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- PDB-2bjc: NMR structure of a protein-DNA complex of an altered specificity ... -

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Basic information

Entry
Database: PDB / ID: 2bjc
TitleNMR structure of a protein-DNA complex of an altered specificity mutant of the lac repressor headpiece that mimics the gal repressor
Components
  • 5'-D(*GP*AP*AP*TP*TP*GP*TP*AP*AP*GP *CP*GP*CP*TP*TP*AP*CP*AP*AP*TP*TP*C)-3'
  • LACTOSE OPERON REPRESSOR
KeywordsTRANSCRIPTION REGULATOR / SYMMETRIC DNA-BINDING / DNA-BINDING / HTH / LAC OPERON / LAC REPRESSOR / ALTERED SPECIFICITY / MUTANT / REPRESSOR / TRANSCRIPTION REGULATION / TRANSCRIPTION REGULATOR/DNA / GAL REPRESSOR / GAL OPERON / LAC HEADPIECE / SYMMETRIC DIMER
Function / homology
Function and homology information


DNA-binding transcription repressor activity / cis-regulatory region sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / identical protein binding / cytosol
Similarity search - Function
LacI-type HTH domain signature. / Transcriptional regulator LacI/GalR-like, sensor domain / Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / lambda repressor-like DNA-binding domains / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily ...LacI-type HTH domain signature. / Transcriptional regulator LacI/GalR-like, sensor domain / Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / lambda repressor-like DNA-binding domains / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Periplasmic binding protein-like I / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Lactose operon repressor
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodSOLUTION NMR / HADDOCK
AuthorsSalinas, R.K. / Folkers, G.E. / Bonvin, A.M.J.J. / Das, D. / Boelens, R. / Kaptein, R.
Citation
Journal: Chembiochem / Year: 2005
Title: Altered Specificity in DNA Binding by the Lac Repressor: A Mutant Lac Headpiece that Mimics the Gal Repressor
Authors: Salinas, R.K. / Folkers, G.E. / Bonvin, A.M.J.J. / Das, D. / Boelens, R. / Kaptein, R.
#1: Journal: Embo J. / Year: 2002
Title: Plasticity in Protein-DNA Recognition: Lac Repressor Interacts with its Natural Operator O1 Through Alternative Conformations of its DNA Binding Domain
Authors: Kalodimos, C.G. / Bonvin, A.M.J.J. / Salinas, R.K. / Wechselberger, R. / Boelens, R. / Kaptein, R.
#2: Journal: Embo J. / Year: 1987
Title: The Interaction of the Recognition Helix of Lac Repressor with Lac Operator
Authors: Lehming, N. / Sartorius, J. / Niemoler, M. / Genenger, G. / Wilcken-Bergmann, B. / Muller-Hill, B.
History
DepositionFeb 1, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 15, 2020Group: Other / Category: pdbx_database_status
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LACTOSE OPERON REPRESSOR
B: LACTOSE OPERON REPRESSOR
C: 5'-D(*GP*AP*AP*TP*TP*GP*TP*AP*AP*GP *CP*GP*CP*TP*TP*AP*CP*AP*AP*TP*TP*C)-3'
D: 5'-D(*GP*AP*AP*TP*TP*GP*TP*AP*AP*GP *CP*GP*CP*TP*TP*AP*CP*AP*AP*TP*TP*C)-3'


Theoretical massNumber of molelcules
Total (without water)26,9044
Polymers26,9044
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)16 / 50RMSD TO AVERAGE STRUCTURE AND LOWEST ENERGY
RepresentativeModel #3

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Components

#1: Protein LACTOSE OPERON REPRESSOR


Mass: 6701.661 Da / Num. of mol.: 2 / Fragment: DNA BINDING DOMAIN, LAC HEADPIECE RESIDUES 1-62 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN IS A DIMER. DISULFIDE BOND BETWEEN CYS52 IN TWO MONOMERS FORMS A COVALENT DIMER
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: DH9 / Plasmid: PET3A / PGP1-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH9 / References: UniProt: P03023
#2: DNA chain 5'-D(*GP*AP*AP*TP*TP*GP*TP*AP*AP*GP *CP*GP*CP*TP*TP*AP*CP*AP*AP*TP*TP*C)-3' / LAC-GAL OPERATOR


Mass: 6750.390 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: ALTERED LAC SYML OPERATOR
Compound detailsENGINEERED RESIDUES TYR 17 VAL, GLN 18 ALA AND VAL 52 CYS IN CHAINS A AND B
Has protein modificationY
Sequence detailsRESIDUES 1-62 OF LAC REPRESSOR (P03023) WITH THE SUBSTITUTIONS Y17V Q18A AND V52C ALTERED ...RESIDUES 1-62 OF LAC REPRESSOR (P03023) WITH THE SUBSTITUTIONS Y17V Q18A AND V52C ALTERED PALINDROME OF THE LEFT SIDE OF THE LAC OPERATOR O1 LACKING THE CENTRAL BASE PAIR.ORIGINAL BASE PAIR GC7 WAS SUBSTITUTED BY AT

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D 15N NOESY-HSQC 3D 13C NOESY-HSQC 2D NOESY 2D NOESY WITH X-FILTERS 3D CBCA(CO)NH 3D HNCO 3D HBHA(CO)NH 3D (H)CC(CO)NH 3D (H)CCH-TOCSY 2D 1H-13C HSQC 2D 1H-15N HSQC 2D 1H-15N J- MODULATED HSQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY ON A 13C, 15N LABELED PROTEIN AND UNLABELED DNA.

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Sample preparation

DetailsContents: 95% WATER/5% D2O
Sample conditionsIonic strength: 20 mM / pH: 6 / Pressure: 1.0 atm / Temperature: 315.0 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
CNSstructure solution
RefinementMethod: HADDOCK / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: RMSD TO AVERAGE STRUCTURE AND LOWEST ENERGY
Conformers calculated total number: 50 / Conformers submitted total number: 16

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