-proline biosynthetic process / phosphorylation / magnesium ion binding / protein homodimerization activity / RNA binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
Glutamate 5-kinase / Glutamate-5-kinase domain / Glutamate 5-kinase/delta-1-pyrroline-5-carboxylate synthase / Glutamate 5-kinase, conserved site / Glutamate 5-kinase signature. / PUA domain / PUA domain / Glutamate/acetylglutamate kinase / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase ...Glutamate 5-kinase / Glutamate-5-kinase domain / Glutamate 5-kinase/delta-1-pyrroline-5-carboxylate synthase / Glutamate 5-kinase, conserved site / Glutamate 5-kinase signature. / PUA domain / PUA domain / Glutamate/acetylglutamate kinase / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain profile. / PUA domain superfamily / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / PUA-like superfamily / Roll / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / Glutamate 5-kinase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMarco-Marin, C. / Gil-Ortiz, F. / Perez-Arellano, I. / Cervera, J. / Fita, I. / Rubio, V.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: A Novel Two-Domain Architecture within the Amino Acid Kinase Enzyme Family Revealed by the Crystal Structure of Escherichia Coli Glutamate 5-Kinase.
Authors: Marco-Marin, C. / Gil-Ortiz, F. / Perez-Arellano, I. / Cervera, J. / Fita, I. / Rubio, V.
History
DepositionSep 19, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_conn.ptnr2_label_seq_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_ncs_dom_lim.end_label_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTAMATE 5-KINASE
B: GLUTAMATE 5-KINASE
C: GLUTAMATE 5-KINASE
D: GLUTAMATE 5-KINASE
E: GLUTAMATE 5-KINASE
F: GLUTAMATE 5-KINASE
G: GLUTAMATE 5-KINASE
H: GLUTAMATE 5-KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)316,15356
Polymers312,7158
Non-polymers3,43848
Water1,856103
1
A: GLUTAMATE 5-KINASE
B: GLUTAMATE 5-KINASE
C: GLUTAMATE 5-KINASE
D: GLUTAMATE 5-KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,08828
Polymers156,3584
Non-polymers1,73024
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11380 Å2
ΔGint-55.8 kcal/mol
Surface area67810 Å2
MethodPISA
2
E: GLUTAMATE 5-KINASE
F: GLUTAMATE 5-KINASE
G: GLUTAMATE 5-KINASE
H: GLUTAMATE 5-KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,06528
Polymers156,3584
Non-polymers1,70824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13900 Å2
ΔGint-44.1 kcal/mol
Surface area67750 Å2
MethodPISA
3
A: GLUTAMATE 5-KINASE
B: GLUTAMATE 5-KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,07415
Polymers78,1792
Non-polymers89513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-96.6 kcal/mol
Surface area28370 Å2
MethodPISA
4
G: GLUTAMATE 5-KINASE
H: GLUTAMATE 5-KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,85612
Polymers78,1792
Non-polymers67710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-71.3 kcal/mol
Surface area27950 Å2
MethodPISA
5
E: GLUTAMATE 5-KINASE
F: GLUTAMATE 5-KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,21016
Polymers78,1792
Non-polymers1,03114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-83 kcal/mol
Surface area29210 Å2
MethodPISA
6
C: GLUTAMATE 5-KINASE
D: GLUTAMATE 5-KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,01413
Polymers78,1792
Non-polymers83511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-84.4 kcal/mol
Surface area28590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.302, 124.108, 144.927
Angle α, β, γ (deg.)90.00, 93.96, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 3 - 367 / Label seq-ID: 3 - 367

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH

NCS oper:
IDCodeMatrixVector
1given(0.66619, -0.73797, -0.1077), (-0.73427, -0.67431, 0.07849), (-0.13054, 0.02679, -0.99108)-11.40808, -62.97409, 229.03127
2given(-0.72894, 0.6755, -0.11113), (0.67664, 0.68628, -0.26677), (-0.10394, -0.26965, -0.95733)118.03104, -13.79059, 208.95186
3given(-0.96598, 0.05816, 0.252), (0.0324, -0.93949, 0.34104), (0.25658, 0.3376, 0.90564)-8.38251, -72.63773, 19.70603
4given(-0.97127, -0.02003, 0.23712), (0.07398, -0.9725, 0.22086), (0.22617, 0.23206, 0.94604)53.74158, -127.41484, 8.55533
5given(-0.68675, 0.69979, -0.19668), (0.70834, 0.58351, -0.3972), (-0.16319, -0.41209, -0.89641)36.20375, -0.11562, 205.43961
6given(0.99999, -0.00464, 0.00166), (0.0047, 0.99901, -0.04425), (-0.00145, 0.04426, 0.99902)65.06425, -58.88403, 7.47517
7given(0.64914, -0.75674, -0.07716), (-0.75337, -0.65361, 0.07227), (-0.10512, 0.01122, -0.9944)74.88105, -66.88284, 211.58546
DetailsCONTACTS BETWEEN DIMERS ARE WEAK, BUT GEL FILTRATION EXPERIMENTS SHOW THAT THE PROTEIN IS TETRAMERIC AND THE TETRAMERS FORMED IN THE CRYSTAL ARE EQUIVALENT TO THOSE FOUNDIN A DIFFERENT CRYSTAL OF THIS PROTEIN (WITH DIFFERENT SPACEGROUP).

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
GLUTAMATE 5-KINASE / / GAMMA-GLUTAMYL KINASE / GK


Mass: 39089.430 Da / Num. of mol.: 8 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A7B5, glutamate 5-kinase

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Non-polymers , 5 types, 151 molecules

#2: Chemical
ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ILE 129 TO VAL ENGINEERED RESIDUE IN CHAIN B, ILE 129 TO VAL ...ENGINEERED RESIDUE IN CHAIN A, ILE 129 TO VAL ENGINEERED RESIDUE IN CHAIN B, ILE 129 TO VAL ENGINEERED RESIDUE IN CHAIN C, ILE 129 TO VAL ENGINEERED RESIDUE IN CHAIN D, ILE 129 TO VAL ENGINEERED RESIDUE IN CHAIN E, ILE 129 TO VAL ENGINEERED RESIDUE IN CHAIN F, ILE 129 TO VAL ENGINEERED RESIDUE IN CHAIN G, ILE 129 TO VAL ENGINEERED RESIDUE IN CHAIN H, ILE 129 TO VAL

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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: 2.77 Å3/Da / Density % sol: 55.2 %
Crystal growpH: 6.5 / Details: 1.45 M MGSO4, 20 MM CACL2, 0.1 M MES PH 6.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 6, 2005 / Details: TOROIDAL MIRRORS
RadiationMonochromator: SI(111) AND SI (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 74908 / % possible obs: 99.3 % / Observed criterion σ(I): 2.9 / Redundancy: 4.5 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 9.7
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.9 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PARTIALLY-REFINED MODEL OF PBD ENTRY 2J5V

2j5v


Resolution: 2.9→25 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.874 / SU B: 35.798 / SU ML: 0.302 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.401 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FINAL STRUCTURE ENCOMPASSES THE ENTIRE POLYPEPTIDE CHAIN FROM RESIDUE 3 IN SUBUNITS D AND E, BUT LACKS THE FOLLOWING RESIDUES IN THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FINAL STRUCTURE ENCOMPASSES THE ENTIRE POLYPEPTIDE CHAIN FROM RESIDUE 3 IN SUBUNITS D AND E, BUT LACKS THE FOLLOWING RESIDUES IN THE OTHER SUBUNITS, 202-211 (A), 202-213 AND 367 (B), 203-211 (G AND C), 176-185 AND 196- 213 (H), 203-213 (F).
RfactorNum. reflection% reflectionSelection details
Rfree0.246 3771 5 %RANDOM
Rwork0.197 ---
obs0.199 70989 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.57 Å2
Baniso -1Baniso -2Baniso -3
1--2.13 Å20 Å20.38 Å2
2--3.82 Å20 Å2
3----1.63 Å2
Refinement stepCycle: LAST / Resolution: 2.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21321 0 188 103 21612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02121752
X-RAY DIFFRACTIONr_bond_other_d0.0020.0220630
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.97129455
X-RAY DIFFRACTIONr_angle_other_deg0.745347605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.79652826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.9623.516930
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.532153669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.68215205
X-RAY DIFFRACTIONr_chiral_restr0.0610.23471
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0224490
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024227
X-RAY DIFFRACTIONr_nbd_refined0.1980.24369
X-RAY DIFFRACTIONr_nbd_other0.1760.220330
X-RAY DIFFRACTIONr_nbtor_refined0.1640.210448
X-RAY DIFFRACTIONr_nbtor_other0.0830.212845
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2455
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.246
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1850.2156
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.521.518189
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.538222421
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.77438407
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.2814.57034
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4994 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.410.5
2Bmedium positional0.420.5
3Cmedium positional0.370.5
4Dmedium positional0.340.5
5Emedium positional0.370.5
6Fmedium positional0.290.5
7Gmedium positional0.380.5
8Hmedium positional0.340.5
1Amedium thermal0.242
2Bmedium thermal0.162
3Cmedium thermal0.182
4Dmedium thermal0.22
5Emedium thermal0.212
6Fmedium thermal0.212
7Gmedium thermal0.232
8Hmedium thermal0.172
LS refinement shellResolution: 2.9→2.97 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.345 267
Rwork0.276 5142
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)
11.6457-0.005-0.19540.15810.11870.7771-0.01080.0140.0629-0.0070.0028-0.0159-0.05930.0310.008-0.14390.0250.0236-0.24370.012-0.175867.3903-61.973993.8984
21.8786-0.6032-0.1361.09510.53311.1709-0.1266-0.766-0.03430.35850.1464-0.07920.29480.2119-0.0198-0.01910.0877-0.02930.12170.0185-0.106469.4179-62.4212125.6015
30.3697-0.108-0.39641.01220.45041.61280.0783-0.06610.13640.0299-0.14080.1667-0.2369-0.28320.0625-0.01010.03490.0339-0.0769-0.0629-0.045216.2667-36.2343128.7095
41.55480.30990.1010.4060.11010.5380.0180.04230.23680.0054-0.0460.13970.0038-0.190.028-0.0830.0345-0.0035-0.092-0.0283-0.043710.7729-44.567298.1857
51.4779-0.2524-0.13530.5120.22970.97780.00380.2297-0.0919-0.0353-0.08190.15170.0551-0.10430.078-0.11620.0195-0.0251-0.1365-0.0444-0.0759-53.93518.943789.7171
61.6093-0.7610.17121.162-0.13451.3058-0.155-0.23460.06010.13210.09880.0937-0.1777-0.0450.0563-0.03550.02940.0013-0.1808-0.0156-0.1485-47.021931.7435118.5264
72.3663-0.27670.01350.18280.08070.5812-0.0911-0.0748-0.03720.0395-0.01430.04860.00410.06890.1054-0.10950.04370.0343-0.2154-0.0012-0.152.22120.782486.3597
82.0187-1.6088-0.16331.29930.08430.6212-0.366-0.89210.06760.43920.3804-0.22310.15220.1026-0.01440.09780.1918-0.02310.2121-0.03950.07834.24631.5253117.0851
90.0025-0.01150.00340.0542-0.01610.0048-0.0060.0378-0.02550.056-0.00010.0299-0.0124-0.02210.0061-0.0002-0.0012-0.00010.00060.00010.000414.1423-20.4832103.1232
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 367
2X-RAY DIFFRACTION2B3 - 367
3X-RAY DIFFRACTION3C3 - 367
4X-RAY DIFFRACTION4D3 - 367
5X-RAY DIFFRACTION5E3 - 367
6X-RAY DIFFRACTION6F3 - 367
7X-RAY DIFFRACTION7G3 - 367
8X-RAY DIFFRACTION8H3 - 367
9X-RAY DIFFRACTION9A2001 - 2017
10X-RAY DIFFRACTION9B2001 - 2008
11X-RAY DIFFRACTION9C2001 - 2010
12X-RAY DIFFRACTION9D2001 - 2014
13X-RAY DIFFRACTION9E2001 - 2014
14X-RAY DIFFRACTION9F2001 - 2012
15X-RAY DIFFRACTION9G2001 - 2013
16X-RAY DIFFRACTION9H2001 - 2015

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