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- PDB-3o4h: Structure and Catalysis of Acylaminoacyl Peptidase -

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Basic information

Entry
Database: PDB / ID: 3o4h
TitleStructure and Catalysis of Acylaminoacyl Peptidase
ComponentsAcylamino-acid-releasing enzyme
KeywordsHYDROLASE / 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
Peptidase/esterase 'gauge' domain / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / 7 Propeller / Methylamine Dehydrogenase; Chain H / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Acylamino-acid-releasing enzyme
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsHarmat, V. / Domokos, K. / Menyhard, D.K. / Pallo, A. / Szeltner, Z. / Szamosi, I. / Beke-Somfai, T. / Naray-Szabo, G. / Polgar, L.
CitationJournal: 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
DepositionJul 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Oct 6, 2021Group: 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_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_label_asym_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_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acylamino-acid-releasing enzyme
B: Acylamino-acid-releasing enzyme
C: Acylamino-acid-releasing enzyme
D: Acylamino-acid-releasing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,76511
Polymers252,2584
Non-polymers5067
Water16,718928
1
A: Acylamino-acid-releasing enzyme
B: Acylamino-acid-releasing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,4286
Polymers126,1292
Non-polymers2994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-30 kcal/mol
Surface area39700 Å2
MethodPISA
2
C: Acylamino-acid-releasing enzyme
D: Acylamino-acid-releasing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,3365
Polymers126,1292
Non-polymers2073
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-31 kcal/mol
Surface area39930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.405, 97.979, 98.797
Angle α, β, γ (deg.)105.69, 103.52, 100.36
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13A
23C
14B
24D

NCS domain segments:

Refine code: 3

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROSERSERAA6 - 106 - 10
211PROPROSERSERCC6 - 106 - 10
121ILEILEALAALAAA12 - 2112 - 21
221ILEILEALAALACC12 - 2112 - 21
131LEULEUSERSERAA322 - 344322 - 344
231LEULEUSERSERCC322 - 344322 - 344
141VALVALALAALAAA346 - 430346 - 430
241VALVALALAALACC346 - 430346 - 430
151GLUGLUGLYGLYAA432 - 434432 - 434
251GLUGLUGLYGLYCC432 - 434432 - 434
161ALAALAALAALAAA436 - 541436 - 541
261ALAALAALAALACC436 - 541436 - 541
171GLYGLYGLUGLUAA543 - 580543 - 580
271GLYGLYGLUGLUCC543 - 580543 - 580
112VALVALALAALABB7 - 217 - 21
212VALVALALAALADD7 - 217 - 21
122LEULEUPHEPHEBB322 - 341322 - 341
222LEULEUPHEPHEDD322 - 341322 - 341
132GLYGLYSERSERBB343 - 344343 - 344
232GLYGLYSERSERDD343 - 344343 - 344
142VALVALALAALABB346 - 427346 - 427
242VALVALALAALADD346 - 427346 - 427
152TRPTRPALAALABB429 - 430429 - 430
252TRPTRPALAALADD429 - 430429 - 430
162SERSERARGARGBB433 - 579433 - 579
262SERSERARGARGDD433 - 579433 - 579
113LEULEUGLYGLYAA27 - 4027 - 40
213LEULEUGLYGLYCC27 - 4027 - 40
123SERSERLEULEUAA42 - 31742 - 317
223SERSERLEULEUCC42 - 31742 - 317
114TYRTYRHISHISBB25 - 7125 - 71
214TYRTYRHISHISDD25 - 7125 - 71
124GLYGLYTHRTHRBB73 - 9773 - 97
224GLYGLYTHRTHRDD73 - 9773 - 97
134ARGARGASPASPBB99 - 15899 - 158
234ARGARGASPASPDD99 - 15899 - 158
144ARGARGLEULEUBB160 - 317160 - 317
244ARGARGLEULEUDD160 - 317160 - 317

NCS ensembles :
ID
1
2
3
4
DetailsThe biological assembly is homodimer. One dimer consists of chains A and B, and the other dimer consists of chains C and D.

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Components

#1: Protein
Acylamino-acid-releasing enzyme / AARE / Acyl-peptide hydrolase / APH / Acylaminoacyl-peptidase


Mass: 63064.543 Da / Num. of mol.: 4 / Mutation: D524A
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 928 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.34 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8148 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Dec 11, 2009 / Details: mirror
RadiationMonochromator: Double crystal Si(111), horizontally focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8148 Å / Relative weight: 1
ReflectionResolution: 1.82→30 Å / Num. all: 206854 / Num. obs: 206854 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.88 % / Rmerge(I) obs: 0.028 / Net I/σ(I): 22.72
Reflection shellResolution: 1.82→1.87 Å / Redundancy: 1.88 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 2.26 / Num. unique all: 15188 / % possible all: 94.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Hydrolase and propeller domains of PDB entry 2HU5.

2hu5


Resolution: 1.82→24.62 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 8.964 / SU ML: 0.118 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23366 10388 5 %RANDOM
Rwork0.20314 ---
all0.20468 196431 --
obs0.20468 196431 95.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.26 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20.03 Å20.04 Å2
2--0.09 Å20.06 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.82→24.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17118 0 32 928 18078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02217614
X-RAY DIFFRACTIONr_bond_other_d0.0080.0211984
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.97423937
X-RAY DIFFRACTIONr_angle_other_deg1.426329051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.33552322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.21822.442692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.42152720
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.00615152
X-RAY DIFFRACTIONr_chiral_restr0.0980.22694
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02119995
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023712
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7751.511413
X-RAY DIFFRACTIONr_mcbond_other0.4831.54756
X-RAY DIFFRACTIONr_mcangle_it1.157218228
X-RAY DIFFRACTIONr_scbond_it2.02636201
X-RAY DIFFRACTIONr_scangle_it2.9244.55699
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1553TIGHT POSITIONAL0.060.05
1A1739LOOSE POSITIONAL0.165
1A1553TIGHT THERMAL0.260.5
1A1739LOOSE THERMAL0.2210
2B1566TIGHT POSITIONAL0.070.05
2B1745LOOSE POSITIONAL0.175
2B1566TIGHT THERMAL0.230.5
2B1745LOOSE THERMAL0.1910
3A1680TIGHT POSITIONAL0.060.05
3A1814LOOSE POSITIONAL0.145
3A1680TIGHT THERMAL0.20.5
3A1814LOOSE THERMAL0.1910
4B1680TIGHT POSITIONAL0.10.05
4B1793LOOSE POSITIONAL0.175
4B1680TIGHT THERMAL0.230.5
4B1793LOOSE THERMAL0.1910
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 737 -
Rwork0.33 14326 -
obs--94.08 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.8710.44960.41641.14080.00981.381-0.1367-0.11960.1605-0.0977-0.09230.154-0.3306-0.22060.22910.18810.1188-0.09930.0898-0.05280.1993-16.1077-6.6514-0.0263
21.68881.30340.84251.39081.15482.94270.13730.3967-0.1774-0.07470.33-0.1340.31120.6555-0.46730.23110.1552-0.08110.2671-0.12620.217416.18476.04572.3542
30.95550.62620.82883.01010.58272.1834-0.00070.1874-0.2160.07150.1576-0.17980.00830.2972-0.1570.040.01120.03580.0698-0.00580.1201-18.514731.2688-29.4688
41.01190.13350.81123.25991.95552.6193-0.0723-0.00190.03920.02890.3581-0.48620.04980.3254-0.28580.0629-0.00380.05380.1121-0.05060.1885-23.85252.9426-49.5696
50.79190.2050.19020.81880.21341.49080.0184-0.0775-0.0039-0.1318-0.08250.05230.0654-0.15020.06420.0762-0.00320.03020.05210.02610.086-12.4343-34.1199-2.1774
61.3053-0.15770.3021.5333-0.34680.93260.05730.1708-0.03060.0105-0.04030.1297-0.08060.0987-0.01690.0715-0.01940.06230.1563-0.01160.083416.605932.606121.4787
72.21740.21160.5261.64360.21231.72930.21390.1949-0.3610.2212-0.0918-0.47890.06810.3851-0.12210.145-0.0511-0.05930.18350.04860.27420.881346.5323-43.0351
81.78610.10570.16612.11450.15831.5290.0097-0.54590.01530.3101-0.00510.18060.1309-0.2821-0.00470.1277-0.06270.07040.31220.03760.0973-55.1609-5.3036-48.2023
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 23
2X-RAY DIFFRACTION1A319 - 581
3X-RAY DIFFRACTION2B7 - 23
4X-RAY DIFFRACTION2B319 - 580
5X-RAY DIFFRACTION3C5 - 23
6X-RAY DIFFRACTION3C319 - 581
7X-RAY DIFFRACTION4D7 - 23
8X-RAY DIFFRACTION4D319 - 581
9X-RAY DIFFRACTION5A24 - 318
10X-RAY DIFFRACTION6B24 - 318
11X-RAY DIFFRACTION7C24 - 318
12X-RAY DIFFRACTION8D24 - 318

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