PDB-5y77: Crystal structure of Pseudomonas fluorescens Kynurenine 3-monooxy...

ID or keywords:

Entry

Database: PDB / ID: 5y77

Title

Crystal structure of Pseudomonas fluorescens Kynurenine 3-monooxygenase in complex with L-KYN (seMet derivative)

Components

Kynurenine 3-monooxygenase

Keywords

OXIDOREDUCTASE / KMO / L-KYN /

enzyme / 3-hydroxy-L-kynurenine (L-3OHKyn)

Function / homology

Function and homology information

kynurenine 3-monooxygenase /

kynurenine 3-monooxygenase activity / kynurenine metabolic process / quinolinate biosynthetic process / anthranilate metabolic process / NAD(P)H oxidase H2O2-forming activity / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process / NAD metabolic process / FAD binding
Similarity search - Function

Biological species

Pseudomonas fluorescens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.6 Å

Authors

Xiang, Y. / Gao, J.J. / Zhu, D.Y.

Funding support

China, 1items

Citation

Journal: FASEB J. / Year: 2018
Title: Biochemistry and structural studies of kynurenine 3-monooxygenase reveal allosteric inhibition by Ro 61-8048
Authors: Gao, J. / Yao, L. / Xia, T. / Liao, X. / Zhu, D. / Xiang, Y.

History

Deposition	Aug 16, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 27, 2017	Provider: repository / Type: Initial release
Revision 1.1	Feb 28, 2018	Group: Database references / Category: citation Item: _citation.page_first / _citation.page_last / _citation.year
Revision 1.2	Apr 11, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5y77.cif.gz	394.1 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y7/5y77 ftp://data.pdbj.org/pub/pdb/validation_reports/y7/5y77	HTTPS FTP

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Related structure data

Related structure data	5y66C 5y7aC C: citing same article (ref.)
Similar structure data	5fn0-1 5mzi-2 5y7a-d 6fox-1 5na5-2 5nah-1 5nae-2 5mzk-2 5nag-2 5mzi-1 5nah-2 6fph-1 5fn0-3 5n7t-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

5y66C

5y7aC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Kynurenine 3-monooxygenase

B: Kynurenine 3-monooxygenase

hetero molecules

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

1

A: Kynurenine 3-monooxygenase

hetero molecules

defined by author&software
Evidence: gel filtration
53.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Kynurenine 3-monooxygenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	69.555, 52.448, 135.712
Angle α, β, γ (deg.)	90.00, 104.33, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Kynurenine 3-monooxygenase / / PfKMO / Kynurenine 3-hydroxylase Mass: 52769.598 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: kmo, qbsG / Production host: Escherichia coli (E. coli) / References: UniProt: Q84HF5, kynurenine 3-monooxygenase
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Chemical	ChemComp-KYN / (2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid / L-KYNURENINE / Kynurenine Type: L-peptide linking / Mass: 208.214 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₂N₂O₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1054 / 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: 2.3 Å³/Da / Density % sol: 46.55 %
Crystal grow	Temperature: 293 K / Method: evaporation / pH: 6 Details: 20% w/v PEG3350, 0.2 M NaCl, 0.1 M Bis-Tris at pH 6.0 and 5 mM DTT

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9789 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 11, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9789 Å / Relative weight: 1
Reflection	Resolution: 1.6→50 Å / Num. obs: 232059 / % possible obs: 94.7 % / Redundancy: 3.4 % / Net I/σ(I): 23.6

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Processing

Software

Name	Version	Classification
PHENIX	1.8.2_1309	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Resolution: 1.6→34.776 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.91

	R_factor	Num. reflection	% reflection
R_free	0.2172	5969	5.01 %
R_work	0.1852	-	-
obs	0.1867	119147	95 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.6→34.776 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7013	0	136	1054	8203

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.018	7549
X-RAY DIFFRACTION	f_angle_d	1.956	10321
X-RAY DIFFRACTION	f_dihedral_angle_d	14.872	2845
X-RAY DIFFRACTION	f_chiral_restr	0.147	1146
X-RAY DIFFRACTION	f_plane_restr	0.01	1367

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 (%)
1.6003-1.6185	0.2336	206	0.2128	3821	X-RAY DIFFRACTION	95
1.6185-1.6375	0.2688	193	0.2066	3901	X-RAY DIFFRACTION	98
1.6375-1.6575	0.2495	203	0.2023	3858	X-RAY DIFFRACTION	99
1.6575-1.6785	0.2295	189	0.1919	3879	X-RAY DIFFRACTION	99
1.6785-1.7005	0.2296	211	0.1968	3904	X-RAY DIFFRACTION	99
1.7005-1.7238	0.2254	191	0.1945	3877	X-RAY DIFFRACTION	99
1.7238-1.7485	0.241	224	0.1898	3953	X-RAY DIFFRACTION	99
1.7485-1.7746	0.226	200	0.1899	3862	X-RAY DIFFRACTION	99
1.7746-1.8023	0.2413	213	0.193	3860	X-RAY DIFFRACTION	99
1.8023-1.8318	0.2353	206	0.1923	3898	X-RAY DIFFRACTION	99
1.8318-1.8634	0.2376	224	0.203	3892	X-RAY DIFFRACTION	98
1.8634-1.8973	0.3176	192	0.2841	3536	X-RAY DIFFRACTION	90
1.8973-1.9338	0.2893	215	0.2697	3930	X-RAY DIFFRACTION	98
1.9338-1.9733	0.229	210	0.2352	3619	X-RAY DIFFRACTION	93
1.9733-2.0162	0.1901	200	0.1846	3937	X-RAY DIFFRACTION	99
2.0162-2.0631	0.2235	197	0.1775	3955	X-RAY DIFFRACTION	99
2.0631-2.1146	0.2286	193	0.1782	3917	X-RAY DIFFRACTION	99
2.1146-2.1718	0.2003	202	0.1733	3980	X-RAY DIFFRACTION	99
2.1718-2.2357	0.2268	178	0.1883	3343	X-RAY DIFFRACTION	85
2.2357-2.3078	0.2241	150	0.2088	2705	X-RAY DIFFRACTION	69
2.3078-2.3903	0.2062	212	0.1817	3967	X-RAY DIFFRACTION	99
2.3903-2.486	0.2303	207	0.1776	3958	X-RAY DIFFRACTION	100
2.486-2.5991	0.2051	219	0.1746	3936	X-RAY DIFFRACTION	100
2.5991-2.7361	0.2185	215	0.178	3957	X-RAY DIFFRACTION	100
2.7361-2.9074	0.2042	211	0.1795	4006	X-RAY DIFFRACTION	100
2.9074-3.1318	0.2233	186	0.1758	3971	X-RAY DIFFRACTION	100
3.1318-3.4467	0.1965	208	0.1679	3982	X-RAY DIFFRACTION	99
3.4467-3.9448	0.231	91	0.1752	2035	X-RAY DIFFRACTION	50
3.9448-4.9678	0.1657	210	0.1538	3857	X-RAY DIFFRACTION	96
4.9678-34.7843	0.2315	213	0.1976	3882	X-RAY DIFFRACTION	94

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	3.3874	-0.7393	-0.7711	2.2191	-0.0014	1.2179	-0.0524	-0.1172	0.0005	0.1092	0.0123	-0.1324	0.0338	0.0272	0.032	0.073	0.0019	-0.0045	0.0633	-0.0103	0.0361	1.44	36.9027	66.4154
2	2.0289	0.2541	0.5681	1.9974	0.3419	2.5664	-0.0101	0.0234	-0.2286	-0.1247	-0.0602	0.1891	0.161	-0.2663	0.0467	0.1713	0.006	0.0346	0.1302	-0.0024	0.1644	-10.2191	19.9338	56.6322
3	3.3007	1.2353	1.9934	2.701	1.3114	3.2683	-0.0365	0.156	-0.2072	-0.0507	0.0159	0.146	0.214	-0.018	0.0646	0.0991	-0.0226	0.0491	0.1126	0.0157	0.1001	-8.833	20.1067	58.3957
4	1.0057	0.4513	0.1695	0.7316	0.2494	0.6947	-0.0923	0.1632	0.1377	-0.1524	0.0868	0.0392	-0.0913	-0.0038	0.018	0.1277	0.0107	0.0016	0.1075	0.0419	0.1086	-9.5733	35.5153	48.5529
5	2.6838	0.3844	0.972	0.5993	0.0849	0.7291	-0.0268	0.0352	-0.0657	-0.1176	0.0375	0.0193	0.0431	-0.0547	-0.0192	0.1642	-0.002	0.0276	0.1321	0.0154	0.1375	-0.5332	29.9594	49.1793
6	1.2196	-0.7817	-0.5513	2.5921	2.0557	1.8415	-0.03	0.2006	-0.0911	-0.1433	-0.2158	0.1754	0.1485	-0.159	0.1949	0.3272	0.0172	0.0797	0.2145	-0.0144	0.209	1.8209	8.9377	39.786
7	1.7048	-0.2516	-1.0835	0.3339	-0.4163	2.9059	-0.003	-0.0979	-0.0556	0.5606	-0.0814	0.2822	0.8492	0.448	0.0604	0.5708	0.1216	0.1075	0.334	-0.0165	0.2968	6.154	0.525	36.795
8	1.115	0.1957	-1.1536	2.6599	-0.561	1.4298	-0.015	0.2554	0.202	-0.0342	-0.081	-0.1437	-0.0329	0.0625	0.0451	0.113	-0.0296	-0.0222	0.1854	0.0282	0.1076	20.034	7.2736	0.7414
9	4.7441	-0.529	2.8653	1.4367	-0.5054	4.1125	0.1946	-0.0404	-0.798	0.0823	-0.0137	-0.1772	0.3608	0.3339	-0.1993	0.2453	0.0147	-0.0132	0.2159	-0.0049	0.3182	26.1776	-13.7945	11.7636
10	1.8117	-0.5872	0.3516	1.073	-0.331	0.8563	-0.1318	-0.0339	0.2847	0.1655	0.1102	-0.1513	-0.1523	0.0741	0.0195	0.1615	-0.0417	-0.011	0.1586	-0.0404	0.1935	24.8888	6.6439	12.4826
11	1.8791	-0.6214	0.1102	1.5377	0.3961	1.7745	-0.0379	-0.2079	0.1687	0.206	0.2175	-0.4375	-0.1149	0.4806	-0.079	0.1959	-0.0571	-0.0136	0.2532	-0.0889	0.2484	26.1038	3.7489	19.3758
12	0.1178	0.1953	-0.4411	1.2062	-1.284	1.7573	-0.0707	-0.2651	-0.3268	0.034	-0.0486	-0.0444	0.2772	0.1561	0.1629	0.2847	0.0056	0.0615	0.1899	0.0007	0.2383	15.3294	-9.3328	23.4888
13	0.7258	0.526	-0.4089	2.9125	-3.1167	4.1514	-0.0991	-0.0927	-0.1295	-0.2394	0.0426	0.1183	0.4313	-0.0846	0.0554	0.3542	-0.0232	0.1075	0.1945	-0.013	0.2627	11.6349	-19.8208	27.1538

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 7 through 46 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 47 through 91 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 92 through 125 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 126 through 269 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 270 through 374 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 375 through 432 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 433 through 461 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 8 through 58 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 59 through 105 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 106 through 247 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 248 through 343 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 344 through 395 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 396 through 458 )

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