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- PDB-3a7a: Crystal structure of E. coli lipoate-protein ligase A in complex ... -

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Basic information

Entry
Database: PDB / ID: 3a7a
TitleCrystal structure of E. coli lipoate-protein ligase A in complex with octyl-amp and apoH-protein
Components
  • Glycine cleavage system H protein
  • Lipoate-protein ligase A
KeywordsLIGASE / ADENIYLATE-FORMING ENZYME / ATP-binding / Nucleotide-binding / Transferase / Lipoyl
Function / homology
Function and homology information


lipoyltransferase activity / lipoate-protein ligase / lipoate-protein ligase activity / glycine decarboxylation via glycine cleavage system / glycine cleavage complex / protein lipoylation / one-carbon metabolic process / ATP binding / cytoplasm / cytosol
Similarity search - Function
Lipoate-protein ligase A / Lipoate protein ligase, C-terminal / Bacterial lipoate protein ligase C-terminus / Lipoyltransferase/lipoate-protein ligase / Glycine cleavage system H-protein, subgroup / Glycine cleavage system H-protein / Glycine cleavage system H-protein/Simiate / Glycine cleavage H-protein / Lipoyl protein ligase A/B catalytic domain / CO dehydrogenase flavoprotein, C-terminal domain ...Lipoate-protein ligase A / Lipoate protein ligase, C-terminal / Bacterial lipoate protein ligase C-terminus / Lipoyltransferase/lipoate-protein ligase / Glycine cleavage system H-protein, subgroup / Glycine cleavage system H-protein / Glycine cleavage system H-protein/Simiate / Glycine cleavage H-protein / Lipoyl protein ligase A/B catalytic domain / CO dehydrogenase flavoprotein, C-terminal domain / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile. / Biotin/lipoate A/B protein ligase family / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Enolase-like; domain 1 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / N-OCTANE / Glycine cleavage system H protein / Lipoate-protein ligase A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsFujiwara, K. / Hosaka, H. / Nakagawa, A.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Global conformational change associated with the two-step reaction catalyzed by Escherichia coli lipoate-protein ligase A.
Authors: Fujiwara, K. / Maita, N. / Hosaka, H. / Okamura-Ikeda, K. / Nakagawa, A. / Taniguchi, H.
History
DepositionSep 20, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipoate-protein ligase A
B: Glycine cleavage system H protein
C: Lipoate-protein ligase A
D: Glycine cleavage system H protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,9828
Polymers103,0594
Non-polymers9234
Water00
1
A: Lipoate-protein ligase A
B: Glycine cleavage system H protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9914
Polymers51,5302
Non-polymers4612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Lipoate-protein ligase A
D: Glycine cleavage system H protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9914
Polymers51,5302
Non-polymers4612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.013, 102.016, 159.934
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 Lipoate-protein ligase A / Lipoate-protein ligase


Mass: 37840.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: lplA, yjjF, b4386, JW4349 / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P32099, Ligases; Forming carbon-nitrogen bonds; Other carbon-nitrogen ligases
#2: Protein Glycine cleavage system H protein / apoH-protein


Mass: 13688.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: gcvH, b2904, JW2872 / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P0A6T9
#3: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM

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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: 2.77 Å3/Da / Density % sol: 55.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 16.2% PEG 3350, 0.045M MgSO4, 0.045M NaCl, 1mM NiCl2, 2% Polyethylene glycol monomethyl ether 2000, 0.01M Tris-Cl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Mar 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.96→50 Å / Num. obs: 23803 / % possible obs: 98.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.7
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 2 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E5A

2e5a


Resolution: 3.1→20 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.877 / SU B: 23.909 / SU ML: 0.433 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.513 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27855 1626 7.7 %RANDOM
Rwork0.22839 ---
obs0.23223 19375 98.29 %-
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: 48.457 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7238 0 62 0 7300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0227452
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.6361.96210120
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2645924
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04824.389360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.186151216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6841552
X-RAY DIFFRACTIONr_chiral_restr0.0430.21124
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0215712
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.2321.54614
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.42527394
X-RAY DIFFRACTIONr_scbond_it0.32132838
X-RAY DIFFRACTIONr_scangle_it0.5884.52726
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 119 -
Rwork0.319 1393 -
obs--98.69 %
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)
10.7780.752-0.10031.0044-0.27780.3510.01530.1037-0.0033-0.07750.0361-0.11670.0696-0.1287-0.05140.19170.06890.01840.26980.00520.1867-5.6606-18.669829.9611
21.49140.71130.27364.34460.39833.1703-0.17770.33880.0769-0.60990.0795-0.23410.18630.14350.09820.30510.06030.08730.44620.08030.043-6.6258-13.52991.6707
31.35640.4979-0.65250.8401-0.13350.84190.0693-0.1290.0052-0.16190.00370.0502-0.25390.0971-0.0730.2741-0.02730.0110.18150.0130.150822.339925.532717.074
42.68071.0124-0.65264.42262.5894.8373-0.30320.1144-0.3896-0.28020.06450.20750.02420.28660.23870.19690.08440.09780.1016-0.02520.292831.13262.04371.5412
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 337
2X-RAY DIFFRACTION2B2 - 128
3X-RAY DIFFRACTION3C1 - 337
4X-RAY DIFFRACTION4D2 - 128

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