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- PDB-9f3m: Crystal structure of Kluyveromyces lactis glucokinase mutant H304... -

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Basic information

Entry
Database: PDB / ID: 9f3m
TitleCrystal structure of Kluyveromyces lactis glucokinase mutant H304Q in complex with fructose
ComponentsGlucokinase-1
KeywordsTRANSFERASE / sugar metabolism
Function / homology
Function and homology information


glucokinase / mannokinase activity / hexokinase / fructokinase activity / glucokinase activity / D-glucose binding / intracellular glucose homeostasis / glycolytic process / glucose metabolic process / mitochondrion ...glucokinase / mannokinase activity / hexokinase / fructokinase activity / glucokinase activity / D-glucose binding / intracellular glucose homeostasis / glycolytic process / glucose metabolic process / mitochondrion / ATP binding / cytosol
Similarity search - Function
Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. / ATPase, nucleotide binding domain
Similarity search - Domain/homology
beta-D-fructofuranose / MALONATE ION / Glucokinase-1
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsWeisse, R.H. / Strater, N.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: To be published
Title: Structural basis of hexose specificity and catalytic properties of Kluyveromyces lactis glucokinase KlGlk1
Authors: Weisse, R.H. / Kettner, K. / Lilie, H. / Funk, L. / Roedel, G. / Tittmann, K. / Strater, N. / Kriegel, T.M.
History
DepositionApr 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucokinase-1
B: Glucokinase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,90313
Polymers107,6242
Non-polymers1,27911
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, equilibrium of monomer and homodimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint37 kcal/mol
Surface area37680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.116, 207.116, 89.376
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and (resid 2 through 481 or resid 500 through 512))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERTYRTYRAA2 - 4812 - 481
d_12FRUFRUFRUFRUAC501
d_13MLIMLIMLIMLIAD502
d_14MLIMLIMLIMLIAE503
d_15MLIMLIMLIMLIAF504
d_21SERSERTYRTYRBB2 - 4812 - 481
d_22FRUFRUFRUFRUBH501
d_23MLIMLIMLIMLIAG505
d_24MLIMLIMLIMLIBI502
d_25MLIMLIMLIMLIBJ503

NCS oper: (Code: givenMatrix: (-0.998055558117, 0.0483515221151, 0.0393348855574), (-0.0610857987174, -0.884247259824, -0.463006812788), (0.0123946806217, -0.464509325851, 0.885481483765)Vector: 39. ...NCS oper: (Code: given
Matrix: (-0.998055558117, 0.0483515221151, 0.0393348855574), (-0.0610857987174, -0.884247259824, -0.463006812788), (0.0123946806217, -0.464509325851, 0.885481483765)
Vector: 39.0255091512, 120.700115669, 28.2408864164)

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Components

#1: Protein Glucokinase-1 / Glucose kinase 1 / GLK-1 / Hexokinase GLK1


Mass: 53812.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Strain: JA6 / Gene: GLK1, KLLA0C01155g / Production host: Kluyveromyces lactis (yeast) / Strain (production host): JA6 / References: UniProt: Q6CUZ3, glucokinase, hexokinase
#2: Sugar ChemComp-FRU / beta-D-fructofuranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DFrufbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructofuranoseCOMMON NAMEGMML 1.0
b-D-FrufIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 4.45 Å3/Da / Density % sol: 72.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: droplet: 1:1 mixture of protein and reservoir protein supplemented with: 9.8 mM fructose 9.8 mM DTT reservoir solution: 1.4 M sodium malonate pH 6.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.6→73.23 Å / Num. obs: 58352 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 94.84 Å2 / CC1/2: 0.997 / Net I/σ(I): 7.9
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 0.2 / Num. unique obs: 4493 / CC1/2: 0.349 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALS1.dev.877-g8f078f0data reduction
Aimless0.5.31data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.6→51.78 Å / SU ML: 0.4221 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.2732
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2584 1458 2.62 %
Rwork0.2475 54280 -
obs0.2478 55738 95.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 120.23 Å2
Refinement stepCycle: LAST / Resolution: 2.6→51.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7536 0 87 35 7658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00187760
X-RAY DIFFRACTIONf_angle_d0.487810495
X-RAY DIFFRACTIONf_chiral_restr0.03751196
X-RAY DIFFRACTIONf_plane_restr0.00291366
X-RAY DIFFRACTIONf_dihedral_angle_d12.94082862
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.43414172477 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.690.35921150.39154123X-RAY DIFFRACTION72.86
2.69-2.80.3471610.37475342X-RAY DIFFRACTION95.04
2.8-2.930.35751540.38745588X-RAY DIFFRACTION98.97
2.93-3.080.37451250.38315637X-RAY DIFFRACTION99.09
3.08-3.280.41741540.3495543X-RAY DIFFRACTION98.48
3.28-3.530.3271350.3275538X-RAY DIFFRACTION97.49
3.53-3.880.35311340.30715508X-RAY DIFFRACTION96.56
3.88-4.440.25551530.24115540X-RAY DIFFRACTION97.58
4.45-5.60.22261490.21375677X-RAY DIFFRACTION99.13
5.6-51.780.20581780.1885784X-RAY DIFFRACTION99.75
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)
13.962935875960.9180380983341.009525380614.237495239450.7588105937093.559399918440.30710187128-0.406118150128-0.04819866209650.07872948811830.1367368921080.7363820309490.256069314893-0.651090676928-0.4129840272280.564586617720.148286522843-0.1331365246041.019183438580.05800961499830.9339367030934.0769109604970.44210886099.07015450113
22.27831994984-0.6469897269840.3787323957453.26268709385-0.08668087935783.742319070950.00345051729054-0.3969900961040.0378228629116-0.5934985886640.293678577710.5823199753880.0994629968356-0.514262577438-0.2827812024240.906514257817-0.051759611142-0.4674023489971.12472907524-0.03033237641911.21699864044-5.7455465433470.8422124138-14.8473744982
33.15165537216-0.912694502838-0.2051227445173.29943431308-0.573170703822.705218039150.4712673679770.165964199126-0.368068950114-0.539539596759-0.1301168351230.2679737260180.4592593735740.0936131095267-0.3307024235060.970509973940.478139821964-0.2310357305840.952045342368-0.201381358170.6515288802838.606566535953.88737358213.65149262274
43.23991871377-0.102661803895-1.656603963153.080026665911.771459711595.526369564220.257703894136-0.1112973900980.387798509523-0.6435018238630.00120153014022-0.0836149899092-0.281931690715-0.171920831082-0.2707333926380.9881835296620.4650554554440.0876405312960.9575865917580.06270914211970.68795907490447.818552986265.4303953053-17.9840521487
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain A and (resi 2:63 or resi 205:463)AA2 - 4632 - 462
22chain A and (resi 64:204 or resi 464:481)AA64 - 48163 - 480
33chain B and (resi 2:63 or resi 205:463)BG2 - 4632 - 462
44chain B and (resi 64:204 or resi 464:481)BG64 - 48163 - 480

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