PDB-6f3n: Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pse...

ID or keywords:

Entry

Database: PDB / ID: 6f3n

Title

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa cocrystallized with SAH in the presence of K+ and Zn2+ cations

Components

Adenosylhomocysteinase

Keywords

HYDROLASE / REGULATION OF SAM-DEPENDENT METHYLATION REACTIONS

Function / homology

Function and homology information

L-homocysteine biosynthetic process / adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / one-carbon metabolic process / cytosol
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Czyrko, J. / Brzezinski, K.

Funding support

Poland, 1items

Citation

Journal: Sci Rep / Year: 2018
Title: Metal-cation regulation of enzyme dynamics is a key factor influencing the activity of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa.
Authors: Czyrko, J. / Sliwiak, J. / Imiolczyk, B. / Gdaniec, Z. / Jaskolski, M. / Brzezinski, K.

History

Deposition	Nov 28, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 8, 2018	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6f3n.cif.gz	744.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6f3n.ent.gz	614.7 KB	Display	PDB format
PDBx/mmJSON format	6f3n.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6f3n_validation.pdf.gz	3.7 MB	Display	wwPDB validaton report
Full document	6f3n_full_validation.pdf.gz	3.7 MB	Display
Data in XML	6f3n_validation.xml.gz	80.7 KB	Display
Data in CIF	6f3n_validation.cif.gz	121 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f3/6f3n ftp://data.pdbj.org/pub/pdb/validation_reports/f3/6f3n	HTTPS FTP

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Related structure data

Related structure data	6f3mC 6f3oC 6f3pC 6f3qC C: citing same article (ref.)
Similar structure data	6f3p-1 6f3m-d 6f3q-d 6aph-1 3g1u-d 1k0u-1 4pgf-1 6f3o-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.18430/M36F3N / Data set type: diffraction image data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#265 - Jan 2022 Golgi Casein Kinase similarity (1)

Deposited unit

A: Adenosylhomocysteinase

B: Adenosylhomocysteinase

C: Adenosylhomocysteinase

D: Adenosylhomocysteinase

hetero molecules

212 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, light scattering

Unit cell

Length a, b, c (Å)	170.585, 99.275, 111.721
Angle α, β, γ (deg.)	90.00, 101.90, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	D-729- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

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

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	TYR	TYR	A	A	10 - 469	13 - 472
2	1	TYR	TYR	B	B	10 - 469	13 - 472
1	2	TYR	TYR	A	A	10 - 469	13 - 472
2	2	TYR	TYR	C	C	10 - 469	13 - 472
1	3	ARG	ARG	A	A	10 - 468	13 - 471
2	3	ARG	ARG	D	D	10 - 468	13 - 471
1	4	TYR	TYR	B	B	10 - 469	13 - 472
2	4	TYR	TYR	C	C	10 - 469	13 - 472
1	5	ARG	ARG	B	B	10 - 468	13 - 471
2	5	ARG	ARG	D	D	10 - 468	13 - 471
1	6	ARG	ARG	C	C	10 - 468	13 - 471
2	6	ARG	ARG	D	D	10 - 468	13 - 471

NCS ensembles :

ID
1
2
3
4
5
6

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Adenosylhomocysteinase / S-adenosyl-L-homocysteine hydrolase / AdoHcyase Mass: 51735.031 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Gene: ahcY, sahH, PA0432 / Plasmid: pMCSG57 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus RILP / References: UniProt: Q9I685, adenosylhomocysteinase

#1: Protein

Adenosylhomocysteinase / S-adenosyl-L-homocysteine hydrolase / AdoHcyase

Mass: 51735.031 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Gene: ahcY, sahH, PA0432 / Plasmid: pMCSG57 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus RILP / References: UniProt: Q9I685, adenosylhomocysteinase

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Non-polymers , 7 types, 1632 molecules

#2: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#5: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#6: Chemical	ChemComp-ADN / ADENOSINE Mass: 267.241 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₅O₄
#7: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1611 / 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: 2.24 Å³/Da / Density % sol: 45 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 50 mM KH2PO4, 20% (w/v) PEG8000, 1 mM S-adenosyl-L-homocysteine

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.895 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 6, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.895 Å / Relative weight: 1
Reflection	Resolution: 1.85→25 Å / Num. obs: 152489 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / R_merge(I) obs: 0.082 / Net I/σ(I): 10.2
Reflection shell	Resolution: 1.85→1.92 Å

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0155	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing
ARP/wARP		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.85→24.82 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.953 / SU B: 5.215 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.109 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.17648	1485	1 %	RANDOM
R_work	0.15111	-	-	-
obs	0.15136	150603	97.89 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 20.83 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.31 Å²	-0 Å²	-0.17 Å²
2-	-	0.04 Å²	0 Å²
3-	-	-	0.31 Å²

Refinement step

Cycle: 1 / Resolution: 1.85→24.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14196	0	286	1611	16093

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.019	15128
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	14537
X-RAY DIFFRACTION	r_angle_refined_deg	1.599	1.949	20567
X-RAY DIFFRACTION	r_angle_other_deg	0.962	3	33539
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.326	5	1915
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.654	25.161	653
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.851	15	2668
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.142	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	2318
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	17938
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	3306
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.565	1.2	7468
X-RAY DIFFRACTION	r_mcbond_other	0.566	1.2	7467
X-RAY DIFFRACTION	r_mcangle_it	0.889	1.798	9360
X-RAY DIFFRACTION	r_mcangle_other	0.889	1.798	9361
X-RAY DIFFRACTION	r_scbond_it	0.806	1.335	7660
X-RAY DIFFRACTION	r_scbond_other	0.806	1.335	7659
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.273	1.968	11179
X-RAY DIFFRACTION	r_long_range_B_refined	3.778	15.702	17755
X-RAY DIFFRACTION	r_long_range_B_other	3.555	15.056	17327
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

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

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	30938	0.07
1	2	B	30938	0.07
2	1	A	31058	0.06
2	2	C	31058	0.06
3	1	A	31112	0.06
3	2	D	31112	0.06
4	1	B	30894	0.06
4	2	C	30894	0.06
5	1	B	30790	0.06
5	2	D	30790	0.06
6	1	C	30894	0.06
6	2	D	30894	0.06

LS refinement shell

Resolution: 1.85→1.898 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.253	85	-
R_work	0.224	10674	-
obs	-	-	94.03 %

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	1.0462	0.0862	-0.2687	0.471	-0.0092	1.2562	-0.0088	0.0172	-0.0002	0.0096	-0.0126	-0.0993	-0.0235	0.2332	0.0214	0.052	-0.0022	-0.0009	0.0951	0.0142	0.0362	72.3708	15.9927	19.2938
2	0.4537	-0.27	0.3044	0.7496	-0.1366	1.2373	-0.023	-0.0242	0.1128	0.0818	-0.0155	-0.0981	-0.1832	0.1105	0.0385	0.0898	-0.0254	0.0002	0.0337	0.0021	0.0394	54.2749	36.9774	27.8079
3	1.5993	0.0713	0.1199	0.5219	-0.0941	0.5276	0.032	0.2446	-0.0947	-0.0977	-0.0114	-0.067	0.0761	0.1031	-0.0205	0.0729	0.0245	0.0179	0.0574	-0.0055	0.0323	57.3503	8.1062	6.9043
4	0.7918	0.0953	-0.1924	0.692	0.0757	1.0054	-0.0087	0.0761	-0.0367	-0.0922	-0.0209	0.011	-0.0027	-0.0558	0.0296	0.0604	0.0119	0.0042	0.0216	-0.0006	0.0041	25.1484	24.6861	-8.3276
5	1.6491	-0.2936	-0.1379	0.5504	-0.1232	0.5328	-0.0292	0.0695	-0.2111	-0.0052	-0.0144	0.0524	0.0943	-0.0436	0.0435	0.0639	-0.0041	0.0163	0.0064	-0.0107	0.0305	26.966	5.7107	13.9302
6	0.89	0.0803	0.8952	0.7507	0.0336	1.0869	-0.0252	0.1807	0.0458	-0.1422	0.0001	-0.1279	-0.0875	0.2287	0.0251	0.079	-0.0107	0.0377	0.0544	0.0091	0.0352	44.0744	31.7571	-1.923
7	1.0403	-0.4346	-0.031	1.1144	0.2957	1.558	-0.1137	-0.1829	-0.0065	0.3093	0.0954	-0.0302	0.0943	0.0487	0.0183	0.2087	0.0272	-0.033	0.063	-0.0133	0.0274	48.5693	26.4912	61.4235
8	1.6578	0.1609	-0.0087	0.562	0.0281	0.3991	-0.0449	-0.1251	-0.1826	0.0766	-0.011	-0.0363	0.0924	0.0666	0.0559	0.1012	0.0062	0.0116	0.0386	0.024	0.0287	46.0746	5.5727	41.5606
9	1.1591	-0.2877	0.752	0.6657	0.0357	0.8319	-0.1171	-0.2271	0.0633	0.276	0.0395	0.0415	-0.0837	-0.1828	0.0776	0.1834	0.0111	0.0187	0.0649	-0.0269	0.0367	30.3509	34.7475	55.3908
10	0.9714	-0.1698	-0.0341	0.412	0.0854	1.1568	-0.0139	-0.0667	0.0103	0.0378	-0.0274	0.0473	-0.0029	-0.1577	0.0413	0.0584	-0.0113	0.0228	0.0603	-0.0094	0.0142	1.2276	18.8331	35.1565
11	0.601	0.0769	0.4221	0.4887	0.1113	1.6456	-0.0216	-0.0174	0.1048	-0.0099	-0.0402	0.0378	-0.2459	-0.1086	0.0619	0.0957	0.0101	0.016	0.0206	-0.0099	0.0267	20.965	38.7542	25.3106
12	0.7852	-0.0667	-0.0165	0.2506	0.0766	0.1567	-0.0227	-0.1916	-0.0757	0.0887	0.0146	-0.0006	0.0605	-0.0511	0.0081	0.0923	-0.0088	0.0206	0.0729	0.0116	0.0175	15.3151	11.9842	46.7561

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	10 - 204
2	X-RAY DIFFRACTION	2	A	205 - 382
3	X-RAY DIFFRACTION	3	A	383 - 469
4	X-RAY DIFFRACTION	4	B	10 - 198
5	X-RAY DIFFRACTION	5	B	199 - 381
6	X-RAY DIFFRACTION	6	B	382 - 469
7	X-RAY DIFFRACTION	7	C	10 - 205
8	X-RAY DIFFRACTION	8	C	206 - 382
9	X-RAY DIFFRACTION	9	C	383 - 469
10	X-RAY DIFFRACTION	10	D	9 - 205
11	X-RAY DIFFRACTION	11	D	206 - 374
12	X-RAY DIFFRACTION	12	D	375 - 469

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