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- PDB-2mkx: Solution structure of LysM the peptidoglycan binding domain of au... -

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Basic information

Entry
Database: PDB / ID: 2mkx
TitleSolution structure of LysM the peptidoglycan binding domain of autolysin AtlA from Enterococcus faecalis
ComponentsAutolysin
KeywordsHYDROLASE / protein
Function / homology
Function and homology information


amidase activity / cytolysis / hydrolase activity, acting on glycosyl bonds / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / division septum assembly / metabolic process / cell wall organization / defense response to bacterium / extracellular region
Similarity search - Function
Membrane-bound Lytic Murein Transglycosylase D; Chain A / LysM domain / Lysozyme subfamily 2 / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain ...Membrane-bound Lytic Murein Transglycosylase D; Chain A / LysM domain / Lysozyme subfamily 2 / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterococcus faecalis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsBaxter, N.J. / Williamson, M.P.
CitationJournal: Nat Commun / Year: 2014
Title: Molecular basis for bacterial peptidoglycan recognition by LysM domains.
Authors: Mesnage, S. / Dellarole, M. / Baxter, N.J. / Rouget, J.B. / Dimitrov, J.D. / Wang, N. / Fujimoto, Y. / Hounslow, A.M. / Lacroix-Desmazes, S. / Fukase, K. / Foster, S.J. / Williamson, M.P.
History
DepositionFeb 14, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Autolysin


Theoretical massNumber of molelcules
Total (without water)6,4001
Polymers6,4001
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Autolysin / Beta-glycosidase / Peptidoglycan hydrolase


Mass: 6400.250 Da / Num. of mol.: 1
Fragment: LysM peptidoglycan binding domain of autolysin AtlA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: ATCC 700802 / V583 / Gene: EF_0799 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3)
References: UniProt: P37710, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: 1H, 15N, 13C chemical shift assignments and solution structure
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CO)CA
1413D HNCO
1513D HN(CA)CO
1613D HN(CA)CB
1713D CBCA(CO)NH
1813D 1H-15N TOCSY
1912D 1H-13C HSQC
11013D (H)CCH-TOCSY
11113D CCH-TOCSY
11213D 1H-15N/13C NOESY aliphatic
11312D 1H-13C HSQC aromatic
11412D H(N)CO

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Sample preparation

DetailsContents: 0.6 mM [U-100% 13C; U-100% 15N] lysm, 40 mM potassium phosphate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMlysm-1[U-100% 13C; U-100% 15N]1
40 mMpotassium phosphate-21
Sample conditionsIonic strength: 40 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix2007Accelrys Software Inc.chemical shift assignment
Felix2007Accelrys Software Inc.peak picking
Felix2007Accelrys Software Inc.processing
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
TopSpin1.3Bruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: in explicit waters using ARIA protocol
NMR constraintsNOE constraints total: 430 / NOE intraresidue total count: 14 / NOE long range total count: 142 / NOE medium range total count: 106 / NOE sequential total count: 168 / Hydrogen bond constraints total count: 32 / Protein chi angle constraints total count: 19 / Protein phi angle constraints total count: 41 / Protein psi angle constraints total count: 38
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0.1 Å / Maximum torsion angle constraint violation: 10.1 ° / Maximum upper distance constraint violation: 0.3 Å
NMR ensemble rmsDistance rms dev: 0.037 Å / Distance rms dev error: 0.001 Å

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