Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  REFINED SOLUTION STRUCTURE OF A DIMER OF LAC REPRESSOR DNA-BINDING DOMAIN COMPLEXED TO ITS NATURAL OPERATOR O1
 
Authors :  J. Romanuka, G. Folkers, N. Biris, E. Tishchenko, H. Wienk, R. Kaptein, R. Boelens
Date :  30 Jan 09  (Deposition) - 19 May 09  (Release) - 07 Jul 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C,D  (20x)
Keywords :  Lac Repressor, Lac Operators, Nmr, Protein-Dna Complex, Dna- Binding, Repressor, Transcription, Transcription Regulation, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Romanuka, G. E. Folkers, N. Biris, E. Tishchenko, H. Wienk, A. M. Bonvin, R. Kaptein, R. Boelens
Specificity And Affinity Of Lac Repressor For The Auxiliary Operators O2 And O3 Are Explained By The Structures Of Their Protein-Dna Complexes.
J. Mol. Biol. V. 390 478 2009
PubMed-ID: 19450607  |  Reference-DOI: 10.1016/J.JMB.2009.05.022
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LACTOSE OPERON REPRESSOR
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainDH9
    Expression System Taxid562
    FragmentUNP RESIDUES 1-62
    GeneLACI, B0345, JW0336
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    StrainK-12
 
Molecule 2 - DNA (5'- D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*GP*AP*TP*AP*AP*CP*AP *AP*TP*TP*T)-3')
    ChainsC
    EngineeredYES
    SyntheticYES
 
Molecule 3 - DNA (5'- D(P*AP*AP*AP*TP*TP*GP*TP*TP*AP*TP*CP*CP*GP*CP*TP*CP*AP*CP*A P*AP*TP*TP*C)-3')
    ChainsD
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2KEI)

(-) Sites  (0, 0)

(no "Site" information available for 2KEI)

(-) SS Bonds  (1, 1)

NMR Structure
No.Residues
1A:52 -B:52

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2KEI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2KEI)

(-) PROSITE Motifs  (2, 4)

NMR Structure (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LACI_2PS50932 LacI-type HTH domain profile.LACI_ECOLI4-58
 
  2A:4-58
B:4-58
2HTH_LACI_1PS00356 LacI-type HTH domain signature.LACI_ECOLI6-24
 
  2A:6-24
B:6-24

(-) Exons   (0, 0)

(no "Exon" information available for 2KEI)

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:62
 aligned with LACI_ECOLI | P03023 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:62
                                    10        20        30        40        50        60  
            LACI_ECOLI    1 MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSL 62
               SCOP domains d2keia_ A: Lac repressor (LacR), N-terminal domain             SCOP domains
               CATH domains 2keiA00 A:1-62 lambda repressor-like DNA-binding domains       CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhhhhhhhhh...hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---HTH_LACI_2  PDB: A:4-58 UniProt: 4-58                  ---- PROSITE (1)
                PROSITE (2) -----HTH_LACI_1         -------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------- Transcript
                  2kei A  1 MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRCAQQLAGKQSL 62
                                    10        20        30        40        50        60  

Chain B from PDB  Type:PROTEIN  Length:62
 aligned with LACI_ECOLI | P03023 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:62
                                    10        20        30        40        50        60  
            LACI_ECOLI    1 MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSL 62
               SCOP domains d2keib_ B: Lac repressor (LacR), N-terminal domain             SCOP domains
               CATH domains 2keiB00 B:1-62 lambda repressor-like DNA-binding domains       CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhh....hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---HTH_LACI_2  PDB: B:4-58 UniProt: 4-58                  ---- PROSITE (1)
                PROSITE (2) -----HTH_LACI_1         -------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------- Transcript
                  2kei B  1 MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRCAQQLAGKQSL 62
                                    10        20        30        40        50        60  

Chain C from PDB  Type:DNA  Length:23
                                                      
                  2kei C -1 GAATTGTGAGCGGATAACAATTT 22
                            ||       9        19   
                           -1|                     
                             1                     

Chain D from PDB  Type:DNA  Length:23
                                                      
                  2kei D -1 AAATTGTTATCCGCTCACAATTC 22
                            ||       9        19   
                           -1|                     
                             1                     

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

NMR Structure

(-) CATH Domains  (1, 2)

NMR Structure

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2KEI)

(-) Gene Ontology  (8, 8)

NMR Structure(hide GO term definitions)
Chain A,B   (LACI_ECOLI | P03023)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000986    bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0001141    transcriptional repressor activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase in order to stop, prevent, or reduce the frequency, rate or extent of transcription from a bacterial-type RNA polymerase promoter.
biological process
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2kei)
 
  Sites
(no "Sites" information available for 2kei)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2kei)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2kei
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  LACI_ECOLI | P03023
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  LACI_ECOLI | P03023
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        LACI_ECOLI | P030231cjg 1efa 1jwl 1jye 1jyf 1l1m 1lbg 1lbh 1lbi 1lcc 1lcd 1lqc 1ltp 1osl 1tlf 1z04 2bjc 2kej 2kek 2p9h 2paf 2pe5 3edc 4rzs 4rzt

(-) Related Entries Specified in the PDB File

1l1m
2kej SAME PROTEIN BOUND TO ITS NATURAL OPERATOR O2
2kek SAME PROTEIN BOUND TO ITS NATURAL OPERATOR O3