PDB-3o4g: Structure and Catalysis of Acylaminoacyl Peptidase

ID or keywords:

Entry

Database: PDB / ID: 3o4g

Title

Structure and Catalysis of Acylaminoacyl Peptidase

Components

Acylamino-acid-releasing enzyme

Acylaminoacyl-peptidase

Keywords

HYDROLASE /

alpha/beta hydrolase fold /

beta propeller /

oligopeptidase / size selectivity

Function / homology

Function and homology information

acylaminoacyl-peptidase / serine-type peptidase activity /

omega peptidase 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 6, 2023	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 / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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 / _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 / _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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PDBx/mmCIF format	3o4g.cif.gz	850.8 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o4/3o4g ftp://data.pdbj.org/pub/pdb/validation_reports/o4/3o4g	HTTPS FTP

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Related structure data

Related structure data	3o4hC 3o4iC 3o4jC 2hu5S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3o4j-2 3o4h-1 3o4h-2 4re6-2 3o4j-1 1ve7-d 6irt-d 7cmi-d 1ve6-d 4re5-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
126 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	71.212, 97.016, 109.494
Angle α, β, γ (deg.)	89.01, 109.20, 100.21
Int Tables number	1
Space group name H-M	P1

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	ASP	ASP	3	A	A	322 - 510	322 - 510
2	2	1	LEU	LEU	ASP	ASP	3	C	C	322 - 510	322 - 510
1	3	1	ILE	ILE	GLU	GLU	3	A	A	512 - 580	512 - 580
2	3	1	ILE	ILE	GLU	GLU	3	C	C	512 - 580	512 - 580
1	1	2	GLU	GLU	ALA	ALA	3	B	B	8 - 21	8 - 21
2	1	2	GLU	GLU	ALA	ALA	3	D	D	8 - 21	8 - 21
1	2	2	LEU	LEU	GLU	GLU	3	B	B	322 - 580	322 - 580
2	2	2	LEU	LEU	GLU	GLU	3	D	D	322 - 580	322 - 580
1	1	3	TYR	TYR	LEU	LEU	3	A	A	25 - 317	25 - 317
2	1	3	TYR	TYR	LEU	LEU	3	C	C	25 - 317	25 - 317
1	1	4	TYR	TYR	VAL	VAL	3	B	B	25 - 95	25 - 95
2	1	4	TYR	TYR	VAL	VAL	3	D	D	25 - 95	25 - 95
1	2	4	THR	THR	LEU	LEU	4	B	B	97 - 317	97 - 317
2	2	4	THR	THR	LEU	LEU	4	D	D	97 - 317	97 - 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 / Acylaminoacyl-peptidase / AARE / Acyl-peptide hydrolase / APH / Acylaminoacyl-peptidase Mass: 63108.551 Da / Num. of mol.: 4 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 / Glycerol Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.78 Å³/Da / Density % sol: 55.79 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 78mM sodium acetate, 0.44mM EDTA, 6.7mM DITHIOTHREITOL, 2.4% PEG 4000 , pH 5.5, 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: X12 / Wavelength: 0.9786 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2008 / 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: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 2.5→20 Å / Num. all: 88675 / Num. obs: 88675 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.99 % / R_merge(I) obs: 0.089 / Net I/σ(I): 12.55
Reflection shell	Resolution: 2.5→2.56 Å / Redundancy: 1.99 % / R_merge(I) obs: 0.595 / Mean I/σ(I) obs: 2.01 / Num. unique all: 6634 / % possible all: 94.9

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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→19.64 Å / Cor.coef. F_o:F_c: 0.933 / Cor.coef. F_o:F_c free: 0.894 / SU B: 27.672 / SU ML: 0.268 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26166	4439	5 %	RANDOM
R_work	0.2152	-	-	-
all	0.21755	84232	-	-
obs	0.21755	84232	94.38 %	-

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: 37.533 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.03 Å²	0.01 Å²	-0.02 Å²
2-	-	0.02 Å²	0 Å²
3-	-	-	-0.06 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→19.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17159	0	24	340	17523

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	17544
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	11949
X-RAY DIFFRACTION	r_angle_refined_deg	1.218	1.975	23818
X-RAY DIFFRACTION	r_angle_other_deg	0.861	3	28983
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.157	5	2298
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.298	22.642	689
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.958	15	2735
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.081	15	147
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	2681
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	19864
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3658
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	0.316	1.5	11374
X-RAY DIFFRACTION	r_mcbond_other	0.138	1.5	4744
X-RAY DIFFRACTION	r_mcangle_it	0.538	2	18157
X-RAY DIFFRACTION	r_scbond_it	0.947	3	6170
X-RAY DIFFRACTION	r_scangle_it	1.472	4.5	5661
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	1602	TIGHT POSITIONAL	0.03	0.05
1	A	1912	LOOSE POSITIONAL	0.03	5
1	A	1602	TIGHT THERMAL	0.07	0.5
1	A	1912	LOOSE THERMAL	0.07	10
2	B	1592	TIGHT POSITIONAL	0.03	0.05
2	B	1770	LOOSE POSITIONAL	0.04	5
2	B	1592	TIGHT THERMAL	0.06	0.5
2	B	1770	LOOSE THERMAL	0.06	10
3	A	1704	TIGHT POSITIONAL	0.02	0.05
3	A	1932	LOOSE POSITIONAL	0.06	5
3	A	1704	TIGHT THERMAL	0.06	0.5
3	A	1932	LOOSE THERMAL	0.06	10
4	B	415	TIGHT POSITIONAL	0.08	0.05
4	B	2715	MEDIUM POSITIONAL	0.12	0.5
4	B	426	LOOSE POSITIONAL	0.14	5
4	B	415	TIGHT THERMAL	0.26	0.5
4	B	2715	MEDIUM THERMAL	0.35	2
4	B	426	LOOSE THERMAL	0.38	10

LS refinement shell

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

	R_factor	Num. reflection	% reflection
R_free	0.372	321	-
R_work	0.334	6206	-
obs	-	-	94.87 %

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	1.5042	0.489	-0.2716	1.3738	-0.0297	2.0104	-0.1755	-0.103	-0.1303	0.0517	-0.0493	-0.0429	0.2831	0.3908	0.2249	0.0793	0.1027	0.0394	0.0935	0.0162	0.0788	16.0746	5.9527	-2.457
2	1.9603	1.1558	-0.4675	2.0656	-1.9132	3.6305	-0.0769	0.4474	0.1266	-0.0794	0.4564	0.2186	-0.0065	-0.4025	-0.3795	0.0827	0.0846	0.0601	0.1831	0.0756	0.2083	-16.4219	-6.0817	-0.0964
3	1.1219	0.0661	-0.2498	2.0848	-0.3812	1.7826	0.0522	-0.0342	0.0652	0.1236	-0.0406	-0.1396	0.092	-0.0164	-0.0116	0.0921	-0.0142	-0.0408	0.0091	-0.0242	0.036	-29.0607	-0.4296	59.8544
4	2.8535	0.4334	-0.6104	2.1908	-1.04	1.5103	0.0706	-0.2313	0	0.1252	0.0621	0.0918	-0.0692	-0.0727	-0.1326	0.0422	0.0135	-0.0502	0.0263	-0.0078	0.0944	-23.906	27.2165	39.114
5	1.369	0.6178	0.1708	1.2308	0.1483	1.6387	-0.0159	0.1277	0.2136	-0.1683	0.0523	0.15	-0.3913	0.2003	-0.0363	0.1621	-0.019	-0.0305	0.0477	-0.0299	0.0605	13.131	33.754	-4.1532
6	1.7403	-0.0448	-0.5011	2.0904	0.5609	1.1146	0.076	0.2015	0.0238	0.1029	-0.0661	-0.2859	0.2237	-0.0985	-0.0099	0.1207	0.0047	-0.0333	0.0344	0.0172	0.0857	-15.9137	-32.8839	19.798
7	0.9937	-0.1764	-0.165	2.1193	-0.2022	1.3283	0.0433	0.1544	0.1645	0.0456	-0.0672	0.1734	0.2882	-0.5008	0.024	0.081	-0.0978	0.0029	0.2245	-0.0371	0.0886	-48.5318	-15.5807	46.899
8	1.4238	0.8932	-0.1235	2.5245	0.1554	2.0449	0.1179	-0.4881	-0.3405	0.3064	-0.231	-0.3112	-0.2351	0.3831	0.1131	0.0983	-0.0789	-0.0594	0.2312	0.0778	0.1576	8.029	35.5933	41.2192

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 23
2	X-RAY DIFFRACTION	1	A	319 - 581
3	X-RAY DIFFRACTION	2	B	7 - 23
4	X-RAY DIFFRACTION	2	B	319 - 581
5	X-RAY DIFFRACTION	3	C	6 - 23
6	X-RAY DIFFRACTION	3	C	319 - 581
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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