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- PDB-1spu: STRUCTURE OF OXIDOREDUCTASE -

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Basic information

Entry
Database: PDB / ID: 1spu
TitleSTRUCTURE OF OXIDOREDUCTASE
ComponentsCOPPER AMINE OXIDASE
KeywordsOXIDOREDUCTASE / COPPER / TPQ / PERIPLASMIC
Function / homology
Function and homology information


phenylethylamine catabolic process / primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / L-phenylalanine catabolic process / amine metabolic process / quinone binding / periplasmic space / copper ion binding / calcium ion binding
Similarity search - Function
Copper amine oxidase-like, N-terminal domain / Copper amine oxidase-like, N-terminal / Copper amine oxidase-like, N-terminal domain superfamily / Copper amine oxidase N-terminal domain / Copper Amine Oxidase; Chain A, domain 1 / Copper amine oxidase, N3-terminal / Copper amine oxidase, N2-terminal / Copper amine oxidase, N2 domain / Copper amine oxidase, N3 domain / Copper amine oxidase, catalytic domain ...Copper amine oxidase-like, N-terminal domain / Copper amine oxidase-like, N-terminal / Copper amine oxidase-like, N-terminal domain superfamily / Copper amine oxidase N-terminal domain / Copper Amine Oxidase; Chain A, domain 1 / Copper amine oxidase, N3-terminal / Copper amine oxidase, N2-terminal / Copper amine oxidase, N2 domain / Copper amine oxidase, N3 domain / Copper amine oxidase, catalytic domain / Copper amine oxidase copper-binding site signature. / Copper amine oxidase topaquinone signature. / Nuclear Transport Factor 2; Chain: A, - #40 / Copper amine oxidase / Copper amine oxidase, catalytic domain / Copper amine oxidase, N-terminal / Copper amine oxidase, catalytic domain superfamily / Copper amine oxidase, enzyme domain / Beta-galactosidase; Chain A, domain 5 / Nuclear Transport Factor 2; Chain: A, / Distorted Sandwich / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / Primary amine oxidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / LEAST SQUARES REFINEMENT / Resolution: 2 Å
AuthorsWilmot, C.M. / Phillips, S.E.V.
Citation
Journal: Biochemistry / Year: 1997
Title: Catalytic mechanism of the quinoenzyme amine oxidase from Escherichia coli: exploring the reductive half-reaction.
Authors: Wilmot, C.M. / Murray, J.M. / Alton, G. / Parsons, M.R. / Convery, M.A. / Blakeley, V. / Corner, A.S. / Palcic, M.M. / Knowles, P.F. / McPherson, M.J. / Phillips, S.E.
#1: Journal: Structure / Year: 1995
Title: Crystal Structure of a Quinoenzyme: Copper Amine Oxidase of Escherichia Coli at 2 A Resolution
Authors: Parsons, M.R. / Convery, M.A. / Wilmot, C.M. / Yadav, K.D. / Blakeley, V. / Corner, A.S. / Phillips, S.E. / McPherson, M.J. / Knowles, P.F.
History
DepositionNov 13, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COPPER AMINE OXIDASE
B: COPPER AMINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,2078
Polymers162,9202
Non-polymers2876
Water19,1681064
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14550 Å2
ΔGint-118 kcal/mol
Surface area49390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.460, 166.070, 79.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.35161, -0.936, -0.01658), (-0.93596, -0.35184, 0.01343), (-0.0184, 0.01079, -0.99977)
Vector: 89.26835, 128.63486, 6.62689)

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Components

#1: Protein COPPER AMINE OXIDASE


Mass: 81459.859 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Cellular location: PERIPLASM / References: UniProt: P46883, EC: 1.4.3.6
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1064 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIN THE NATIVE ENZYME, RESIDUE 466 IS 2,4,5-TRIHYDROXYPHENYLALANINE QUINONE (TPQ) FORMED BY POST- ...IN THE NATIVE ENZYME, RESIDUE 466 IS 2,4,5-TRIHYDROXYPHENYLALANINE QUINONE (TPQ) FORMED BY POST-TRANSLATIONAL MODIFICATION OF TYROSINE. IN THE COMPLEX THE PRIMARY AMINE GROUP OF 2-HYDRAZINOPYRIDINE (2-HP) HAS COVALENTLY REACTED WITH THE 5 POSITION OF THE TPQ RING. THE CHEMICALLY MODIFIED COFACTOR IS IDENTIFIED BY THP IN THE SITE RECORDS BELOW.
Nonpolymer detailsE. COLI AMINE OXIDASE IS A HOMODIMER. EACH SUBUNIT ACTIVE SITE CONTAINS ONE COPPER AND A REDOX ...E. COLI AMINE OXIDASE IS A HOMODIMER. EACH SUBUNIT ACTIVE SITE CONTAINS ONE COPPER AND A REDOX COFACTOR, TPQ, WHICH HAS BEEN CHEMICALLY MODIFIED BY A SUICIDE INHIBITOR, 2-HYDRAZINOPYRIDINE. THIS COMPLEX IS A MIMIC OF THE SUBSTRATE SCHIFF BASE INTERMEDIATE OF THE CATALYTIC MECHANISM.

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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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growpH: 7.2
Details: 1.4M SODIUM CITRATE, 0.1M HEPES BUFFER, PH 7.2 PROTEIN SOLUTION CONCENTRATION 6.5 MG/ML INHIBITOR SOAKING SOLUTION 0.375MM 2-HYDRAZINOPYRIDINE MADE UP IN 1.4M SODIUM CITRATE, 0.1M HEPES ...Details: 1.4M SODIUM CITRATE, 0.1M HEPES BUFFER, PH 7.2 PROTEIN SOLUTION CONCENTRATION 6.5 MG/ML INHIBITOR SOAKING SOLUTION 0.375MM 2-HYDRAZINOPYRIDINE MADE UP IN 1.4M SODIUM CITRATE, 0.1M HEPES BUFFER, PH 7.2. CRYSTAL SOAKED FOR 30 DAYS. CRYOPROTECTANT 20% GLYCEROL, 1.44M SODIUM CITRATE BUFFER, PH 6.4
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 mg/mlenzyme1drop
210 mMpotassium phosphate1drop
31.1 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1996 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 100550 / % possible obs: 83.7 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 24.21 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 8.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 2 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 3.3 / % possible all: 72.9
Reflection
*PLUS
Num. measured all: 264608
Reflection shell
*PLUS
Num. measured obs: 12938

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Processing

Software
NameVersionClassification
CCP4IMPLEMENTATION OF PROLSQmodel building
PROLSQrefinement
MOSFLMdata reduction
CCP4data scaling
CCP4IMPLEMENTATION OF PROLSQphasing
RefinementMethod to determine structure: LEAST SQUARES REFINEMENT
Starting model: PDB ENTRY 1OAC

1oac


Resolution: 2→20 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.206 --
obs-100550 83.7 %
Displacement parametersBiso mean: 27.62 Å2
Refine analyzeLuzzati d res low obs: 8 Å / Luzzati sigma a obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11319 0 48 1064 12431
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.01
X-RAY DIFFRACTIONp_angle_d0.0350.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0480.04
X-RAY DIFFRACTIONp_hb_or_metal_coord0.030.01
X-RAY DIFFRACTIONp_mcbond_it5.1374
X-RAY DIFFRACTIONp_mcangle_it6.6255
X-RAY DIFFRACTIONp_scbond_it7.5825
X-RAY DIFFRACTIONp_scangle_it10.1296
X-RAY DIFFRACTIONp_plane_restr0.010.01
X-RAY DIFFRACTIONp_chiral_restr0.110.07
X-RAY DIFFRACTIONp_singtor_nbd0.1850.3
X-RAY DIFFRACTIONp_multtor_nbd0.2130.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1940.3
X-RAY DIFFRACTIONp_planar_tor2.373
X-RAY DIFFRACTIONp_staggered_tor17.67115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor24.10220
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor obs: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS

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