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- PDB-1ehi: D-ALANINE:D-LACTATE LIGASE (LMDDL2) OF VANCOMYCIN-RESISTANT LEUCO... -

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Basic information

Entry
Database: PDB / ID: 1ehi
TitleD-ALANINE:D-LACTATE LIGASE (LMDDL2) OF VANCOMYCIN-RESISTANT LEUCONOSTOC MESENTEROIDES
ComponentsD-ALANINE:D-LACTATE LIGASE
KeywordsLIGASE / ATP-binding. Grasp motif for ATP.
Function / homology
Function and homology information


D-alanine-D-alanine ligase / D-alanine-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / ATP binding / metal ion binding / cytosol
Similarity search - Function
D-alanine--D-alanine ligase/VANA/B/C, conserved site / D-alanine--D-alanine ligase / D-alanine--D-alanine ligase, N-terminal domain / D-ala D-ala ligase N-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / D-alanine--D-alanine ligase, C-terminal / D-ala D-ala ligase C-terminus / Rossmann fold - #20 / ATP-grasp fold, A domain ...D-alanine--D-alanine ligase/VANA/B/C, conserved site / D-alanine--D-alanine ligase / D-alanine--D-alanine ligase, N-terminal domain / D-ala D-ala ligase N-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / D-alanine--D-alanine ligase, C-terminal / D-ala D-ala ligase C-terminus / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, subdomain 1 / ATP-grasp fold, B domain / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-PHY / D-alanine--D-alanine ligase / D-alanine--D-alanine ligase
Similarity search - Component
Biological speciesLeuconostoc mesenteroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 3-wavelength MAD near Se edge (x12c at BNL) / Resolution: 2.38 Å
AuthorsKuzin, A.P. / Sun, T. / Jorczak-Baillass, J. / Healy, V.L. / Walsh, C.T. / Knox, J.R.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: Enzymes of vancomycin resistance: the structure of D-alanine-D-lactate ligase of naturally resistant Leuconostoc mesenteroides.
Authors: Kuzin, A.P. / Sun, T. / Jorczak-Baillass, J. / Healy, V.L. / Walsh, C.T. / Knox, J.R.
#1: Journal: Science / Year: 1994
Title: Vancomycin Resistance: Structure of D-alanine:D-alanine Ligase at 2.3 A Resolution
Authors: Fan, C. / Moews, P.C. / Walsh, C.T. / Knox, J.R.
#2: Journal: Biochemistry / Year: 1997
Title: D-alanine:D-alanine ligase: Phosphonate and Phosphinate Intermediates with Wild-type and the Y216F Mutant
Authors: Fan, C. / Park, I.-S. / Walsh, C.T. / Knox, J.R.
History
DepositionFeb 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.4Feb 7, 2024Group: 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 / 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_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
Revision 1.5Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-ALANINE:D-LACTATE LIGASE
B: D-ALANINE:D-LACTATE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4856
Polymers83,7342
Non-polymers7514
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-62 kcal/mol
Surface area27050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.200, 90.800, 82.100
Angle α, β, γ (deg.)90.00, 92.10, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe ligase is a dimer formed of chain A and B. However, part of chain B is missing in the crystallographic model.

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Components

#1: Protein D-ALANINE:D-LACTATE LIGASE / LMDDL2


Mass: 41866.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leuconostoc mesenteroides (bacteria) / Plasmid: PLMDDL2 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5A AND BL21(DE3)
References: UniProt: P71454, UniProt: Q03ZI1*PLUS, D-alanine-D-alanine ligase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Details: Made by Prof. Paul A. Bartlett, Dept. of Chem., UC Berkeley
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-PHY / 1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC ACID


Mass: 275.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15NO7P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.6 Å3/Da / Density % sol: 53.2 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5
Details: PEG8000 15%, 0.1 M ammonium sulfate, 50mM NaCl, 2.4mM DTT, 1mM MgCl2, 3mM ATP, 3mM phosphinic acid, 50mM MES buffer., pH 6.5, VAPOR DIFFUSION, SITTING DROP
Temp details: 293-295
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
13.5 mg/mlprotein1drop
215 %PEG80001drop
30.1 Mammonium sulfate1drop
450 mM1dropNaCl
51 mM1dropMgCl2
63 mMATP1drop
73 mMphosphinate1drop
850 mMMES1drop
930 %PEG1reservoiror mPEG
100.2 Mammonium sulfate1reservoir
110.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorType: ADSC / Detector: CCD / Date: Aug 15, 1997
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2.38→100 Å / Num. all: 30564 / Num. obs: 30564 / % possible obs: 82 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 11
Reflection shellResolution: 2.38→2.48 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1738 / % possible all: 47
Reflection
*PLUS
% possible obs: 82 % / Num. measured all: 94338
Reflection shell
*PLUS
% possible obs: 47 % / Num. unique obs: 1738 / Num. measured obs: 4374

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Processing

Software
NameVersionClassification
SOLVEphasing
X-PLOR3.851refinement
DENZO(DENZO)data reduction
SCALEPACK(DENZO)data scaling
RefinementMethod to determine structure: 3-wavelength MAD near Se edge (x12c at BNL)
Resolution: 2.38→100 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: bulk solvent correction. A 3-wavelength MAD method was used to determine structure of the selenomet-protein. A native data set (A1 at CHESS) was used to refine structure.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 951 -random
Rwork0.184 ---
all0.184 28899 --
obs0.184 27948 82 %-
Refinement stepCycle: LAST / Resolution: 2.38→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5531 0 45 213 5789
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_improper_angle_d1.2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 100 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2

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