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- PDB-1mly: Crystal Structure of 7,8-Diaminopelargonic Acid Synthase in compl... -

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Basic information

Entry
Database: PDB / ID: 1mly
TitleCrystal Structure of 7,8-Diaminopelargonic Acid Synthase in complex with the cis isomer of amiclenomycin
Components7,8-diamino-pelargonic acid aminotransferase
KeywordsTRANSFERASE / Aminotransferase / Fold type I / subclass II / amiclenomycin
Function / homology
Function and homology information


adenosylmethionine-8-amino-7-oxononanoate transaminase / adenosylmethionine-8-amino-7-oxononanoate transaminase activity / biotin biosynthetic process / pyridoxal phosphate binding / protein homodimerization activity / cytoplasm
Similarity search - Function
Adenosylmethionine--8-amino-7-oxononanoate aminotransferase BioA / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...Adenosylmethionine--8-amino-7-oxononanoate aminotransferase BioA / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CIS-AMICLENOMYCIN / PYRIDOXAL-5'-PHOSPHATE / Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsSandmark, J. / Mann, S. / Marquet, A. / Schneider, G.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structural basis for the inhibition of the biosynthesis of biotin by the antibiotic amiclenomycin
Authors: Sandmark, J. / Mann, S. / Marquet, A. / Schneider, G.
History
DepositionSep 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 7, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999sequence The crystallized protein differs from the Swissprot sequence at residue 14. In the ...sequence The crystallized protein differs from the Swissprot sequence at residue 14. In the Swissprot sequence number 14 is a tryptophan while here it is a leucin. This is confirmed by DNA sequencing and was also reported for the original WT structure (1qj5).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 7,8-diamino-pelargonic acid aminotransferase
B: 7,8-diamino-pelargonic acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5548
Polymers94,6212
Non-polymers9336
Water9,674537
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12680 Å2
ΔGint-98 kcal/mol
Surface area26700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.655, 56.073, 116.174
Angle α, β, γ (deg.)90.00, 109.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 7,8-diamino-pelargonic acid aminotransferase / Adenosylmethionine-8-amino-7-oxononanoate aminotransferase / DAPA aminotransferase


Mass: 47310.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bioA / Plasmid: pET24 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P12995, adenosylmethionine-8-amino-7-oxononanoate transaminase
#2: Chemical ChemComp-ACZ / CIS-AMICLENOMYCIN / 2-AMINO-4-(4-AMINO-CYCLOHEXA-2,5-DIENYL)-BUTYRIC ACID


Mass: 196.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 537 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsIn both subunits the cofactor pyridoxal-5'-phosphate forms a covalent adduct with the inhibitor ...In both subunits the cofactor pyridoxal-5'-phosphate forms a covalent adduct with the inhibitor amiclenomycin, followed by aromatization of amiclenomycin hexadiene ring. The binding mode for the inhibitor is different in the two subunits. The electron density for the covalent adduct between amiclenomycin and pyridoxal-5'-phosphate is better in monomer A. For details see the primary citation.

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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: 2.08 Å3/Da / Density % sol: 40.91 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG4000, MPD, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Method: vapor diffusion / Details: Kack, H., (1998) Acta Crystallogr., D54, 1397.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
221 %PEG40001reservoir
312 %2-propanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.968 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 16, 2001
RadiationMonochromator: Si(111) monocromator crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.81→40.16 Å / Num. all: 70391 / Num. obs: 70391 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.1 Å2 / Rsym value: 0.062 / Net I/σ(I): 17.4
Reflection shellResolution: 1.81→1.91 Å / Mean I/σ(I) obs: 3.4 / Rsym value: 0.259 / % possible all: 94.1
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 69507 / Num. measured all: 276229 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
Lowest resolution: 1.9 Å / % possible obs: 94.1 % / Rmerge(I) obs: 0.259

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.533 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: In monomer A two stretches of residues are disordered, 159-168 and 180-189 resp. In monomer B three stretches of residues are disordered, 159-168, 180-189 and 299-303 resp. Residue 429 was ...Details: In monomer A two stretches of residues are disordered, 159-168 and 180-189 resp. In monomer B three stretches of residues are disordered, 159-168, 180-189 and 299-303 resp. Residue 429 was excluded from both monomers. A number of side chains on the surface of the protein are disordered. The occupancy for these is estimated to 0 in most cases. In four cases the side chains are given the occupancy 0.5.
RfactorNum. reflection% reflectionSelection details
Rfree0.22045 3492 5 %RANDOM
Rwork0.19439 ---
all0.19572 66847 --
obs0.19572 66847 99.9 %-
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: 23.278 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å20 Å2-1.24 Å2
2--1.57 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 1.81→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6588 0 60 537 7185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0216743
X-RAY DIFFRACTIONr_bond_other_d0.0010.026155
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.9489159
X-RAY DIFFRACTIONr_angle_other_deg1.177314223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.863850
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.172151144
X-RAY DIFFRACTIONr_chiral_restr0.090.21014
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027537
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021377
X-RAY DIFFRACTIONr_nbd_refined0.2660.31603
X-RAY DIFFRACTIONr_nbd_other0.2140.36013
X-RAY DIFFRACTIONr_nbtor_other0.1290.53
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.5540
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2550.53
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.317
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2410.341
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3010.519
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.5421.54258
X-RAY DIFFRACTIONr_mcangle_it0.99926809
X-RAY DIFFRACTIONr_scbond_it1.40332485
X-RAY DIFFRACTIONr_scangle_it2.294.52350
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.81→1.858 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.275 208
Rwork0.253 4363
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.22 / Rfactor Rwork: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.376

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