PDB-3o4j: Structure and Catalysis of Acylaminoacyl Peptidase

ID or keywords:

Entry

Database: PDB / ID: 3o4j

Title

Structure and Catalysis of Acylaminoacyl Peptidase

Components

Acylamino-acid-releasing enzyme

Keywords

HYDROLASE / alpha/beta hydrolase fold / beta propeller / oligopeptidase / size selectivity

Function / homology

Function and homology information

acylaminoacyl-peptidase / omega peptidase activity / serine-type endopeptidase activity / proteolysis / cytoplasm
Similarity search - Function

Biological species

Aeropyrum pernix (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Harmat, V. / Domokos, K. / Menyhard, D.K. / Pallo, A. / Szeltner, Z. / Szamosi, I. / Beke-Somfai, T. / Naray-Szabo, G. / Polgar, L.

Citation

Journal: J.Biol.Chem. / Year: 2011
Title: Structure and Catalysis of Acylaminoacyl Peptidase: CLOSED AND OPEN SUBUNITS OF A DIMER OLIGOPEPTIDASE.
Authors: Harmat, V. / Domokos, K. / Menyhard, D.K. / Pallo, A. / Szeltner, Z. / Szamosi, I. / Beke-Somfai, T. / Naray-Szabo, G. / Polgar, L.

History

Deposition	Jul 27, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 17, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Sep 27, 2017	Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3	Oct 6, 2021	Group: Data collection / Database references / Derived calculations Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Sep 6, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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	3o4j.cif.gz	881.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3o4j_validation.pdf.gz	469.2 KB	Display	wwPDB validaton report
Full document	3o4j_full_validation.pdf.gz	502.2 KB	Display
Data in XML	3o4j_validation.xml.gz	84.6 KB	Display
Data in CIF	3o4j_validation.cif.gz	118 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o4/3o4j ftp://data.pdbj.org/pub/pdb/validation_reports/o4/3o4j	HTTPS FTP

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Related structure data

Related structure data	3o4gC 3o4hC 3o4iC 2hu5S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4re6-2 4re6-1 3o4g-2 3c1n-3 3c20-d 3o4g-1 2cdq-d 3o4h-1 3ohn-3 3o4i-d 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#202 - Oct 2016 Dipeptidyl Peptidase 4 similarity (2)

Deposited unit

A: Acylamino-acid-releasing enzyme

B: Acylamino-acid-releasing enzyme

C: Acylamino-acid-releasing enzyme

D: Acylamino-acid-releasing enzyme

hetero molecules

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

1

A: Acylamino-acid-releasing enzyme

B: Acylamino-acid-releasing enzyme

hetero molecules

defined by author&software
126 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Acylamino-acid-releasing enzyme

D: Acylamino-acid-releasing enzyme

hetero molecules

defined by author&software
127 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	184.270, 227.524, 110.684
Angle α, β, γ (deg.)	90.00, 100.37, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

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

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	PRO	PRO	ALA	ALA	3	A	A	6 - 21	6 - 21
2	1	1	PRO	PRO	ALA	ALA	3	C	C	6 - 21	6 - 21
1	2	1	LEU	LEU	GLU	GLU	3	A	A	322 - 580	322 - 580
2	2	1	LEU	LEU	GLU	GLU	3	C	C	322 - 580	322 - 580
1	1	2	PRO	PRO	ALA	ALA	3	B	B	6 - 21	6 - 21
2	1	2	PRO	PRO	ALA	ALA	3	D	D	6 - 21	6 - 21
1	2	2	LEU	LEU	SER	SER	3	B	B	322 - 340	322 - 340
2	2	2	LEU	LEU	SER	SER	3	D	D	322 - 340	322 - 340
1	3	2	ASP	ASP	GLU	GLU	3	B	B	342 - 580	342 - 580
2	3	2	ASP	ASP	GLU	GLU	3	D	D	342 - 580	342 - 580
1	1	3	TYR	TYR	LEU	LEU	3	A	A	25 - 187	25 - 187
2	1	3	TYR	TYR	LEU	LEU	3	C	C	25 - 187	25 - 187
1	2	3	VAL	VAL	LEU	LEU	4	A	A	189 - 317	189 - 317
2	2	3	VAL	VAL	LEU	LEU	4	C	C	189 - 317	189 - 317
1	1	4	TYR	TYR	LEU	LEU	3	B	B	25 - 317	25 - 317
2	1	4	TYR	TYR	LEU	LEU	3	D	D	25 - 317	25 - 317

NCS ensembles :

ID
1
2
3
4

Details

The biological assembly is homodimer. One dimer consists of chains A and B, and the other dimer consists of chains C and D.

#1: Protein	Acylamino-acid-releasing enzyme / AARE / Acyl-peptide hydrolase / APH / Acylaminoacyl-peptidase Mass: 63107.566 Da / Num. of mol.: 4 / Mutation: D524N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeropyrum pernix (archaea) / Gene: APE_1547.1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YBQ2, acylaminoacyl-peptidase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 535 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 4.52 Å³/Da / Density % sol: 72.79 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 170mM sodium acetate, 0.4mM EDTA, 10% dimethyl sulphoxide, 2.5% PEG 4000 , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8148 Å
Detector	Type: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Dec 12, 2009 / Details: mirror
Radiation	Monochromator: Double crystal Si(111), horizontally focussing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8148 Å / Relative weight: 1
Reflection	Resolution: 2.5→30 Å / Num. all: 149375 / Num. obs: 149375 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / R_merge(I) obs: 0.092 / Net I/σ(I): 11.43
Reflection shell	Resolution: 2.5→2.6 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.642 / Mean I/σ(I) obs: 2.48 / Num. unique all: 16732 / % possible all: 98.8

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Processing

Software

Name	Version	Classification
MAR345dtb		data collection
MOLREP		phasing
REFMAC	5.5.0102	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: Hydrolase and propeller domains of PDB entry 2HU5.

2hu5

Resolution: 2.5→29.52 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.92 / SU B: 17.687 / SU ML: 0.17 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23589	7519	5 %	RANDOM
R_work	0.19914	-	-	-
all	0.20099	141856	-	-
obs	0.20099	141856	96.89 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 35.233 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.02 Å²	0 Å²	-0.02 Å²
2-	-	0.11 Å²	0 Å²
3-	-	-	-0.09 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→29.52 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17452	0	33	535	18020

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.022	17965
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	12417
X-RAY DIFFRACTION	r_angle_refined_deg	1.748	1.974	24378
X-RAY DIFFRACTION	r_angle_other_deg	1.12	3	30039
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.245	5	2330
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.229	22.487	760
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.887	15	2874
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.254	15	174
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	2705
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	20338
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	3816
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	0.642	1.5	11445
X-RAY DIFFRACTION	r_mcbond_other	0.354	1.5	4770
X-RAY DIFFRACTION	r_mcangle_it	1.065	2	18333
X-RAY DIFFRACTION	r_scbond_it	1.855	3	6520
X-RAY DIFFRACTION	r_scangle_it	2.818	4.5	6033
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	1606	TIGHT POSITIONAL	0.04	0.05
1	A	1965	LOOSE POSITIONAL	0.1	5
1	A	1606	TIGHT THERMAL	0.16	0.5
1	A	1965	LOOSE THERMAL	0.16	10
2	B	1581	TIGHT POSITIONAL	0.05	0.05
2	B	1878	LOOSE POSITIONAL	0.13	5
2	B	1581	TIGHT THERMAL	0.16	0.5
2	B	1878	LOOSE THERMAL	0.16	10
3	A	939	TIGHT POSITIONAL	0.08	0.05
3	A	1667	MEDIUM POSITIONAL	0.12	0.5
3	A	1062	LOOSE POSITIONAL	0.22	5
3	A	939	TIGHT THERMAL	0.67	0.5
3	A	1667	MEDIUM THERMAL	0.8	2
3	A	1062	LOOSE THERMAL	0.96	10
4	B	1700	TIGHT POSITIONAL	0.04	0.05
4	B	1984	LOOSE POSITIONAL	0.08	5
4	B	1700	TIGHT THERMAL	0.16	0.5
4	B	1984	LOOSE THERMAL	0.15	10

LS refinement shell

Resolution: 2.5→2.564 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.412	519	-
R_work	0.345	10589	-
obs	-	-	98.01 %

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	1.4875	0.3444	-0.6158	1.8152	-0.1209	2.0207	-0.132	0.1256	0.0044	-0.3521	0.1681	0.1767	0.0804	-0.3727	-0.0361	0.2268	-0.2145	-0.0306	0.2845	-0.0208	0.1339	-38.7161	-12.1574	-39.166
2	1.6748	0.9444	-0.6865	2.1468	0.6791	2.685	-0.1758	0.1998	0.0472	-0.2323	0.1961	0.0316	0.022	-0.0717	-0.0203	0.0326	-0.0191	-0.0169	0.1068	-0.0012	0.1005	-19.9995	11.4554	-21.6441
3	1.405	-0.1534	-0.075	1.7691	-0.153	1.1558	0.0751	0.0482	-0.0637	-0.2044	-0.061	-0.0574	0.2717	0.1542	-0.0141	0.1157	0.083	0.0115	0.1457	-0.0039	0.0775	33.8684	0.4366	-37.2396
4	1.5289	0.5073	0.8146	3.0698	-1.1158	2.7182	-0.1191	0.0415	-0.2188	-0.2851	0.2159	0.3703	0.0191	-0.1221	-0.0968	0.1151	0.093	0.0118	0.1799	0.0235	0.2842	17.0992	-22.557	-17.1486
5	1.3218	0.5079	-0.6168	1.9723	-0.2233	2.2087	-0.2507	0.1211	-0.2325	-0.5058	0.1453	-0.3095	0.6878	0.1316	0.1054	0.4546	-0.1362	0.1464	0.2243	-0.1266	0.2621	-23.5215	-35.5086	-38.2769
6	1.7	-0.5429	0.4474	2.6938	-0.1785	1.4631	0.0508	0.0776	0.0004	-0.3148	-0.0276	0.338	-0.1494	-0.2214	-0.0232	0.0655	0.0569	-0.0483	0.1223	-0.0201	0.1407	-40.716	31.3309	-5.502
7	1.4061	0.1335	0.3455	1.1378	-0.2657	1.6703	-0.0141	0.0444	0.1014	-0.1434	-0.0221	0.0291	-0.0774	-0.0335	0.0363	0.0277	0.0146	-0.0109	0.0866	0.0085	0.083	19.3873	24.248	-34.3941
8	1.7032	-0.7392	-0.5782	2.9293	0.4437	1.7656	0.1303	0.105	-0.0039	-0.0971	0.0145	-0.079	0.0537	0.0631	-0.1447	0.1676	0.1143	-0.0195	0.1294	0.0705	0.1803	39.2274	-42.9765	-4.5539

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 23
2	X-RAY DIFFRACTION	1	A	319 - 581
3	X-RAY DIFFRACTION	2	B	6 - 23
4	X-RAY DIFFRACTION	2	B	319 - 581
5	X-RAY DIFFRACTION	3	C	4 - 23
6	X-RAY DIFFRACTION	3	C	319 - 582
7	X-RAY DIFFRACTION	4	D	6 - 23
8	X-RAY DIFFRACTION	4	D	319 - 581
9	X-RAY DIFFRACTION	5	A	24 - 318
10	X-RAY DIFFRACTION	6	B	24 - 318
11	X-RAY DIFFRACTION	7	C	24 - 318
12	X-RAY DIFFRACTION	8	D	24 - 318

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