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- PDB-1bu6: CRYSTAL STRUCTURES OF ESCHERICHIA COLI GLYCEROL KINASE AND THE MU... -

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Basic information

Entry
Database: PDB / ID: 1bu6
TitleCRYSTAL STRUCTURES OF ESCHERICHIA COLI GLYCEROL KINASE AND THE MUTANT A65T IN AN INACTIVE TETRAMER: CONFORMATIONAL CHANGES AND IMPLICATIONS FOR ALLOSTERIC REGULATION
ComponentsPROTEIN (GLYCEROL KINASE)
KeywordsTRANSFERASE / ALLOSTERY / COOPERATIVITY / GLYCEROL KINASE
Function / homology
Function and homology information


glycerol-3-phosphate metabolic process / glycerol kinase / glycerol kinase activity / glycerol metabolic process / glycerol catabolic process / DNA damage response / zinc ion binding / ATP binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function
FGGY family of carbohydrate kinases signature 1. / Glycerol kinase / FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain ...FGGY family of carbohydrate kinases signature 1. / Glycerol kinase / FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsFeese, M.D. / Faber, H.R. / Bystrom, C.E. / Pettigrew, D.W. / Remington, S.J.
Citation
Journal: Structure / Year: 1998
Title: Glycerol kinase from Escherichia coli and an Ala65-->Thr mutant: the crystal structures reveal conformational changes with implications for allosteric regulation.
Authors: Feese, M.D. / Faber, H.R. / Bystrom, C.E. / Pettigrew, D.W. / Remington, S.J.
#1: Journal: J.Bacteriol. / Year: 1996
Title: A Single Amino Acid Change in Escherichia Coli Glycerol Kinase Abolishes Glucose Control of Glycerol Utilization in Vivo
Authors: Pettigrew, D.W. / Liu, W.Z. / Holmes, C. / Meadow, N.D. / Roseman, S.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Cation Promoted Association (Cpa) of a Regulatory and Target Protein is Controlled by Protein Phosphorylation
Authors: Feese, M.D. / Pettigrew, D.W. / Meadow, N.D. / Roseman, S. / Remington, S.J.
#3: Journal: Biochemistry / Year: 1994
Title: Escherichia Coli Glycerol Kinase: Role of a Tetramer Interface in Regulation by Fructose-1,6-Bisphosphate and Phosphotransferase System Regulatory Protein Iiiglc
Authors: Liu, W.Z. / Faber, H.R. / Feese, M.D. / Remington, S.J. / Pettigrew, D.W.
#4: Journal: Science / Year: 1993
Title: Structure of the Regulatory Complex of Escherichia Coli III==Glc== with Glycerol Kinase
Authors: Hurley, J.H. / Faber, H.R. / Worthylake, D. / Meadow, N.D. / Roseman, S. / Pettigrew, D.W. / Remington, S.J.
History
DepositionAug 30, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
O: PROTEIN (GLYCEROL KINASE)
Y: PROTEIN (GLYCEROL KINASE)
Z: PROTEIN (GLYCEROL KINASE)
X: PROTEIN (GLYCEROL KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,71414
Polymers224,7704
Non-polymers94510
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12650 Å2
ΔGint-144 kcal/mol
Surface area64400 Å2
MethodPISA
2
O: PROTEIN (GLYCEROL KINASE)
Y: PROTEIN (GLYCEROL KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,8577
Polymers112,3852
Non-polymers4725
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
Z: PROTEIN (GLYCEROL KINASE)
X: PROTEIN (GLYCEROL KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,8577
Polymers112,3852
Non-polymers4725
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.900, 119.000, 109.300
Angle α, β, γ (deg.)90.00, 103.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PROTEIN (GLYCEROL KINASE)


Mass: 56192.379 Da / Num. of mol.: 4 / Mutation: A65T
Source method: isolated from a genetically manipulated source
Details: GLYCEROL SULPHATE / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GLPK / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6F3, glycerol kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.65 Å3/Da / Density % sol: 53.1 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: 20-22% (W/V) POLYETHYLENE GLYCOL MR 4000 0.2 M LISO4 0.1 M TRIS PH 8.5 - 8.8 CRYSTALLIZED BY HANGING DROP VAPOR DIFFUSION AT ROOM TEMPERATURE., vapor diffusion - hanging drop
PH range: 8.5-8.8 / Temp details: room temp
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Faber, H.R., (1989) J. Mol. Biol., 207, 637. / PH range low: 7 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110-30 mg/mlprotein1drop
250 mMsodium potassium phosphate1drop
310 mMglycerol1drop
42 mMbeta-mercaptoethanol1drop
5300-500 mM1reservoirNaCl
620 %(w/w)PEG15501reservoirPEG1550 to 20000
750 mMsodium potassium phosphate1reservoir
8100 mMADP1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Aug 15, 1994
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.37→20 Å / Num. obs: 69682 / % possible obs: 74 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 32.3 Å2 / Rmerge(I) obs: 0.068
Reflection
*PLUS
Lowest resolution: 37 Å / % possible obs: 74 % / Num. measured all: 132331

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Processing

Software
NameVersionClassification
FRFSUM(WOLFGANG KABSCH)model building
UNPUBLISHEDPROGRAMS BY SJRmodel building
TNT5F-6refinement
SDMSdata reduction
SDMSdata scaling
FRFSUM(WOLFGANG KABSCH)phasing
UNPUBLISHEDPROGRAMS BY SJRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GLF

1glf


Resolution: 2.37→20 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
Details: BSOL AND KSOL SET BY USER GLYCEROL KINASE EXISTS AT PHYSIOLOGICAL CONCENTRATIONS IN AN EQUILIBRIUM BETWEEN FUNCTIONAL DIMERS AND TETRAMERS. THE CRYSTAL ASYMMETRIC UNIT CONTAINS A TETRAMER OF ...Details: BSOL AND KSOL SET BY USER GLYCEROL KINASE EXISTS AT PHYSIOLOGICAL CONCENTRATIONS IN AN EQUILIBRIUM BETWEEN FUNCTIONAL DIMERS AND TETRAMERS. THE CRYSTAL ASYMMETRIC UNIT CONTAINS A TETRAMER OF GLYCEROL KINASE WITH NEARLY EXACT 222 POINT-GROUP SYMMETRY, UNLIKE THE PREVIOUSLY SUBMITTED GLYCEROL KINASE - FACTOR IIIGLC COMPLEX IN WHICH THE 222 POINT GROUP SYMMETRY WAS CRYSTALLOGRAPHICALLY ENFORCED
RfactorNum. reflection% reflection
Rwork0.167 --
obs-69682 74 %
Solvent computationSolvent model: TNT SOLVENT MODELING / Bsol: 300 Å2 / ksol: 0.8 e/Å3
Refinement stepCycle: LAST / Resolution: 2.37→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15621 0 54 140 15815
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.019159821.5
X-RAY DIFFRACTIONt_angle_deg2.928216203
X-RAY DIFFRACTIONt_dihedral_angle_d20.52895290
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0184172.2
X-RAY DIFFRACTIONt_gen_planes0.01923277.7
X-RAY DIFFRACTIONt_it9.34159381
X-RAY DIFFRACTIONt_nbd0.03274220
Software
*PLUS
Name: TNT / Version: 5F-6 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor obs: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeWeightDev ideal
X-RAY DIFFRACTIONt_bond_d1.5
X-RAY DIFFRACTIONt_angle_deg3
X-RAY DIFFRACTIONt_dihedral_angle_d0
X-RAY DIFFRACTIONt_planar_d2.20.018
X-RAY DIFFRACTIONt_plane_restr7.70.019

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