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- PDB-9f3j: Crystal structure of Kluyveromyces lactis glucokinase in complex ... -

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Basic information

Entry
Database: PDB / ID: 9f3j
TitleCrystal structure of Kluyveromyces lactis glucokinase in complex with mannose
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
alpha-D-mannopyranose / MALONATE ION / Glucokinase-1
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.35 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)109,12715
Polymers107,6442
Non-polymers1,48313
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, in solution exists an equilibrium of monomer and homodimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint37 kcal/mol
Surface area37100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.890, 187.890, 92.151
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_1(chain "A" and (resid 2 through 109 or resid 111...
d_2ens_1(chain "B" and (resid 2 through 109 or resid 111...

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_11SERSERPHEPHEAA2 - 1092 - 109
d_12ASPASPASPASPAA111 - 112111 - 112
d_13HISHISTRPTRPAA114 - 168114 - 168
d_14LYSLYSTYRTYRAA173 - 481173 - 481
d_15MANMANMANMANAC501
d_16MLIMLIMLIMLIAD502
d_17MLIMLIMLIMLIAE503
d_18MLIMLIMLIMLIAF504
d_19MLIMLIMLIMLIAG505
d_110MLIMLIMLIMLIBI501
d_21SERSERPHEPHEBB2 - 1092 - 109
d_22ASPASPASPASPBB111 - 112111 - 112
d_23HISHISTRPTRPBB114 - 168114 - 168
d_24LYSLYSTYRTYRBB173 - 481173 - 481
d_25MANMANMANMANBJ502
d_26MLIMLIMLIMLIBK503
d_27MLIMLIMLIMLIBL504
d_28MLIMLIMLIMLIBM505
d_29MLIMLIMLIMLIBN506
d_210MLIMLIMLIMLIBO507

NCS oper: (Code: givenMatrix: (-0.792057654424, -0.00533371604862, -0.610422987397), (-0.0177082884111, -0.999340245738, 0.0317094586691), (-0.610189387478, 0.0359252657701, 0.791440640028)Vector: - ...NCS oper: (Code: given
Matrix: (-0.792057654424, -0.00533371604862, -0.610422987397), (-0.0177082884111, -0.999340245738, 0.0317094586691), (-0.610189387478, 0.0359252657701, 0.791440640028)
Vector: -131.091444666, -47.1378749977, -43.9136520188)

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Components

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


Mass: 53822.020 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-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 3.78 Å3/Da / Density % sol: 67.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: droplet: 1:1 mixture of protein and reservoir protein supplemented with: 9.8 mM mannose 9.8 mM DTT reservoir solution: 1.6 M sodium malonate, pH 6.0

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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: Nov 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.35→46.97 Å / Num. obs: 66871 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 42.81 Å2 / CC1/2: 0.994 / Net I/σ(I): 7.4
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4469 / CC1/2: 0.341 / % 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: 2.35→42.01 Å / SU ML: 0.3173 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.0064
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2152 1645 2.46 %
Rwork0.1914 65199 -
obs0.192 66844 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.44 Å2
Refinement stepCycle: LAST / Resolution: 2.35→42.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7538 0 101 201 7840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027825
X-RAY DIFFRACTIONf_angle_d0.496810583
X-RAY DIFFRACTIONf_chiral_restr0.03811204
X-RAY DIFFRACTIONf_plane_restr0.0031380
X-RAY DIFFRACTIONf_dihedral_angle_d12.88072887
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.47217643992 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.420.3031340.30135379X-RAY DIFFRACTION99.93
2.42-2.50.31571460.28525399X-RAY DIFFRACTION99.96
2.5-2.590.28141010.27245431X-RAY DIFFRACTION100
2.59-2.690.29991430.25275413X-RAY DIFFRACTION100
2.69-2.810.28421080.26065469X-RAY DIFFRACTION100
2.81-2.960.25191740.22865358X-RAY DIFFRACTION100
2.96-3.150.24661180.21475416X-RAY DIFFRACTION100
3.15-3.390.22581530.19525429X-RAY DIFFRACTION100
3.39-3.730.20111440.17685421X-RAY DIFFRACTION100
3.73-4.270.16381540.14275457X-RAY DIFFRACTION99.98
4.27-5.380.17651370.1455474X-RAY DIFFRACTION100
5.38-42.010.19221330.17675553X-RAY DIFFRACTION99.77
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)
10.9948880771320.3577491043140.6448482837981.199550688580.481215050021.232447738260.0002897113700270.07127337431180.0844838891744-0.0743090447617-0.0243145819621-0.0366110198123-0.152903887836-0.0665719735392-8.03606587045E-70.3411795597150.039424143295-0.01829805433220.319093083599-0.006988809286950.30054444266-61.8332109678-6.11585395472-55.5999418107
21.41893143469-0.658273107693-0.9052612476481.609040975781.046838454261.70946058062-0.0490427948123-0.1197910127350.1077821081010.154881959976-0.002552728098790.134549321531-0.0868603985921-0.0270597030434-1.6124489354E-60.479762890294-0.000514990785324-0.02306920690390.294847778427-0.07064580200530.3908291676-62.37536897932.9720557432-31.7219999849
31.86221201737-0.237760132584-0.101496259170.652055765127-0.2518697664451.03107594742-0.120150365762-0.0571498848247-0.0249976282714-0.07693805513660.09100889620520.03230003190740.104439998239-0.0215844203262-1.73625433025E-60.3091914276550.0343082129753-0.03261597671470.296138529821-0.05228639520880.277443516599-47.9962694615-41.546562636-50.4065381273
40.659445029861-0.124178252258-0.2343598233170.928698172161-0.6324620509442.18542654751-0.0644882989762-0.0416699544223-0.06789517139130.0460731882330.09140412711710.08706396432310.0926932525089-0.2835847117521.2618142267E-60.4182995786580.032792626464-0.007741426141270.4690108196020.04950904364450.461511522293-63.2838366054-49.9787318679-30.6866094079
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)BK2 - 4632 - 462
44chain B and (resi 64:204 or resi 464:481)BK64 - 48163 - 480

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