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- PDB-3fw0: Structure of Peptidyl-alpha-hydroxyglycine alpha-Amidating Lyase ... -

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Basic information

Entry
Database: PDB / ID: 3fw0
TitleStructure of Peptidyl-alpha-hydroxyglycine alpha-Amidating Lyase (PAL) bound to alpha-hydroxyhippuric acid (non-peptidic substrate)
ComponentsPeptidyl-glycine alpha-amidating monooxygenase
KeywordsLYASE / BETA PROPELLER / ZINC / CALCIUM / MERCURY / PEPTIDE AMIDATION / SUBSTRATE / HYDROXYHIPPURIC ACID / Alternative splicing / Cleavage on pair of basic residues / Copper / Cytoplasmic vesicle / Glycoprotein / Membrane / Metal-binding / Monooxygenase / Multifunctional enzyme / Oxidoreductase / Phosphoprotein / Sulfation / Transmembrane / Vitamin C
Function / homology
Function and homology information


peptidylglycine monooxygenase / peptidylamidoglycolate lyase / peptide amidation / peptidylglycine monooxygenase activity / peptidylamidoglycolate lyase activity / fatty acid primary amide biosynthetic process / toxin metabolic process / ovulation cycle process / long-chain fatty acid metabolic process / peptide metabolic process ...peptidylglycine monooxygenase / peptidylamidoglycolate lyase / peptide amidation / peptidylglycine monooxygenase activity / peptidylamidoglycolate lyase activity / fatty acid primary amide biosynthetic process / toxin metabolic process / ovulation cycle process / long-chain fatty acid metabolic process / peptide metabolic process / mitotic chromosome condensation / response to pH / L-ascorbic acid binding / response to copper ion / limb development / response to zinc ion / transport vesicle membrane / maternal process involved in female pregnancy / condensed chromosome / response to glucocorticoid / lactation / secretory granule / regulation of actin cytoskeleton organization / trans-Golgi network / response to estradiol / heart development / perikaryon / response to hypoxia / response to xenobiotic stimulus / copper ion binding / neuronal cell body / chromatin binding / calcium ion binding / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / perinuclear region of cytoplasm / cell surface / extracellular space / zinc ion binding / extracellular region / identical protein binding
Similarity search - Function
Peptidylglycine alpha-hydroxylating monooxygenase/peptidyl-hydroxyglycine alpha-amidating lyase / Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-2 conserved site / Copper type II, ascorbate-dependent monooxygenases signature 2. / Copper type II, ascorbate-dependent monooxygenase, N-terminal / Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-1 conserved site / Copper type II ascorbate-dependent monooxygenase, C-terminal / Copper type II, ascorbate-dependent monooxygenase, N-terminal domain superfamily / Copper type II ascorbate-dependent monooxygenase, N-terminal domain / Copper type II ascorbate-dependent monooxygenase, C-terminal domain / Copper type II, ascorbate-dependent monooxygenases signature 1. ...Peptidylglycine alpha-hydroxylating monooxygenase/peptidyl-hydroxyglycine alpha-amidating lyase / Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-2 conserved site / Copper type II, ascorbate-dependent monooxygenases signature 2. / Copper type II, ascorbate-dependent monooxygenase, N-terminal / Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-1 conserved site / Copper type II ascorbate-dependent monooxygenase, C-terminal / Copper type II, ascorbate-dependent monooxygenase, N-terminal domain superfamily / Copper type II ascorbate-dependent monooxygenase, N-terminal domain / Copper type II ascorbate-dependent monooxygenase, C-terminal domain / Copper type II, ascorbate-dependent monooxygenases signature 1. / PHM/PNGase F domain superfamily / Copper type II, ascorbate-dependent monooxygenase-like, C-terminal / NHL repeat profile. / NHL repeat / NHL repeat / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
: / (2S)-hydroxy[(phenylcarbonyl)amino]ethanoic acid / Peptidylglycine alpha-amidating monooxygenase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsChufan, E.E. / De, M. / Eipper, B.A. / Mains, R.E. / Amzel, L.M.
CitationJournal: Structure / Year: 2009
Title: Amidation of bioactive peptides: the structure of the lyase domain of the amidating enzyme.
Authors: Chufan, E.E. / De, M. / Eipper, B.A. / Mains, R.E. / Amzel, L.M.
History
DepositionJan 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 3, 2024Group: 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 / 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 / _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.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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-glycine alpha-amidating monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5515
Polymers36,9141
Non-polymers6364
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.930, 75.080, 97.026
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidyl-glycine alpha-amidating monooxygenase / PAM / Peptidylglycine alpha-hydroxylating monooxygenase / PHM / Peptidyl-alpha-hydroxyglycine alpha- ...PAM / Peptidylglycine alpha-hydroxylating monooxygenase / PHM / Peptidyl-alpha-hydroxyglycine alpha-amidating lyase / Peptidylamidoglycolate lyase / PAL


Mass: 36914.090 Da / Num. of mol.: 1
Fragment: Peptidyl-alpha-hydroxyglycine alpha-Amidating Lyase catalytic core
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pam / Cell line (production host): Ovary cells / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P14925, peptidylamidoglycolate lyase
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-HH3 / (2S)-hydroxy[(phenylcarbonyl)amino]ethanoic acid / alpha-hydroxyhippuric acid


Mass: 195.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9NO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

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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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1M sodium acetate pH=4.8, 0.5mM mercury(II) acetate - 0.2ml mother liquor in reservoir. Then, crystals soaked in 5mM hydroxyhippuric acid for several hours, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1.00724 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 9, 2008 / Details: Monochromator Kohzu HLD-4 Double Crystal
RadiationMonochromator: Kohzu HLD-4 Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00724 Å / Relative weight: 1
ReflectionResolution: 2.5→59.34 Å / Num. all: 13347 / Num. obs: 13347 / % possible obs: 99.6 % / Redundancy: 6.8 % / Rsym value: 0.075 / Net I/σ(I): 23.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 1306 / Rsym value: 0.48 / % possible all: 98.9

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PALcc native, being deposited at the same time as this structure

Resolution: 2.52→59.34 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.899 / SU B: 18.474 / SU ML: 0.216 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.689 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26019 655 4.9 %RANDOM
Rwork0.20672 ---
obs0.20939 12648 99.09 %-
all-13347 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.912 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å20 Å2
2--0.24 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 2.52→59.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2619 0 17 118 2754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212721
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.9263694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5525330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24724.317139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.92515413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7851511
X-RAY DIFFRACTIONr_chiral_restr0.1150.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022155
X-RAY DIFFRACTIONr_nbd_refined0.1950.21170
X-RAY DIFFRACTIONr_nbtor_refined0.310.21762
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2136
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.28
X-RAY DIFFRACTIONr_mcbond_it0.311.51676
X-RAY DIFFRACTIONr_mcangle_it0.54122664
X-RAY DIFFRACTIONr_scbond_it1.21331163
X-RAY DIFFRACTIONr_scangle_it1.2374.51030
LS refinement shellResolution: 2.515→2.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 48 -
Rwork0.274 846 -
obs-1306 92.64 %

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