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- PDB-5cm5: Structure of Hydroxyethylthiazole Kinase ThiM from Staphylococcus... -

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Basic information

Entry
Database: PDB / ID: 5cm5
TitleStructure of Hydroxyethylthiazole Kinase ThiM from Staphylococcus aureus
ComponentsHydroxyethylthiazole kinase
KeywordsTRANSFERASE / Bacterial Thiamine Biosynthesis / Hydroxyethylthiazole Kinase
Function / homology
Function and homology information


hydroxyethylthiazole kinase / hydroxyethylthiazole kinase activity / thiamine biosynthetic process / thiamine diphosphate biosynthetic process / magnesium ion binding / ATP binding
Similarity search - Function
Hydroxyethylthiazole kinase / Hydroxyethylthiazole kinase family / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Hydroxyethylthiazole kinase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus MRSA252 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsDrebes, J. / Kuenz, M. / Eberle, R.J. / Oberthuer, D. / Cang, H. / Wrenger, C. / Betzel, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
LEXI-SDI Germany
CitationJournal: Sci Rep / Year: 2016
Title: Structure of ThiM from Vitamin B1 biosynthetic pathway of Staphylococcus aureus - Insights into a novel pro-drug approach addressing MRSA infections.
Authors: Julia Drebes / Madeleine Künz / Björn Windshügel / Alexey G Kikhney / Ingrid B Müller / Raphael J Eberle / Dominik Oberthür / Huaixing Cang / Dmitri I Svergun / Markus Perbandt / ...Authors: Julia Drebes / Madeleine Künz / Björn Windshügel / Alexey G Kikhney / Ingrid B Müller / Raphael J Eberle / Dominik Oberthür / Huaixing Cang / Dmitri I Svergun / Markus Perbandt / Christian Betzel / Carsten Wrenger /
Abstract: Infections caused by the methicillin-resistant Staphylococcus aureus (MRSA) are today known to be a substantial threat for global health. Emerging multi-drug resistant bacteria have created a ...Infections caused by the methicillin-resistant Staphylococcus aureus (MRSA) are today known to be a substantial threat for global health. Emerging multi-drug resistant bacteria have created a substantial need to identify and discover new drug targets and to develop novel strategies to treat bacterial infections. A promising and so far untapped antibiotic target is the biosynthesis of vitamin B1 (thiamin). Thiamin in its activated form, thiamin pyrophosphate, is an essential co-factor for all organisms. Therefore, thiamin analogous compounds, when introduced into the vitamin B1 biosynthetic pathway and further converted into non-functional co-factors by the bacterium can function as pro-drugs which thus block various co-factor dependent pathways. We characterized one of the key enzymes within the S. aureus vitamin B1 biosynthetic pathway, 5-(hydroxyethyl)-4-methylthiazole kinase (SaThiM; EC 2.7.1.50), a potential target for pro-drug compounds and analyzed the native structure of SaThiM and complexes with the natural substrate 5-(hydroxyethyl)-4-methylthiazole (THZ) and two selected substrate analogues.
History
DepositionJul 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydroxyethylthiazole kinase
B: Hydroxyethylthiazole kinase
C: Hydroxyethylthiazole kinase
D: Hydroxyethylthiazole kinase
E: Hydroxyethylthiazole kinase
F: Hydroxyethylthiazole kinase


Theoretical massNumber of molelcules
Total (without water)178,9676
Polymers178,9676
Non-polymers00
Water9,944552
1
A: Hydroxyethylthiazole kinase
B: Hydroxyethylthiazole kinase
C: Hydroxyethylthiazole kinase


Theoretical massNumber of molelcules
Total (without water)89,4833
Polymers89,4833
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-29 kcal/mol
Surface area28570 Å2
MethodPISA
2
D: Hydroxyethylthiazole kinase
E: Hydroxyethylthiazole kinase
F: Hydroxyethylthiazole kinase


Theoretical massNumber of molelcules
Total (without water)89,4833
Polymers89,4833
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-28 kcal/mol
Surface area27440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.561, 103.519, 126.180
Angle α, β, γ (deg.)90.00, 99.48, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALAA1 - 2621 - 262
21VALVALBB1 - 2621 - 262
12VALVALAA1 - 2621 - 262
22VALVALCC1 - 2621 - 262
13VALVALAA1 - 2621 - 262
23VALVALDD1 - 2621 - 262
14VALVALAA1 - 2621 - 262
24VALVALEE1 - 2621 - 262
15GLUGLUAA1 - 2611 - 261
25GLUGLUFF1 - 2611 - 261
16VALVALBB1 - 2621 - 262
26VALVALCC1 - 2621 - 262
17GLUGLUBB1 - 2641 - 264
27GLUGLUDD1 - 2641 - 264
18GLUGLUBB1 - 2611 - 261
28GLUGLUEE1 - 2611 - 261
19GLNGLNBB1 - 2601 - 260
29GLNGLNFF1 - 2601 - 260
110VALVALCC1 - 2621 - 262
210VALVALDD1 - 2621 - 262
111VALVALCC1 - 2621 - 262
211VALVALEE1 - 2621 - 262
112GLUGLUCC1 - 2611 - 261
212GLUGLUFF1 - 2611 - 261
113VALVALDD1 - 2621 - 262
213VALVALEE1 - 2621 - 262
114GLUGLUDD1 - 2611 - 261
214GLUGLUFF1 - 2611 - 261
115GLNGLNEE1 - 2601 - 260
215GLNGLNFF1 - 2601 - 260

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Hydroxyethylthiazole kinase / 4-methyl-5-beta-hydroxyethylthiazole kinase / Thz kinase


Mass: 29827.801 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus MRSA252 (bacteria)
Gene: thiM, SAR2181 / Plasmid: pASK-IBA3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6GEY3, hydroxyethylthiazole kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.38 %
Crystal growTemperature: 293.2 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 18 - 22 % PEG 3,350 (w/v), 0.2 M magnesium formate, 5 % isopropanol (v/v),

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.81 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 2.09→20 Å / Num. obs: 93740 / % possible obs: 99.9 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 13.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C3Q

1c3q


Resolution: 2.09→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 11.459 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2304 4693 5 %RANDOM
Rwork0.20342 ---
obs0.20479 88976 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.648 Å2
Baniso -1Baniso -2Baniso -3
1--2.76 Å20 Å2-1.24 Å2
2--6.68 Å2-0 Å2
3----3.32 Å2
Refinement stepCycle: 1 / Resolution: 2.09→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11439 0 0 552 11991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01911625
X-RAY DIFFRACTIONr_bond_other_d0.0090.0211483
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.97815821
X-RAY DIFFRACTIONr_angle_other_deg1.455326382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52151524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.56926.308474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.54151973
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.761536
X-RAY DIFFRACTIONr_chiral_restr0.0950.21946
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02113297
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022383
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4521.3066105
X-RAY DIFFRACTIONr_mcbond_other1.451.3066104
X-RAY DIFFRACTIONr_mcangle_it2.3821.9467616
X-RAY DIFFRACTIONr_mcangle_other2.3821.9467617
X-RAY DIFFRACTIONr_scbond_it1.7731.5175520
X-RAY DIFFRACTIONr_scbond_other1.7731.5165518
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8352.1868203
X-RAY DIFFRACTIONr_long_range_B_refined5.90910.85713163
X-RAY DIFFRACTIONr_long_range_B_other5.86210.59312968
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A152760.08
12B152760.08
21A156010.09
22C156010.09
31A152670.09
32D152670.09
41A152770.09
42E152770.09
51A150820.09
52F150820.09
61B153120.09
62C153120.09
71B156060.08
72D156060.08
81B154460.08
82E154460.08
91B151750.08
92F151750.08
101C151790.09
102D151790.09
111C153130.08
112E153130.08
121C151220.09
122F151220.09
131D152890.09
132E152890.09
141D148840.1
142F148840.1
151E149680.09
152F149680.09
LS refinement shellResolution: 2.09→2.144 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 378 -
Rwork0.273 6439 -
obs--99.97 %
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)
11.1539-0.0846-0.20381.7138-0.18061.0325-0.0461-0.2084-0.11140.03980.05510.1380.1422-0.0922-0.0090.2643-0.0160.02530.05480.02770.2942-4.588-0.54660.4
21.3705-0.0883-0.12731.46760.41141.3560.00320.23920.1129-0.22750.00740.0487-0.0113-0.0827-0.01050.2234-0.01670.00690.04640.02450.2703-8.2169.73329.63
32.3726-0.4916-0.15330.93060.08251.03550.0003-0.10310.19090.0871-0.0261-0.1733-0.03120.15510.02580.1951-0.01880.02740.030.00240.346819.66417.74446.592
41.7482-0.04890.29440.7908-0.59372.20050.05560.27210.0234-0.1016-0.03640.06580.1752-0.0665-0.01920.3038-0.0078-0.00560.05570.0180.286616.80321.65288.206
52.50660.34360.25470.6477-0.21991.7757-0.01060.1175-0.146-0.0846-0.057-0.12670.16250.50030.06750.23640.02320.00740.2090.07740.301240.39915.508110.724
61.27260.3230.1422.4162-0.61011.7187-0.0096-0.39260.30.40440.11020.1327-0.3637-0.2357-0.10050.33250.05250.040.1651-0.01060.428113.60732.196118.87
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 262
2X-RAY DIFFRACTION2B1 - 264
3X-RAY DIFFRACTION3C1 - 262
4X-RAY DIFFRACTION4D1 - 265
5X-RAY DIFFRACTION5E1 - 262
6X-RAY DIFFRACTION6F1 - 261

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