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- PDB-9f3l: Crystal structure of Kluyveromyces lactis glucokinase mutant H304... -

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Basic information

Entry
Database: PDB / ID: 9f3l
TitleCrystal structure of Kluyveromyces lactis glucokinase mutant H304Q 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: 2.48 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
C: Glucokinase-1
D: Glucokinase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,90827
Polymers215,2484
Non-polymers2,65923
Water2,162120
1
A: Glucokinase-1
B: Glucokinase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,69911
Polymers107,6242
Non-polymers1,0759
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Glucokinase-1
D: Glucokinase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,20916
Polymers107,6242
Non-polymers1,58514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)202.412, 88.340, 212.450
Angle α, β, γ (deg.)90.000, 89.920, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -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 84 or resid 86...
d_2ens_1(chain "B" and (resid 2 through 84 or resid 86...
d_3ens_1(chain "C" and (resid 2 through 84 or resid 86...
d_4ens_1(chain "D" and (resid 2 through 84 or resid 86...

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_11SERSERVALVALAA2 - 842 - 84
d_12SERSERPHEPHEAA86 - 12186 - 121
d_13HISHISTHRTHRAA123 - 412123 - 412
d_14ALAALAVALVALAA414 - 459414 - 459
d_15LEULEUTYRTYRAA461 - 481461 - 481
d_16MANMANMANMANAE501
d_17MLIMLIMLIMLIAF502
d_18MLIMLIMLIMLIAG503
d_21SERSERVALVALBB2 - 842 - 84
d_22SERSERPHEPHEBB86 - 12186 - 121
d_23HISHISTHRTHRBB123 - 412123 - 412
d_24ALAALAVALVALBB414 - 459414 - 459
d_25LEULEUTYRTYRBB461 - 481461 - 481
d_26MANMANMANMANBI501
d_27MLIMLIMLIMLIAH504
d_28MLIMLIMLIMLIBJ502
d_31SERSERVALVALCC2 - 842 - 84
d_32SERSERPHEPHECC86 - 12186 - 121
d_33HISHISTHRTHRCC123 - 412123 - 412
d_34ALAALAVALVALCC414 - 459414 - 459
d_35LEULEUTYRTYRCC461 - 481461 - 481
d_36MANMANMANMANCN501
d_37MLIMLIMLIMLICO502
d_38MLIMLIMLIMLICP503
d_41SERSERVALVALDD2 - 842 - 84
d_42SERSERPHEPHEDD86 - 12186 - 121
d_43HISHISTHRTHRDD123 - 412123 - 412
d_44ALAALAVALVALDD414 - 459414 - 459
d_45LEULEUTYRTYRDD461 - 481461 - 481
d_46MANMANMANMANDU501
d_47MLIMLIMLIMLICT507
d_48MLIMLIMLIMLIDV502

NCS oper:
IDCodeMatrixVector
1given(-0.999408166774, 0.00698851941948, -0.0336819949059), (-0.00883329709048, 0.894175791404, 0.447628894208), (0.0332458876709, 0.447661495623, -0.893584856793)43.7170466529, -30.6487004186, 126.989255534
2given(-0.0185117585244, 0.481412681851, -0.876298547613), (-0.0350966480106, 0.87559570695, 0.481767976591), (0.999212459938, 0.0396735141252, 0.000687155150667)21.9986657876, 13.2709743566, 63.6738472174
3given(0.0587859384744, -6.68888234664E-5, 0.998270609085), (-0.00278004327528, 0.999996109057, 0.000230715012589), (-0.998266740304, -0.00278879829224, 0.0587855237878)-106.518081517, 46.0645943796, 100.676380265

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Components

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


Mass: 53812.004 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Strain: JA6 / Gene: GLK1, KLLA0C01155g / Production host: Kluyveromyces (fungus) / 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.: 4 / 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.: 19 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 4.41 Å3/Da / Density % sol: 72.12 %
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 6.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.48→146.45 Å / Num. obs: 130184 / % possible obs: 97.9 % / Redundancy: 4 % / Biso Wilson estimate: 69.98 Å2 / CC1/2: 0.995 / Net I/σ(I): 7.4
Reflection shellResolution: 2.48→2.52 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 6479 / CC1/2: 0.285 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALS1.dev.877-g8f078f0data reduction
Aimless0.5.32data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.48→64.28 Å / SU ML: 0.3931 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.0499
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2368 6451 4.97 %
Rwork0.2114 123349 -
obs0.2126 129800 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.42 Å2
Refinement stepCycle: LAST / Resolution: 2.48→64.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15072 0 181 120 15373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004315558
X-RAY DIFFRACTIONf_angle_d0.610221045
X-RAY DIFFRACTIONf_chiral_restr0.04112401
X-RAY DIFFRACTIONf_plane_restr0.00472743
X-RAY DIFFRACTIONf_dihedral_angle_d12.94085750
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS2.74319156919
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS2.53105384943
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS1.96280453226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.510.38952100.39534048X-RAY DIFFRACTION96.86
2.51-2.540.36162350.3714084X-RAY DIFFRACTION97.74
2.54-2.570.36342260.35944105X-RAY DIFFRACTION98.3
2.57-2.60.37872100.35594176X-RAY DIFFRACTION97.81
2.6-2.640.35182450.35654032X-RAY DIFFRACTION98.12
2.64-2.670.40411990.39694111X-RAY DIFFRACTION97.8
2.67-2.710.44811930.40934064X-RAY DIFFRACTION97.55
2.71-2.750.39372370.38134103X-RAY DIFFRACTION97.7
2.75-2.790.38112150.36134110X-RAY DIFFRACTION97.78
2.79-2.840.31941920.33883937X-RAY DIFFRACTION93.06
2.84-2.890.30432080.31653995X-RAY DIFFRACTION95.85
2.89-2.940.29392210.27164178X-RAY DIFFRACTION98.85
2.94-30.30672320.27074106X-RAY DIFFRACTION98.79
3-3.060.29972220.25964179X-RAY DIFFRACTION98.77
3.06-3.120.28451850.27044180X-RAY DIFFRACTION98.55
3.12-3.20.27742050.27274095X-RAY DIFFRACTION97.99
3.2-3.280.28352180.2724135X-RAY DIFFRACTION97.95
3.28-3.370.30222520.28474076X-RAY DIFFRACTION98.32
3.37-3.460.26521640.22844092X-RAY DIFFRACTION96.27
3.46-3.580.25951860.23283962X-RAY DIFFRACTION93.32
3.58-3.70.22922200.21554159X-RAY DIFFRACTION98.78
3.7-3.850.22122290.18684150X-RAY DIFFRACTION98.65
3.85-4.030.1981980.1834233X-RAY DIFFRACTION98.47
4.03-4.240.1912520.17484092X-RAY DIFFRACTION98.75
4.24-4.510.17692040.15884201X-RAY DIFFRACTION97.98
4.51-4.850.16181890.15323958X-RAY DIFFRACTION93.89
4.85-5.340.18332150.15784223X-RAY DIFFRACTION99.08
5.34-6.110.22262270.1814235X-RAY DIFFRACTION98.94
6.11-7.70.2182380.18274053X-RAY DIFFRACTION95.55
7.7-64.280.2042240.16114277X-RAY DIFFRACTION97.21
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)
10.7719695780540.2117426109920.04170714692971.362152850530.224903419891.893221462930.100425414779-0.0751972431333-0.0355802013378-0.17295207026-0.129655556907-0.0465032396509-0.0751019301412-0.152270881936-1.16099935294E-60.5869530397160.0774428009310.2116964287580.6575797801230.1230848423820.62758730196437.8067165634-11.440314616755.8764692977
21.87297883074-0.8443869532480.5516924676391.41178911365-0.5296069828542.06616819127-0.09524654370290.0645320037508-0.450084682869-0.0198193330274-0.07410040070230.425297885920.160073064324-0.154409888729-0.00240212785730.571739806668-0.04037937988210.1399631228070.7958659646540.07530297144540.8986167623683.87433822473-16.008098650673.2357912766
31.79673380603-0.523103214817-0.505480529731.183350425880.7174902221441.196564896830.151229462074-0.373325305813-0.1341691340540.293448772797-0.162956402590.0756782917030.3601377719070.03621577847712.84041685074E-60.963211880534-0.0286116982931-0.1186805144440.8194751777320.02564178633090.56546881311-33.092839719128.9640867403101.117370594
41.81847052929-0.005002214684130.159227685630.918557319037-0.2363980135420.7365822648280.036082195319-0.0889611495870.00891814014158-0.00381930190203-0.1536387941610.01989953006090.029492086436-0.02486526532879.84438388445E-70.667706237330.0576333496394-0.16777623650.467492202272-0.07575826809010.678686799265-48.527689106934.61634035466.2326238745
51.2084165541.10617313506-0.007411112696492.48333581655-0.6631021718920.8999447902220.177384147938-0.151230711939-0.06443617479020.0771363704695-0.0473026000086-0.196980790668-0.4455522772240.0630152851697-1.2361120416E-50.761586422154-0.009871326200220.2467792472010.782631672826-0.03033193752130.72424287556547.25066941449.9299036719567.0538019929
61.32798355238-1.28592947232-0.08469803019081.961796776410.7408659522251.82244469416-0.372245712795-0.02927707899320.1177567512610.08546783559340.05401177766440.29025771279-0.511347127071-0.274035387899-3.73513783525E-50.71840264350.132765055415-0.09219373796770.9195969544330.04150058976220.89999635087-5.683059764037.7886285333273.2425508138
71.599945843030.5846147829530.04563955066191.351600815450.3857802656170.7421139655490.186861553041-0.4664191257550.5706176301580.254673173762-0.05309163660830.0857320824033-0.09735377712990.2425523650171.72009952594E-61.11749590829-0.04682948682220.03992055806651.17080522439-0.3463754907350.75210036412-32.733925398252.5715795314111.341831777
80.702529487648-0.4523428696930.2432536310812.91429723378-1.296420795261.54100595139-0.1484189808150.009676444340290.27883280751-0.0141063444844-0.0752888233271-0.175793965371-0.1231950000020.19792045025-6.81874240887E-60.706450596252-0.0326996880076-0.2035448115780.5715244759990.03769361021720.78683787599-36.875661058756.018050578157.2807998937
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 B and (resi 2:63 or resi 205:463)BF2 - 4632 - 462
33chain C and (resi 2:63 or resi 205:463)CN2 - 4632 - 462
44chain D and (resi 2:63 or resi 205:463)DV2 - 4632 - 462
55chain A and (resi 64:204 or resi 464:481)AA64 - 48163 - 480
66chain B and (resi 64:204 or resi 464:481)BF64 - 48163 - 480
77chain C and (resi 64:204 or resi 464:481)CN64 - 48163 - 480
88chain D and (resi 64:204 or resi 464:481)DV64 - 48163 - 480

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