PDB-7owz: Heterodimeric murine tRNA-guanine transglycosylase in complex wit...

ID or keywords:

Entry

Database: PDB / ID: 7owz

Title

Heterodimeric murine tRNA-guanine transglycosylase in complex with queuine and in the presence of Anderson-Evans type (TEW) and Strandberg type polyoxometalate (POM)

Components

(Queuine tRNA-ribosyltransferase ...) x 2

Keywords

TRANSFERASE / TRANSGLYCOSYLASE / TIM BARREL / DIMER / TGT

Function / homology

Function and homology information

tRNA-guanosine34 queuine transglycosylase / transferase complex / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / mitochondrial outer membrane / tRNA binding / protein heterodimerization activity / protein homodimerization activity / protein-containing complex / mitochondrion ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Sebastiani, M. / Heine, A. / Reuter, K.

Citation

Journal: Acs Chem.Biol. / Year: 2022
Title: Structural and Biochemical Investigation of the Heterodimeric Murine tRNA-Guanine Transglycosylase.
Authors: Sebastiani, M. / Behrens, C. / Dorr, S. / Gerber, H.D. / Benazza, R. / Hernandez-Alba, O. / Cianferani, S. / Klebe, G. / Heine, A. / Reuter, K.

History

Deposition	Jun 21, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 13, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jun 28, 2023	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7owz.cif.gz	354.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7owz.ent.gz	238.4 KB	Display	PDB format
PDBx/mmJSON format	7owz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7owz_validation.pdf.gz	2.1 MB	Display	wwPDB validaton report
Full document	7owz_full_validation.pdf.gz	2.2 MB	Display
Data in XML	7owz_validation.xml.gz	27.1 KB	Display
Data in CIF	7owz_validation.cif.gz	37.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ow/7owz ftp://data.pdbj.org/pub/pdb/validation_reports/ow/7owz	HTTPS FTP

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Related structure data

Related structure data	6h62SC 7b2iC 7ov9C 7ovoC 7ovsC 6fv5S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Queuine tRNA-ribosyltransferase accessory subunit 2

C: Queuine tRNA-ribosyltransferase catalytic subunit 1

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: mass spectrometry

Unit cell

Length a, b, c (Å)	199.500, 199.500, 90.586
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	180
Space group name H-M	P6₂22
Space group name Hall	P6₂2(x,y,z+1/3)
Symmetry operation	#1: x,y,z #2: x-y,x,z+1/3 #3: y,-x+y,z+2/3 #4: -y,x-y,z+2/3 #5: -x+y,-x,z+1/3 #6: x-y,-y,-z #7: -x,-x+y,-z+1/3 #8: -x,-y,z #9: y,x,-z+2/3 #10: -y,-x,-z+2/3 #11: -x+y,y,-z #12: x,x-y,-z+1/3

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Queuine tRNA-ribosyltransferase ... , 2 types, 2 molecules AC

#1: Protein	Queuine tRNA-ribosyltransferase accessory subunit 2 / Queuine tRNA-ribosyltransferase domain-containing protein 1 Mass: 46710.465 Da / Num. of mol.: 1 / Mutation: M1del Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Qtrt2, Qtrtd1 / Production host: Vibrio natriegens (bacteria) / Variant (production host): Vmax References: UniProt: B8ZXI1, tRNA-guanosine34 preQ1 transglycosylase
#2: Protein	Queuine tRNA-ribosyltransferase catalytic subunit 1 / Guanine insertion enzyme / tRNA-guanine transglycosylase Mass: 43428.980 Da / Num. of mol.: 1 / Mutation: M1_L10del Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Qtrt1, Tgt, Tgut / Production host: Vibrio natriegens (bacteria) / Variant (production host): Vmax References: UniProt: Q9JMA2, tRNA-guanosine34 preQ1 transglycosylase

#1: Protein

Queuine tRNA-ribosyltransferase accessory subunit 2 / Queuine tRNA-ribosyltransferase domain-containing protein 1

Mass: 46710.465 Da / Num. of mol.: 1 / Mutation: M1del
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse) / Gene: Qtrt2, Qtrtd1 / Production host:

Vibrio natriegens (bacteria) / Variant (production host): Vmax
References: UniProt: B8ZXI1, tRNA-guanosine34 preQ1 transglycosylase

#2: Protein

Queuine tRNA-ribosyltransferase catalytic subunit 1 / Guanine insertion enzyme / tRNA-guanine transglycosylase

Mass: 43428.980 Da / Num. of mol.: 1 / Mutation: M1_L10del
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse) / Gene: Qtrt1, Tgt, Tgut / Production host:

Vibrio natriegens (bacteria) / Variant (production host): Vmax
References: UniProt: Q9JMA2, tRNA-guanosine34 preQ1 transglycosylase

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Non-polymers , 5 types, 53 molecules

#3: Chemical	ChemComp-TEW / 6-tungstotellurate(VI) Mass: 1614.626 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O₂₄TeW₆
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical	ChemComp-QEI / 2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one / queuine Mass: 277.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₁₅N₅O₃ / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-2I2 / pentadecaoxodiphosphopentatungstate Mass: 1359.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H₁₀O₂₃P₂W₅
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.88 Å³/Da / Density % sol: 57.31 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 100 mM Na/K phosphate pH 6.8, 200 mM Sodium chloride, 14 % (w/v) PEG 1000, 1 mM TEW

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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 PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.6→48.6 Å / Num. obs: 62234 / % possible obs: 99.9 % / Redundancy: 12.75 % / B_iso Wilson estimate: 58.92 Å² / CC_1/2: 1 / Net I/σ(I): 24.06
Reflection shell	Resolution: 2.6→2.75 Å / Num. unique obs: 9974 / CC_1/2: 0.833

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Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
Coot	0.8.9	model building
XDS	1.02	data reduction
XDS	1.02	data scaling
PHASER	7.0.047	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6H62, 6FV5

6h62

6fv5

Resolution: 2.6→48.6 Å / SU ML: 0.326 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.7235 / Stereochemistry target values: CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2394	3124	5.02 %
R_work	0.2138	59104	-
obs	0.2151	62228	99.86 %

Solvent computation

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

Displacement parameters

B_iso mean: 61.78 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→48.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5555	0	114	47	5716

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0025	5822
X-RAY DIFFRACTION	f_angle_d	1.0104	8116
X-RAY DIFFRACTION	f_chiral_restr	0.0477	907
X-RAY DIFFRACTION	f_plane_restr	0.0032	1002
X-RAY DIFFRACTION	f_dihedral_angle_d	15.4708	3431

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 (%)
2.6-2.64	0.3631	139	0.3187	2630	X-RAY DIFFRACTION	97.95
2.64-2.68	0.3114	143	0.2962	2690	X-RAY DIFFRACTION	100
2.68-2.73	0.3012	142		2690	X-RAY DIFFRACTION	99.96
2.73-2.78	0.3034	142	0.2897	2696	X-RAY DIFFRACTION	99.96
2.78-2.83	0.2725	140	0.2681	2682	X-RAY DIFFRACTION	100
2.83-2.89	0.3064	142	0.27	2683	X-RAY DIFFRACTION	100
2.89-2.95	0.2743	144	0.2742	2679	X-RAY DIFFRACTION	100
2.95-3.02	0.298	136	0.2598	2709	X-RAY DIFFRACTION	100
3.02-3.09	0.2506	139		2702	X-RAY DIFFRACTION	100
3.09-3.18	0.3417	141	0.2619	2675	X-RAY DIFFRACTION	100
3.18-3.27	0.2755	148	0.2491	2698	X-RAY DIFFRACTION	100
3.27-3.38	0.2892	141	0.2452	2687	X-RAY DIFFRACTION	99.96
3.38-3.5	0.2797	140	0.2297	2704	X-RAY DIFFRACTION	100
3.5-3.64	0.1925	140		2653	X-RAY DIFFRACTION	99.5
3.64-3.8	0.2707	147	0.21	2681	X-RAY DIFFRACTION	99.96
3.8-4	0.2189	143	0.1983	2692	X-RAY DIFFRACTION	100
4-4.25	0.1934	143	0.1884	2693	X-RAY DIFFRACTION	100
4.25-4.58	0.2073	146	0.1824	2686	X-RAY DIFFRACTION	99.96
4.58-5.04	0.2093	141	0.1789	2696	X-RAY DIFFRACTION	100
5.04-5.77	0.2418	143	0.2107	2677	X-RAY DIFFRACTION	99.86
5.77-7.27	0.2401	139	0.2099	2703	X-RAY DIFFRACTION	100
7.27-48.6	0.1979	145	0.1614	2698	X-RAY DIFFRACTION	99.82

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	1.73504244	-0.259466803949	-0.301117232093	2.1728095658	-0.577237426647	0.66268725503	-0.0781571891847	-0.0987107593227	-0.0957913542294	0.24775861249	0.0628739861554	0.102244471221	0.0715714262679	0.0248154934989	0.0117496195325	0.631033522365	0.0544865489958	-0.0181693948422	0.510130778518	-0.0471896077493	0.54372877711	72.3968497906	51.6071071489	-4.14531852714
2	2.53111482146	-1.28989005144	-1.73155729385	3.56235411013	-0.448981881756	2.52669576548	-0.0194490559299	-0.0136873741203	-0.0381126845951	-0.19966795488	0.221142211544	-0.391927402898	0.277089385006	0.279567352414	-0.213597298851	0.514755118007	0.0630086963479	-0.022309244211	0.57557772205	-0.0660533845159	0.527488101086	85.8445315322	48.7914093389	-13.6481286101
3	0.754034993469	-0.662008964155	-0.963032445011	2.69923636679	-1.16126462234	3.13817659973	-0.0778569605403	-0.0296105668073	0.490563846911	-0.0340265063949	0.060212463663	0.0251112976987	0.510970875886	0.175813030729	-0.146112565949	0.613673193338	0.111033545706	-0.0042748666124	0.614786037433	-0.0787146735017	0.593478287574	80.9156766943	39.4799043899	-10.8418122307
4	0.563695255802	-0.0828954099493	0.119680636944	1.34358249953	-0.169752339464	1.00878871865	-0.447252935418	-0.0477278998547	-0.172112777603	-0.0806192707597	0.0038797933214	0.150048806462	0.27337757026	0.213501809112	0.196684625335	0.775894167048	0.211259190612	0.0231617826277	0.604088830409	-0.0360468535256	0.697378381595	81.9953611748	34.5957471925	-7.87993532973
5	2.41969694288	0.351479607718	-0.248863523022	1.80864011412	-0.499038403071	0.994350149223	-0.141516996155	0.111381048209	-0.32932327616	0.201994197873	0.171604340191	0.323318572696	0.239462304893	0.00611993532144	-0.00650107149035	0.790519013095	0.0609422615526	0.0997190868404	0.440822806458	0.0294778574668	0.733140602922	55.7835766742	36.3460909065	-2.23820224939
6	1.67177847752	-0.252749222245	-0.0555833151151	1.01485181075	-0.426704863103	0.340835462376	-0.32725940601	-0.383651718352	-0.467876032412	0.32676839275	0.266060318167	-0.13661236514	0.230951164969	0.122369010684	0.0508470039834	0.735877895062	0.081733905069	0.0799469973829	0.495518618997	0.0799012123438	0.683464646871	63.8916033773	34.240703427	2.71556824718
7	2.16479376611	1.03465519002	0.123814485841	2.5343846132	-0.113690066928	1.84547521038	0.0471519442148	-0.195594435407	-0.0141541290071	0.103770930959	-0.112367652593	0.152970987121	-0.069076322216	-0.0811109702215	-0.0396785518595	0.637684647356	0.0588020339557	0.0823196741732	0.596466446341	0.0675678159524	0.447857525952	31.7818919737	66.0618415134	13.4070393132
8	1.98625815178	0.178330407949	-0.341604139927	1.33263203658	0.234848092884	0.194518446694	-0.129489652833	0.139869452506	-0.405179138263	-0.0173438163729	0.0568174816651	0.107217487602	0.103673367858	-0.107186991793	0.101544153169	0.678148314916	-0.0181755499578	0.124616886025	0.526491127893	0.0208488589438	0.628173441327	28.5798551334	52.108664839	-0.951995485539
9	2.01615049835	0.597796872453	1.03033539991	1.89711891793	0.337992343561	0.754152986827	-0.19892362334	-0.123900811644	-0.248971423464	0.14597319484	0.139306632932	0.240649757584	0.125990960191	-0.283949979946	0.0644379731623	0.497124128854	0.0257074156197	0.109860327109	0.528807918726	0.061792933299	0.513889579502	23.0782481742	67.4876974469	2.16581252974
10	1.98785134691	-0.612630480036	-0.499625214927	1.24890110874	0.462641584417	0.68229032089	-0.110604020693	-0.10556765778	0.0912799591639	0.201453275021	0.0809517234126	-0.0775448340765	-0.0477588986713	-0.00609756722036	0.0206088578907	0.614150153419	0.0410302447697	0.0194798479575	0.478452632234	0.0185002816407	0.544865297879	47.9048710331	74.2267997338	1.95746640879

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 125 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 126 through 210 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 211 through 229 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 230 through 256 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 257 through 372 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 373 through 414 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 13 through 54 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 55 through 168 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 169 through 294 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 295 through 402 )

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Queuine tRNA-ribosyltransferase ... , 2 types, 2 molecules AC

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Non-polymers , 5 types, 53 molecules

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-Non-polymers , 5 types, 53 molecules

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Queuine tRNA-ribosyltransferase ... , 2 types, 2 molecules AC

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Non-polymers , 5 types, 53 molecules

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Details

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Experimental details

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Processing

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