PDB-9f3i: Crystal structure of Kluyveromyces lactis glucokinase in complex ...

ID or keywords:

Entry

Database: PDB / ID: 9f3i

Title

Crystal structure of Kluyveromyces lactis glucokinase in complex with glucose

Components

Glucokinase-1

Keywords

TRANSFERASE / 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 ...
Similarity search - Function

Biological species

Kluyveromyces lactis (yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 2.65 Å

Authors

Weisse, R.H. / Strater, N.

Funding support

Germany, 1items

Citation

Journal: To Be Published
Title: Structural basis of hexose specificity and catalytic properties of Kluyveromyces lactis glucokinase KlGlk1
Authors: Weisse, R.H. / Strater, N. / Kettner, K. / Lilie, H. / Funk, L. / Roedel, G. / Tittmann, K. / Kriegel, T.M.

History

Deposition	Apr 25, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 14, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9f3i.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb9f3i.ent.gz	931.7 KB	Display	PDB format
PDBx/mmJSON format	9f3i.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9f3i_validation.pdf.gz	2 MB	Display	wwPDB validaton report
Full document	9f3i_full_validation.pdf.gz	2 MB	Display
Data in XML	9f3i_validation.xml.gz	73.3 KB	Display
Data in CIF	9f3i_validation.cif.gz	91.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f3/9f3i ftp://data.pdbj.org/pub/pdb/validation_reports/f3/9f3i	HTTPS FTP

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Related structure data

Related structure data	9f3jC 9f3kC 9f3lC 9f3mC 9f3nC 9f3oC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	SASBDB: SASDU26associated SAS data, KlGlk1 without ligand SASBDB: SASDU36associated SAS data, KlGlk1 without ligand SASBDB: SASDU46associated SAS data, KlGlk1 without ligand SASBDB: SASDU56associated SAS data, KlGlk1 without ligand SASBDB: SASDU66associated SAS data, KlGlk1 without ligand SASBDB: SASDU76associated SAS data, KlGlk1 without ligand SASBDB: SASDU86associated SAS data, KlGlk1 in complex with fructose SASBDB: SASDU96associated SAS data, KlGlk1 in complex with mannose

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (9) #198 - Jun 2016 Beta-galactosidase similarity (1) #75 - Mar 2006 Tissue Factor similarity (1) #77 - May 2006 Glucose Oxidase similarity (1)

Deposited unit

A: Glucokinase-1

B: Glucokinase-1

C: Glucokinase-1

D: Glucokinase-1

hetero molecules

218 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glucokinase-1

B: Glucokinase-1

hetero molecules

defined by author
Evidence: SAXS, is in an equilibrium of a monomeric and a homodimeric state
109 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Glucokinase-1

D: Glucokinase-1

hetero molecules

defined by author
109 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	203.777, 88.108, 212.030
Angle α, β, γ (deg.)	90.000, 90.100, 90.000
Int Tables number	5
Space group name H-M	I121
Space group name Hall	C2y(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:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 2 through 169 or resid 172 through 481 or resid 500 through 512))
d_2	ens_1	(chain "B" and (resid 2 through 169 or resid 172 through 481 or resid 500 through 512))
d_3	ens_1	(chain "C" and (resid 2 through 169 or resid 172 through 481 or resid 500 through 512))
d_4	ens_1	(chain "D" and (resid 2 through 169 or resid 172 through 481 or resid 500 through 512))

NCS domain segments:

Ens-ID: ens_1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
d_1	1	SER	SER	THR	THR	A	A	2 - 169	2 - 169
d_1	2	PHE	PHE	TYR	TYR	A	A	172 - 481	172 - 481
d_1	3	BGC	BGC	BGC	BGC	A	E	501
d_1	4	MLI	MLI	MLI	MLI	A	F	502
d_1	5	MLI	MLI	MLI	MLI	A	G	503
d_1	6	MLI	MLI	MLI	MLI	A	H	504
d_2	1	SER	SER	THR	THR	B	B	2 - 169	2 - 169
d_2	2	PHE	PHE	TYR	TYR	B	B	172 - 481	172 - 481
d_2	3	BGC	BGC	BGC	BGC	B	I	501
d_2	4	MLI	MLI	MLI	MLI	B	J	502
d_2	5	MLI	MLI	MLI	MLI	B	K	503
d_2	6	MLI	MLI	MLI	MLI	B	L	504
d_3	1	SER	SER	THR	THR	C	C	2 - 169	2 - 169
d_3	2	PHE	PHE	TYR	TYR	C	C	172 - 481	172 - 481
d_3	3	BGC	BGC	BGC	BGC	C	M	501
d_3	4	MLI	MLI	MLI	MLI	C	N	502
d_3	5	MLI	MLI	MLI	MLI	C	O	503
d_3	6	MLI	MLI	MLI	MLI	C	P	504
d_4	1	SER	SER	THR	THR	D	D	2 - 169	2 - 169
d_4	2	PHE	PHE	TYR	TYR	D	D	172 - 481	172 - 481
d_4	3	BGC	BGC	BGC	BGC	D	R	501
d_4	4	MLI	MLI	MLI	MLI	D	S	502
d_4	5	MLI	MLI	MLI	MLI	D	T	503
d_4	6	MLI	MLI	MLI	MLI	D	U	504

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.999316655624, 0.00460249885587, -0.03667477058), (-0.0127559656569, 0.888316443658, 0.459054660434), (0.034691600323, 0.459208790127, -0.887650708295)	43.713419683, -31.0817403281, 126.07805882
2	given	(-0.00737373175639, 0.488731843386, -0.872402896224), (-0.0417316091069, 0.871516164969, 0.488587808892), (0.999101646922, 0.0400094920911, 0.0139692398244)	20.8239960196, 12.944496434, 62.6019103918
3	given	(0.0474343927612, 0.00237162894945, 0.998871540169), (0.00274179461133, 0.999993105012, -0.00250449418064), (-0.998870592692, 0.00285749976688, 0.0474275631822)	-106.401928513, 45.802071736, 101.264759498

#1: Protein

Glucokinase-1 / Glucose kinase 1 / GLK-1 / Hexokinase GLK1

Mass: 53822.020 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 lactis (yeast) / Strain (production host): JA6 / References: UniProt: Q6CUZ3, glucokinase, hexokinase

#2: Sugar

ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose

Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₂O₆ / Feature type: SUBJECT OF INVESTIGATION

#3: Chemical

ChemComp-MLI / MALONATE ION

Mass: 102.046 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C₃H₂O₄

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

Has protein modification

N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 4.42 Å³/Da / Density % sol: 72.18 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: droplet: 1:1 mixture of protein and reservoir protein supplemented with: 9.9 mM glucose reservoir solution: 1.5 M sodium malonate, pH 6.3

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.65→146.8 Å / Num. obs: 107657 / % possible obs: 98.5 % / Redundancy: 6.6 % / B_iso Wilson estimate: 65.67 Å² / CC_1/2: 0.991 / Net I/σ(I): 6.2
Reflection shell	Resolution: 2.65→2.7 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 5283 / CC_1/2: 0.274 / % possible all: 98.3

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
DIALS	1.dev.877-g8f078f0	data reduction
Aimless	0.5.31	data scaling

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 2.65→64.72 Å / SU ML: 0.4477 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.6414
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2576	5284	4.93 %
R_work	0.2355	101866	-
obs	0.2366	107150	97.85 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 85.34 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→64.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15076	0	153	69	15298

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0027	15524
X-RAY DIFFRACTION	f_angle_d	0.493	20996
X-RAY DIFFRACTION	f_chiral_restr	0.0384	2397
X-RAY DIFFRACTION	f_plane_restr	0.0034	2729
X-RAY DIFFRACTION	f_dihedral_angle_d	11.8818	5725

Refine LS restraints NCS

Ens-ID	Dom-ID	Asym-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	A	A	X-RAY DIFFRACTION	Torsion NCS	2.1926806306
ens_1	d_3	A	A	X-RAY DIFFRACTION	Torsion NCS	2.19168907512
ens_1	d_4	A	A	X-RAY DIFFRACTION	Torsion NCS	2.63139407753

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.65-2.68	0.4708	153	0.443	3226	X-RAY DIFFRACTION	94.04
2.68-2.71	0.4205	156	0.4191	3225	X-RAY DIFFRACTION	93.97
2.71-2.74	0.3863	175	0.3938	3232	X-RAY DIFFRACTION	92.36
2.74-2.78	0.3545	187	0.3806	3325	X-RAY DIFFRACTION	97.37
2.78-2.82	0.379	158	0.3556	3416	X-RAY DIFFRACTION	99.39
2.82-2.85	0.3453	186	0.3499	3442	X-RAY DIFFRACTION	99.48
2.85-2.9	0.3369	173	0.3322	3457	X-RAY DIFFRACTION	99.59
2.9-2.94	0.3482	185	0.332	3431	X-RAY DIFFRACTION	99.23
2.94-2.98	0.3232	181	0.3157	3371	X-RAY DIFFRACTION	99.47
2.98-3.03	0.3453	195	0.328	3443	X-RAY DIFFRACTION	99.18
3.03-3.09	0.337	188	0.3168	3434	X-RAY DIFFRACTION	99.42
3.09-3.14	0.3436	142	0.3349	3479	X-RAY DIFFRACTION	98.99
3.14-3.2	0.346	170	0.3342	3373	X-RAY DIFFRACTION	97.95
3.2-3.27	0.3229	177	0.3248	3408	X-RAY DIFFRACTION	97.95
3.27-3.34	0.3125	190	0.2956	3233	X-RAY DIFFRACTION	95.67
3.34-3.42	0.2652	167	0.2654	3364	X-RAY DIFFRACTION	95.79
3.42-3.5	0.2862	131	0.2527	3444	X-RAY DIFFRACTION	99.61
3.5-3.6	0.2687	186	0.2503	3458	X-RAY DIFFRACTION	99.51
3.6-3.7	0.2992	174	0.2456	3447	X-RAY DIFFRACTION	99.42
3.7-3.82	0.2628	193	0.2285	3423	X-RAY DIFFRACTION	99.34
3.82-3.96	0.2492	165	0.2201	3472	X-RAY DIFFRACTION	99.15
3.96-4.12	0.2149	192	0.2147	3416	X-RAY DIFFRACTION	99.09
4.12-4.3	0.2284	200	0.1986	3309	X-RAY DIFFRACTION	96.83
4.3-4.53	0.2068	161	0.1899	3284	X-RAY DIFFRACTION	94
4.53-4.81	0.1812	159	0.1773	3525	X-RAY DIFFRACTION	99.46
4.81-5.19	0.2005	185	0.1849	3460	X-RAY DIFFRACTION	99.7
5.19-5.71	0.2084	182	0.1889	3469	X-RAY DIFFRACTION	99.35
5.71-6.53	0.2362	175	0.2151	3334	X-RAY DIFFRACTION	95.41
6.53-8.23	0.214	206	0.1914	3473	X-RAY DIFFRACTION	98.53
8.23-64.72	0.2333	192	0.1781	3493	X-RAY DIFFRACTION	96.42

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.83950307839	-0.042661216598	0.0389837301349	2.40046329312	0.155162802714	3.21190371746	0.0807654317159	0.10885011483	-0.0639926779149	-0.285438549785	-0.127758701313	0.0781898686802	-0.15096700594	-0.202082664884	0.0409555929475	0.454787890168	0.0790926032769	0.195687192736	0.371739348431	0.0657653278092	0.608030101231	37.9865922232	-11.291794614	55.7312413137
2	2.91052320723	-0.724898513973	0.476865399817	2.14294321298	-0.75997644775	4.74400518251	-0.14641148701	-0.121491518321	-0.726350959507	0.0343274822266	-0.0547479179676	0.509924153943	0.327265505365	-0.378232016194	0.168884894917	0.402902951223	0.013049059676	0.0535661144158	0.541272746324	0.0596827379094	0.900092364029	3.60406958872	-15.9136532202	72.8024235936
3	3.09931959357	-0.360963640843	-0.212995731009	1.85962884157	0.558165860655	1.95240277076	0.180843428072	-0.502491844421	-0.260227889081	0.254685413947	-0.091126498843	0.0529758699806	0.609126073902	0.29535744135	-0.0745862840939	0.94623430508	0.0740882907686	-0.32878244171	0.659577213023	0.00559291466715	0.599151532073	-33.5210017968	28.8486282733	100.915911552
4	2.03703730897	0.14250618862	0.393253368499	1.83919502981	-0.237836739763	1.32868618854	0.0567365023363	-0.203564766155	0.0636604841756	0.111174925089	-0.101640300737	-0.0125153908496	0.0662363674969	-0.0269845563247	0.0509684350658	0.707793833458	0.0559926568278	-0.432079170164	0.384208891373	-0.0780557854928	0.862379927325	-48.9165741236	34.4998846631	65.9856817567
5	2.95515535386	1.029978111	-0.473425296764	4.93485689464	-1.02211314762	3.25661596588	0.212848865577	-0.128248524839	0.165734098397	0.135318616956	-0.11687338821	-0.0642140748085	-0.478277501946	-0.171831232678	-0.0908148987105	0.587165099036	-0.00257479380672	0.24141882283	0.414891772842	0.0235994280689	0.586438455912	47.295126768	9.93904592936	66.9650811788
6	3.27439255822	-0.401790090627	-0.791186259135	2.98152226662	0.232378078483	2.86554793023	-0.37743469452	-0.370562279819	0.260389805312	0.150769677656	0.0251664612663	0.13616827478	-0.67809967255	-0.457866297026	0.355620016597	0.724119964315	0.327382630458	-0.299206270263	0.853375991912	-0.0334625395057	0.916627653859	-5.87894129744	7.88018992838	72.9219969846
7	2.80215387518	0.731933135093	0.740773777112	1.9345894654	0.330150685608	4.3971864526	0.275184134491	-0.693586374523	0.607974646997	0.164567700798	-0.0339469781484	0.0545871161272	-0.14428473953	0.595866793706	-0.193827485517	0.820112031897	-0.0505568360672	-0.0795302139146	0.947657156359	-0.416754136091	0.779915350199	-32.9604581047	52.1761287763	111.160897911
8	1.33203963126	-0.507722377052	0.340125353204	3.36019872745	-1.04924965718	2.10576548059	-0.136424006878	-0.10472720149	0.365574636113	0.0586199923678	-0.0504680665171	-0.185755629314	-0.142876327754	0.197542950592	0.188662411805	0.698783981233	0.0136956576328	-0.453483641103	0.45023345417	-0.0234533100161	0.981712271479	-37.248451976	55.7264187874	57.2052261212

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain A and (resi 2:63 or resi 205:463)	A	A	2 - 463	2 - 462
2	2	chain B and (resi 2:63 or resi 205:463)	B	G	2 - 463	2 - 462
3	3	chain C and (resi 2:63 or resi 205:463)	C	M	2 - 463	2 - 462
4	4	chain D and (resi 2:63 or resi 205:463)	D	S	2 - 463	2 - 462
5	5	chain A and (resi 64:204 or resi 464:481)	A	A	64 - 481	63 - 480
6	6	chain B and (resi 64:204 or resi 464:481)	B	G	64 - 481	63 - 480
7	7	chain C and (resi 64:204 or resi 464:481)	C	M	64 - 481	63 - 480
8	8	chain D and (resi 64:204 or resi 464:481)	D	S	64 - 481	63 - 480

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