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- PDB-2v3z: Glu383Ala Escherichia coli aminopeptidase P in complex with substrate -

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Basic information

Entry
Database: PDB / ID: 2v3z
TitleGlu383Ala Escherichia coli aminopeptidase P in complex with substrate
Components
  • TRIPEPTIDE (VALINE-PROLINE-LEUCINE)
  • XAA-PRO AMINOPEPTIDASE
KeywordsHYDROLASE / 'PITA-BREAD' ENZYME / PROLINE- SPECIFIC ENZYME / AMINOPEPTIDASE P / MANGANESE ENZYME / PROTEASE / MANGANESE / METAL-BINDING / METALLOENZYME / AMINOPEPTIDASE / METALLOPROTEASE
Function / homology
Function and homology information


Xaa-Pro aminopeptidase / metalloexopeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / manganese ion binding / protein homotetramerization / protein-containing complex / proteolysis / identical protein binding / cytosol
Similarity search - Function
Aminopeptidase P, N-terminal / Aminopeptidase P, N-terminal domain / Aminopeptidase P, N-terminal domain / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase ...Aminopeptidase P, N-terminal / Aminopeptidase P, N-terminal domain / Aminopeptidase P, N-terminal domain / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Xaa-Pro aminopeptidase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsGraham, S.C. / Guss, J.M.
CitationJournal: Arch.Biochem.Biophys. / Year: 2008
Title: Complexes of Mutants of Escherichia Coli Aminopeptidase P and the Tripeptide Substrate Valproleu.
Authors: Graham, S.C. / Guss, J.M.
History
DepositionJun 25, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Sep 25, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Dec 13, 2023Group: 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_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_seq_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_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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XAA-PRO AMINOPEPTIDASE
B: TRIPEPTIDE (VALINE-PROLINE-LEUCINE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1755
Polymers50,0292
Non-polymers1453
Water13,169731
1
A: XAA-PRO AMINOPEPTIDASE
B: TRIPEPTIDE (VALINE-PROLINE-LEUCINE)
hetero molecules

A: XAA-PRO AMINOPEPTIDASE
B: TRIPEPTIDE (VALINE-PROLINE-LEUCINE)
hetero molecules

A: XAA-PRO AMINOPEPTIDASE
B: TRIPEPTIDE (VALINE-PROLINE-LEUCINE)
hetero molecules

A: XAA-PRO AMINOPEPTIDASE
B: TRIPEPTIDE (VALINE-PROLINE-LEUCINE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,69920
Polymers200,1188
Non-polymers58112
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+4/31
crystal symmetry operation10_666-y+1,-x+1,-z+4/31
Buried area16320 Å2
ΔGint-34 kcal/mol
Surface area84310 Å2
MethodPQS
Unit cell
Length a, b, c (Å)177.695, 177.695, 96.433
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein XAA-PRO AMINOPEPTIDASE / AMINOPEPTIDASE P / X-PRO AMINOPEPTIDASE / AMINOPEPTIDASE P II / APP-II / AMINOACYLPROLINE AMINOPEPTIDASE


Mass: 49702.027 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PPL670 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): AN1459 / References: UniProt: P15034, Xaa-Pro aminopeptidase
#2: Protein/peptide TRIPEPTIDE (VALINE-PROLINE-LEUCINE)


Mass: 327.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TRIPEPTIDE SUBSTRATE OF AMINOPEPTIDASE P / Source: (synth.) ESCHERICHIA COLI (E. coli)
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 731 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 383 TO ALA RELEASE OF ANY N-TERMINAL AMINO ACID, INCLUDING ...ENGINEERED RESIDUE IN CHAIN A, GLU 383 TO ALA RELEASE OF ANY N-TERMINAL AMINO ACID, INCLUDING PROLINE, THAT IS LINKED TO PROLINE, EVEN FROM A DIPEPTIDE OR TRIPEPTIDE
Sequence detailsE383A MUTANT

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.4 Å3/Da / Density % sol: 72.1 %
Description: STARTING MODEL WAS STRIPPED OF LIGANDS, SOLVENT AND ALTERNATE CONFORMERS BEFORE REFINEMENT
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: CRYSTALLISED IN 30% PEG 4K, 0.1 M TRIS PH 8.8 AT 277K. SOAKED IN 30% PEG 4K, 0.1 M TRIS PH 8.5, 1 MM MNCL2, 5 MM VAL-PRO-LEU, 10% MPD FOR 30 MIN AT 277K IMMEDIATELY PRIOR TO DATA COLLECTION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97934
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 22, 2006 / Details: MIRRORS
RadiationMonochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. obs: 125677 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 17.78 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 32.5
Reflection shellResolution: 1.56→1.62 Å / Redundancy: 10 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 4.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WL9

1wl9


Resolution: 1.56→29.66 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.35 / SU ML: 0.026 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.15 3825 3 %RANDOM
Rwork0.14 ---
obs0.14 121838 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.05 Å20 Å2
2--0.11 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.56→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3519 0 3 731 4253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223785
X-RAY DIFFRACTIONr_bond_other_d0.0020.022601
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.9585169
X-RAY DIFFRACTIONr_angle_other_deg0.90236327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8325490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31523.568199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.15615659
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3671538
X-RAY DIFFRACTIONr_chiral_restr0.0820.2568
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024329
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02801
X-RAY DIFFRACTIONr_nbd_refined0.2170.2767
X-RAY DIFFRACTIONr_nbd_other0.1950.22822
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21832
X-RAY DIFFRACTIONr_nbtor_other0.0840.22019
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2470
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3580.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3260.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.249
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.20623033
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.39633738
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.92341698
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.761408
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.56→1.6 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.215 280
Rwork0.195 8915
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)
10.5495-0.104-0.07810.4222-0.15711.07140.03510.05180.0318-0.0088-0.0277-0.015-0.04070.0456-0.00740.00910.0153-0.00650.04510.00330.043365.62573.94647.611
21.3863-0.04240.64130.44730.01050.63-0.10230.03860.13880.05360.01550.017-0.13990.03270.08680.02040.0186-0.02010.01260.0120.034959.32984.8948.863
30.3469-0.14420.09510.4011-0.10360.84610.00580.0159-0.05890.0143-0.0260.05310.176-0.00510.02010.04310.01770.0140.0126-0.00410.039167.19944.54950.41
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 54
2X-RAY DIFFRACTION2A55 - 166
3X-RAY DIFFRACTION3A167 - 440

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