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

ID or keywords:

Entry

Database: PDB / ID: 7ovo

Title

Heterodimeric murine tRNA-guanine transglycosylase in complex with queuine

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: 2.1 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 15, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 22, 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	7ovo.cif.gz	370.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7ovo.ent.gz	249.4 KB	Display	PDB format
PDBx/mmJSON format	7ovo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ov/7ovo ftp://data.pdbj.org/pub/pdb/validation_reports/ov/7ovo	HTTPS FTP

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Related structure data

Related structure data	6h62SC 7b2iC 7ov9C 7ovsC 7owzC 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

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

1

Idetical with deposited unit
defined by author&software
Evidence: mass spectrometry

Unit cell

Length a, b, c (Å)	100.429, 100.429, 202.853
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	95
Space group name H-M	P4₃22
Space group name Hall	P4cw2c
Symmetry operation	#1: x,y,z #2: -y,x,z+3/4 #3: y,-x,z+1/4 #4: x,-y,-z+1/2 #5: -x,y,-z #6: -x,-y,z+1/2 #7: y,x,-z+1/4 #8: -y,-x,-z+3/4

Components on special symmetry positions

ID	Model	Components
1	1	C-681- HOH

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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 / Plasmid: pETDuet-1 / 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 / Plasmid: pETDuet-1 / 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 / Plasmid: pETDuet-1 / 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 / Plasmid: pETDuet-1 / Production host:

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

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Non-polymers , 5 types, 250 molecules

#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#6: 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 / Queuine Mass: 277.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₁₅N₅O₃ / Feature type: SUBJECT OF INVESTIGATION
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.84 Å³/Da / Density % sol: 56.69 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100 mM Citrate pH 6.5, 700 mM Ammonium sulfate, 1 M Lithium sulfate

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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: Nov 28, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. obs: 61375 / % possible obs: 99.9 % / Redundancy: 13.1 % / B_iso Wilson estimate: 44.15 Å² / R_sym value: 7.5 / Net I/σ(I): 20.7
Reflection shell	Resolution: 2.1→2.23 Å / Num. unique obs: 9724 / CC_1/2: 0.894

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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: 2.1→48.74 Å / SU ML: 0.2446 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.5356 / Stereochemistry target values: CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2339	3068	5 %
R_work	0.189	58270	-
obs	0.1912	61338	99.85 %

Solvent computation

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

Displacement parameters

B_iso mean: 57.16 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→48.74 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5617	0	61	239	5917

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0069	5876
X-RAY DIFFRACTION	f_angle_d	0.7899	7987
X-RAY DIFFRACTION	f_chiral_restr	0.0495	910
X-RAY DIFFRACTION	f_plane_restr	0.0063	1027
X-RAY DIFFRACTION	f_dihedral_angle_d	16.6751	3484

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 (%)
2.1-2.13	0.315	136	0.2498	2580	X-RAY DIFFRACTION	99.09
2.13-2.17	0.3054	135	0.2388	2581	X-RAY DIFFRACTION	99.96
2.17-2.2	0.2394	138	0.2381	2610	X-RAY DIFFRACTION	99.96
2.2-2.24	0.341	136	0.2536	2589	X-RAY DIFFRACTION	99.56
2.24-2.29	0.3355	138	0.274	2613	X-RAY DIFFRACTION	99.39
2.29-2.33	0.2675	138	0.2199	2620	X-RAY DIFFRACTION	100
2.33-2.38	0.2417	136	0.2071	2613	X-RAY DIFFRACTION	99.89
2.38-2.44	0.2245	138	0.1974	2619	X-RAY DIFFRACTION	99.89
2.44-2.5	0.2428	138	0.1975	2606	X-RAY DIFFRACTION	99.82
2.5-2.57	0.2858	137	0.1989	2607	X-RAY DIFFRACTION	99.82
2.57-2.64	0.228	139	0.1975	2630	X-RAY DIFFRACTION	99.89
2.64-2.73	0.2359	139	0.1902	2638	X-RAY DIFFRACTION	99.89
2.73-2.83	0.2385	138	0.2	2622	X-RAY DIFFRACTION	100
2.83-2.94	0.2561	139	0.2063	2648	X-RAY DIFFRACTION	100
2.94-3.07	0.246	139	0.2111	2636	X-RAY DIFFRACTION	99.96
3.07-3.24	0.3104	140	0.2026	2668	X-RAY DIFFRACTION	99.96
3.24-3.44	0.2333	141	0.1974	2662	X-RAY DIFFRACTION	100
3.44-3.7	0.2004	140	0.1802	2669	X-RAY DIFFRACTION	100
3.7-4.08	0.1905	141	0.1618	2682	X-RAY DIFFRACTION	100
4.08-4.67	0.1972	143	0.1496	2711	X-RAY DIFFRACTION	100
4.67-5.88	0.207	145	0.1767	2756	X-RAY DIFFRACTION	99.93
5.88-48.74	0.2519	154	0.1933	2910	X-RAY DIFFRACTION	99.74

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	3.57614418549	-1.82882147344	1.20158682693	6.23096305169	1.97979358572	5.78029118814	-0.337849628196	-0.718562622242	0.312823191521	0.113695833178	-0.145336573343	0.482216326454	-0.719690841554	-0.878881783034	0.455800737828	0.404850930333	0.0898194026015	0.0595137415488	0.541089755443	-0.0580134790632	0.535909098916	-27.1102174507	48.0666387242	13.2137314777
2	3.48430085257	0.208407917479	1.71108301318	2.83473310309	-0.533860601459	2.53616428027	-0.297739074163	0.112675768355	0.87470244799	-0.0241183117848	-0.184831118519	-0.360846896211	-0.675641405369	-0.0041113874353	0.422026390668	0.798204769828	0.0895251867996	-0.139735542691	0.442818899549	-0.0391066457172	0.782256016702	-24.8832596299	64.0502143619	2.24140172704
3	1.73628666655	0.564759879604	1.26080988807	6.86431115239	2.69494272438	3.24327718956	-0.0973310349075	-0.172944767334	0.260065135418	0.268750253257	-0.0124397006954	-0.048534589088	-0.0997464282665	0.0353574017388	0.0933504201853	0.316649872035	0.00639438034973	-0.0122122480453	0.485771625102	-0.00497413434596	0.324066040329	-15.8969436994	40.4950046346	6.44087634924
4	5.93365498303	3.14816469619	6.39521999051	3.70075781639	4.30194492353	7.84385321513	-0.322332766943	-0.258532142408	-0.110824176051	0.204780795574	0.113505854981	0.0820104519266	0.0177545480463	0.0586112927048	0.235671427385	0.358401402206	0.0388267710064	0.0278483566362	0.448132642517	-0.00909035587864	0.318957691278	-17.009918582	39.2520093587	12.9175761604
5	2.33768796708	0.470222537021	0.787870122446	3.74778212043	0.484540389839	3.67265762445	-0.0740234949168	-0.125546100395	0.118446933103	0.0847486962211	0.057583789124	0.182290375549	0.06138392642	-0.447041655924	0.0423709171759	0.339385782458	0.0302078110536	0.0624630650078	0.441500470121	0.00510503890601	0.260305874774	-46.5582914303	17.1293195867	-7.92644169599
6	1.96903069639	0.518813274862	-0.405188019696	1.29474890502	-0.203318433616	2.79142958318	-0.0725978853207	-0.112833856953	-0.142542010537	0.0106303839009	-0.0427300566363	-0.104689757584	0.0579768344719	0.0855046471102	0.138290542679	0.322922876983	0.0454845339672	0.00951759949387	0.301078188139	0.015519441636	0.316282351866	-27.27434334	14.2341186435	-17.9035755488
7	2.96069614924	-0.716582754233	-0.564761781076	1.76287312131	0.409937133496	2.04738486175	-0.0186043577048	0.15062031366	0.0391679351852	-0.0836226164759	-0.0601109298045	-0.0219416249656	0.149021259677	-0.316740741718	0.0892381709498	0.354301349255	-0.0707349743355	0.0136223263086	0.354548259235	0.00981626607286	0.269639261023	-44.6690340275	10.5182023496	-24.5138330941
8	3.8168783629	3.81497808484	1.16092039917	7.43427182556	1.54455039084	1.04071670322	-0.10025052885	-0.0335253355801	0.455045618576	0.0433097868934	-0.0249985247821	0.251729076834	-0.259098557002	-0.165478126923	0.124920473058	0.435095159472	0.0949758807966	-0.00260589835707	0.511788852125	0.0140248228981	0.347617097071	-45.1140440922	39.6965933172	-10.9629069592
9	3.14115368141	1.86688735874	-2.56216589102	3.83371814767	1.52365680914	6.54270244203	0.103710310544	0.181792647532	0.303277569967	-0.10525374305	-0.170806708132	0.518863282481	-0.495871606399	-0.956521882806	0.0241042751068	0.345563664126	0.137595989218	-0.0433560585328	0.742013765706	0.0490486364307	0.581196780562	-62.6896422946	27.9605964392	-21.1819994838

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 58 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 59 through 229 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 230 through 372 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 373 through 414 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 11 through 65 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 66 through 150 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 151 through 285 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 286 through 365 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 366 through 402 )

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

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Non-polymers , 5 types, 250 molecules

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-Non-polymers , 5 types, 250 molecules

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

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Non-polymers , 5 types, 250 molecules

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