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- PDB-2y1o: Dual-target Inhibitor of MurD and MurE Ligases: Design, Synthesis... -

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Basic information

Entry
Database: PDB / ID: 2y1o
TitleDual-target Inhibitor of MurD and MurE Ligases: Design, Synthesis and Binding Mode Studies
ComponentsUDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE
KeywordsLIGASE / CELL CYCLE / CELL DIVISION / CELL SHAPE / CELL WALL BIOGENESIS/DEGRADATION
Function / homology
Function and homology information


UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase / UDP-N-acetylmuramoylalanine-D-glutamate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
UDP-N-acetylmuramoylalanine-D-glutamate ligase MurD / Mur ligase MurD-like, N-terminal domain / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain ...UDP-N-acetylmuramoylalanine-D-glutamate ligase MurD / Mur ligase MurD-like, N-terminal domain / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Protein-Tyrosine Phosphatase; Chain A / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-T26 / UDP-N-acetylmuramoylalanine--D-glutamate ligase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsTomasic, T. / Sink, R. / Kovac, A. / Turk, S. / Contreras-Martel, C. / Dessen, A. / Blanot, D. / Gobec, S. / Zega, A. / Kikelj, D. / Peterlin-Masic, L.
CitationJournal: ACS Med Chem Lett / Year: 2012
Title: Dual Inhibitor of MurD and MurE Ligases from Escherichia coli and Staphylococcus aureus.
Authors: Tomasic, T. / Sink, R. / Zidar, N. / Fic, A. / Contreras-Martel, C. / Dessen, A. / Patin, D. / Blanot, D. / Muller-Premru, M. / Gobec, S. / Zega, A. / Kikelj, D. / Masic, L.P.
History
DepositionDec 9, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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: UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,17610
Polymers47,9791
Non-polymers1,1969
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.844, 65.844, 135.747
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE / D-GLUTAMIC ACID-ADDING ENZYME / UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE SYNTHETASE / MURD LIGASE


Mass: 47979.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: DH5[ALPHA] / Plasmid: PABD16/MURD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH5[ALPHA]
References: UniProt: P14900, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase
#2: Chemical ChemComp-T26 / (2R)-2-[[3-[[4-[(Z)-(4-OXO-2-SULFANYLIDENE-1,3-THIAZOLIDIN-5-YLIDENE)METHYL]PHENYL]METHYLAMINO]PHENYL]CARBONYLAMINO]PENTANEDIOIC ACID


Mass: 499.559 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H21N3O6S2
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 3.07 Å3/Da / Density % sol: 59.9 % / Description: NONE
Crystal growpH: 7.4
Details: 6.0 MG/ML MURD, 20 MM HEPES, PH 7.4, 200 MM NACL, 5 MM DITHIOTHREITOL, 0.05% (W/V) NAN3 0.1. M HEPES PH 7.5, 1.9 M AMMONIUM SULPHATE, 7% (W/V) PEG 400, 50 MM NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97238
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97238 Å / Relative weight: 1
ReflectionResolution: 1.49→46.56 Å / Num. obs: 91441 / % possible obs: 82.8 % / Observed criterion σ(I): 3 / Redundancy: 4.5 % / Biso Wilson estimate: 25.693 Å2 / Rsym value: 0.04 / Net I/σ(I): 27.7
Reflection shellResolution: 1.49→1.58 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3 / Rsym value: 0.47 / % possible all: 52.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UAG

1uag


Resolution: 1.49→46.56 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.149 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.22845 8826 10 %RANDOM
Rwork0.20512 ---
obs0.20749 79419 100 %-
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: 23.543 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.49→46.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3278 0 70 415 3763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223483
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.994743
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5445461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.75224.533150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84215582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8281523
X-RAY DIFFRACTIONr_chiral_restr0.1280.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212631
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_it1.6311.52203
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.50523533
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.82931280
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.0654.51196
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: 1.49→1.529 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.502 435 -
Rwork0.48 3990 -
obs--100 %
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)
10.5916-0.2142-0.3760.70970.34990.60040.0106-0.0262-0.004-0.0123-0.0007-0.0142-0.0623-0.0514-0.00990.02320.00570.0020.0410.00130.036-27.005736.268849.0575
20.3574-0.0388-0.19880.11330.16030.2939-0.0023-0.0052-0.0413-0.0081-0.00620.00250.00680.0220.00850.03280.00590.01040.05630.00140.0448-4.931919.434638.4833
31.22080.17910.14570.56120.23630.63040.0111-0.0641-0.0303-0.0075-0.0232-0.0338-0.0177-0.02210.0120.0024-0.01-0.0030.0546-0.00330.03978.642229.428661.0117
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 92
2X-RAY DIFFRACTION2A94 - 295
3X-RAY DIFFRACTION3A304 - 439

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