PDB-3awi: Bifunctional tRNA modification enzyme MnmC from Escherichia coli

ID or keywords:

Entry

Database: PDB / ID: 3awi

Title

Bifunctional tRNA modification enzyme MnmC from Escherichia coli

Components

tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmC

Keywords

TRANSFERASE /

OXIDOREDUCTASE / tRNA modification /

Rossmann Fold /

RNA binding

Function / homology

Function and homology information

Oxidoreductases; Acting on the CH-NH group of donors / tRNA (5-methylaminomethyl-2-thiouridylate)(34)-methyltransferase activity / oxidoreductase activity, acting on the CH-NH group of donors / tRNA 5-(aminomethyl)-2-thiouridylate-methyltransferase / tRNA wobble uridine modification / tRNA methylation / FAD binding /

oxidoreductase activity /

cytoplasm
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3 Å

Authors

Kitamura, A. / Sengoku, T. / Nishimoto, M. / Yokoyama, S. / Bessho, Y.

Citation

Journal: Protein Sci. / Year: 2011
Title: Crystal structure of the bifunctional tRNA modification enzyme MnmC from Escherichia coli
Authors: Kitamura, A. / Sengoku, T. / Nishimoto, M. / Yokoyama, S. / Bessho, Y.

History

Deposition	Mar 23, 2011	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 1, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 12, 2014	Group: Structure summary
Revision 1.3	Mar 13, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3awi.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb3awi.ent.gz	1.2 MB	Display	PDB format
PDBx/mmJSON format	3awi.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/aw/3awi ftp://data.pdbj.org/pub/pdb/validation_reports/aw/3awi	HTTPS FTP

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Related structure data

Similar structure data	3ps9-d 3sgl-d 449 3pvc-d 4i8d-1 3af5-d 5o6d-1 3ekg-d 2ww4-d 4m26-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmC

B: tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmC

C: tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmC

D: tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmC

E: tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmC

F: tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmC

hetero molecules

466 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmC

hetero molecules

defined by author&software
77.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmC

hetero molecules

defined by author&software
77.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmC

hetero molecules

defined by author&software
77.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmC

hetero molecules

defined by author&software
77.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmC

hetero molecules

defined by author&software
77.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

F: tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmC

hetero molecules

defined by author&software
77.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	92.138, 243.022, 175.527
Angle α, β, γ (deg.)	90.00, 90.42, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmC / tRNA mnm(5)s(2)U biosynthesis bifunctional protein / tRNA (mnm(5)s(2)U34)-methyltransferase / FAD- ...tRNA mnm(5)s(2)U biosynthesis bifunctional protein / tRNA (mnm(5)s(2)U34)-methyltransferase / FAD-dependent cmnm(5)s(2)U34 oxidoreductase Mass: 76679.266 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: mnmC, yfcK, b2324, JW5380 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) References: UniProt: P77182, tRNA 5-(aminomethyl)-2-thiouridylate-methyltransferase, Oxidoreductases; Acting on the CH-NH group of donors
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.27 Å³/Da / Density % sol: 71.2 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M Bis-Tris (pH 5.5), 25% PEG 3350, 0.25M ammonium sulfate, 10mM hexamine cobalt(III), VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 17, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3→50 Å / Num. all: 154235 / Num. obs: 151613 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / B_iso Wilson estimate: 58.34 Å²
Reflection shell	Resolution: 3→3.11 Å / % possible all: 94

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7_650)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 3→46.068 Å / FOM work R set: 0.8249 / SU ML: 0.43 / σ(F): 0.01 / Phase error: 24.96 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2514	1685	1.15 %	RANDOM
R_work	0.2045	-	-	-
obs	0.205	146580	95.28 %	-
all	-	153841	-	-

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 44.474 Å² / k_sol: 0.316 e/Å³

Displacement parameters

B_iso mean: 87.7729 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-19.4256 Å²	0 Å²	-2.8705 Å²
2-	-	-7.7211 Å²	0 Å²
3-	-	-	-13.0907 Å²

Refinement step

Cycle: LAST / Resolution: 3→46.068 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	29853	0	373	61	30287

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	32051
X-RAY DIFFRACTION	f_angle_d	1.026	42253
X-RAY DIFFRACTION	f_dihedral_angle_d	15.44	11206
X-RAY DIFFRACTION	f_chiral_restr	0.076	4505
X-RAY DIFFRACTION	f_plane_restr	0.004	5539

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 (%)
3-3.1072	0.3494	148	0.3049	12613	X-RAY DIFFRACTION	83
3.1072-3.2316	0.3063	156	0.2446	13301	X-RAY DIFFRACTION	88
3.2316-3.3786	0.2834	161	0.2304	13993	X-RAY DIFFRACTION	92
3.3786-3.5567	0.261	172	0.2086	14505	X-RAY DIFFRACTION	96
3.5567-3.7794	0.2476	167	0.1973	14780	X-RAY DIFFRACTION	98
3.7794-4.0711	0.2295	175	0.1816	14999	X-RAY DIFFRACTION	99
4.0711-4.4804	0.2313	175	0.1617	15090	X-RAY DIFFRACTION	99
4.4804-5.128	0.2258	176	0.1736	15156	X-RAY DIFFRACTION	100
5.128-6.458	0.2393	174	0.218	15150	X-RAY DIFFRACTION	100
6.458-46.0732	0.2572	181	0.2253	15308	X-RAY DIFFRACTION	100

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	0.6679	-0.6377	0.0766	0.9141	0.2564	0.4933	-0.1022	0.1151	0.0378	-0.1411	0.1857	0.1695	-0.1199	-0.2891	-0.0872	0.5013	0.0479	-0.1032	0.5234	0.1246	0.4676	41.9401	200.8491	61.8362
2	0.685	-0.2788	0.1124	1.1176	-0.6124	0.3702	-0.0099	0.4193	0.2272	-0.318	0.08	-0.0865	0.079	-0.0217	-0.0628	0.4985	-0.0681	-0.0067	0.611	0.103	0.4418	53.4715	199.8824	53.258
3	0.3514	-0.0732	-0.1174	0.0652	0.021	0.3022	-0.068	0.1916	-0.0598	0.0237	0.1682	-0.0481	0.0395	0.0027	-0.0218	0.3541	-0.0565	-0.0714	0.1979	-0.045	0.2885	55.3461	188.5841	64.7357
4	0.3972	-0.0164	0.0665	0.0823	0.1564	0.5377	-0.0445	0.0161	0.005	-0.0694	0.0926	-0.0396	-0.0191	0.1082	-0.0482	0.3392	0.0078	-0.0467	0.2637	-0.0719	0.42	68.159	202.3609	87.5664
5	0.1314	-0.0561	0.1676	0.1712	0.0595	0.2939	-0.1939	0.002	0.1108	0.0716	-0.1248	-0.0368	-0.0364	0.1074	0.2584	0.3133	-0.0166	0.0227	0.3033	-0.0063	0.4159	77.0178	191.5564	79.0017
6	0.2248	-0.0712	-0.1063	0.133	0.0123	0.7991	-0.1172	0.1647	-0.0995	-0.0996	0.0788	0.0293	-0.1009	0.1671	0.0298	0.3415	0.0562	0.0042	0.3699	-0.0801	0.326	69.8108	190.2158	69.698
7	0.4233	0.0516	-0.1965	0.3458	0.0318	0.3314	-0.1447	0.1813	0.1066	0.0211	-0.0073	0.0676	-0.0129	-0.0906	0.1242	0.1443	0.0182	-0.0282	0.1806	-0.0016	0.3585	61.6645	121.8775	48.4459
8	0.2182	-0.096	-0.0229	0.6224	-0.0357	0.0696	0.0918	0.0941	0.2354	0.1719	-0.0909	0.1726	-0.075	-0.0652	0.0025	0.239	-0.0117	0.0048	0.1998	0.0101	0.5062	63.6951	132.5488	58.6704
9	0.4347	-0.2089	-0.0019	0.1381	0.1119	0.2307	0.0193	-0.2996	-0.2557	0.0653	-0.0303	-0.0731	0.0375	0.0075	-0.0073	0.1511	-0.0375	0.0157	0.2594	0.111	0.406	70.0017	101.8747	74.8474
10	0.1283	-0.0298	0.0539	0.1009	-0.1535	0.2842	0.037	0.0013	-0.1963	-0.0004	0.0992	-0.0435	0.0297	-0.0198	-0.1065	0.2398	0.0434	-0.0478	0.1951	-0.0874	0.4397	22.1415	97.4837	53.2011
11	0.0883	0.1177	-0.0247	0.4461	0.1111	0.0978	0.1217	0.1343	-0.1013	0.178	0.0124	-0.1947	0.0286	0.0233	-0.0601	0.0992	0.0399	0.0062	0.1905	-0.0381	0.3654	29.6965	110.2075	55.4284
12	0.3051	0.0161	-0.0697	0.4408	-0.1238	0.1923	0.0323	0.3643	0.0499	-0.1024	0.0847	0.0687	0.0061	0.042	-0.0587	0.2422	0.0269	0.0165	0.6642	-0.0954	0.2733	11.5448	111.3252	23.077
13	0.0908	-0.0803	-0.0483	0.1007	0.0256	0.025	-0.0891	0.0719	0.165	-0.0783	0.2303	0.0358	-0.0406	0.1428	-0.141	0.2373	-0.0155	0.0149	0.5587	-0.0085	0.4974	15.9875	122.4785	36.5308
14	0.249	-0.1729	0.0322	0.133	-0.047	0.0673	-0.2058	-0.049	0.0202	0.0676	0.2006	-0.1289	-0.0592	0.0493	0.0042	0.8631	-0.0781	0.0206	0.2755	-0.0458	0.7211	48.3736	135.9364	95.4704
15	0.3012	-0.0881	-0.0316	0.0482	-0.0102	0.1845	-0.1561	-0.0811	-0.0144	0.4201	0.1822	0.0594	0.007	-0.0683	-0.025	0.5726	0.0052	0.0811	0.2916	-0.0641	0.4771	47.9735	151.2355	89.7395
16	0.2531	0.0075	-0.0251	0.0301	-0.0719	0.2589	-0.2158	0.0015	-0.2221	0.3699	0.0372	-0.3301	0.098	0.0365	0.0855	0.4946	-0.0016	0.0185	0.226	-0.0818	0.602	60.2435	141.5385	81.9786
17	0.1079	0.0947	0.1184	0.5999	-0.1501	0.2674	-0.1879	0.2857	-0.2958	-0.1236	0.2756	1.066	-0.1473	-0.4334	-0.0931	0.1293	-0.1872	0.1149	0.5618	0.0981	1.1055	24.8138	156.1816	73.5645
18	0.1941	-0.0302	0.1122	0.2954	0.1093	0.1887	0.0142	0.0163	0.0045	-0.0404	0.2138	0.0506	0.0854	-0.2042	-0.1864	0.5162	-0.1796	-0.0773	0.9529	0.173	0.3874	85.6734	202.3563	9.4827
19	0.1387	0.1728	0.0924	0.1594	-0.0259	0.2208	0.3102	-0.5482	-0.2996	0.1858	-0.1209	-0.1135	0.0911	-0.7341	0.211	0.3209	-0.2021	-0.485	1.1659	0.3543	-0.1001	94.0112	196.3074	40.9814
20	0.1054	0.0707	-0.0987	0.2502	-0.0109	0.3069	0.1522	0.192	0.2162	0.0699	-0.0072	0.0261	-0.01	-0.0976	-0.1147	0.3879	0.0162	-0.0942	0.9564	0.0021	0.5756	-25.9165	113.4902	13.2649
21	0.0408	-0.0332	0.0031	0.0347	0.003	0.0154	0.0822	0.2149	0.0838	0.0091	-0.1792	0.3007	0.0405	0.0511	0.0512	0.9767	0.023	-0.0997	1.5101	0.106	1.4092	-37.5385	130.1176	9.4598
22	0.0436	-0.0871	0.0439	0.3273	-0.2122	0.1641	-0.0209	0.235	0.1416	-0.0405	0.127	0.3492	-0.0371	-0.1241	-0.0958	1.0183	0.1206	0.0267	1.1821	0.1546	1.3579	-12.9368	141.0894	11.7194
23	0.0522	-0.1126	0.0273	0.5744	-0.1607	0.2424	0.0244	0.0424	0.2795	0.0785	0.1527	0.0941	-0.0153	-0.0223	-0.1595	1.0726	0.0241	-0.0976	1.1597	0.2262	1.3929	-16.7029	144.6818	5.2488
24	0.0085	0.0552	-0.0132	0.6698	-0.1029	0.39	-0.0313	0.2001	0.1669	-0.016	-0.0509	-0.2146	-0.0456	0.2343	0.0619	0.9902	0.1073	0.21	1.1325	0.2844	1.5516	-4.5187	151.2846	10.8462
25	0.4107	-0.2101	-0.3074	0.8003	0.0235	0.2572	-0.0587	0.0839	0.1526	0.2935	-0.0789	-0.2882	0.0337	-0.0621	0.093	1.3014	0.0009	0.0476	1.1728	0.1591	1.8047	-1.9948	160.2537	16.1437
26	0.0389	-0.1126	0.0522	0.3847	-0.1405	0.1526	-0.07	0.4825	-0.1033	0.07	0.013	0.2399	-0.034	0.0526	0.0545	1.0295	0.1952	0.0256	1.3281	0.1686	1.5684	-28.7234	145.0459	13.7165

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 35:129)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 130:230)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 231:294)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 295:554)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 555:596)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 597:662)
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 35:130)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 131:254)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 255:662)
10	X-RAY DIFFRACTION	10	chain 'C' and (resseq 35:130)
11	X-RAY DIFFRACTION	11	chain 'C' and (resseq 131:254)
12	X-RAY DIFFRACTION	12	chain 'C' and (resseq 255:596)
13	X-RAY DIFFRACTION	13	chain 'C' and (resseq 597:662)
14	X-RAY DIFFRACTION	14	chain 'D' and (resseq 1:41)
15	X-RAY DIFFRACTION	15	chain 'D' and (resseq 42:163)
16	X-RAY DIFFRACTION	16	chain 'D' and (resseq 164:238)
17	X-RAY DIFFRACTION	17	chain 'D' and (resseq 239:662)
18	X-RAY DIFFRACTION	18	chain 'E' and (resseq 35:243)
19	X-RAY DIFFRACTION	19	chain 'E' and (resseq 244:662)
20	X-RAY DIFFRACTION	20	chain 'F' and (resseq 35:239)
21	X-RAY DIFFRACTION	21	chain 'F' and (resseq 240:273)
22	X-RAY DIFFRACTION	22	chain 'F' and (resseq 274:368)
23	X-RAY DIFFRACTION	23	chain 'F' and (resseq 369:467)
24	X-RAY DIFFRACTION	24	chain 'F' and (resseq 468:517)
25	X-RAY DIFFRACTION	25	chain 'F' and (resseq 518:554)
26	X-RAY DIFFRACTION	26	chain 'F' and (resseq 555:662)

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Open data

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Download

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Validation report

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Assembly

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Experimental details

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Data collection

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi