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(-) Description

Title :  SOLUTION STRUCTURE OF A DIMER OF LAC REPRESSOR DNA-BINDING DOMAIN COMPLEXED TO ITS NATURAL OPERATOR O3
 
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  (10x)
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
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: DH9
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-62
    Gene: LACI, B0345, JW0336
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12
 
Molecule 2 - DNA (5'- D(*CP*GP*GP*CP*AP*GP*TP*GP*AP*GP*CP*GP*CP*AP*AP*CP*GP*CP*AP *AP*TP*TP*C)-3')
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(P*GP*AP*AP*TP*TP*GP*CP*GP*TP*TP*GP*CP*GP*CP*TP*CP*AP*CP*T P*GP*CP*CP*G)-3')
    Chains: D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (10x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2KEK)

(-) SS Bonds  (1, 1)

NMR Structure
No.Residues
1A:52 -B:52

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 2KEK)

(-) 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 d2keka_ A: Lac repressor (LacR), N-terminal domain             SCOP domains
               CATH domains 2kekA00 A:1-62 lambda repressor-like DNA-binding domains       CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh.hhhhhhhhhhh.......hhhhhhhhhhhh......hhhhhh..... 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
                  2kek 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 d2kekb_ B: Lac repressor (LacR), N-terminal domain             SCOP domains
               CATH domains 2kekB00 B:1-62 lambda repressor-like DNA-binding domains       CATH domains
           Pfam domains (1) ----LacI-2kekB01 B:5-50                           ------------ Pfam domains (1)
           Pfam domains (2) ----LacI-2kekB02 B:5-50                           ------------ Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhh..hhhhhhhhhh....hhhhhhhhhhhhhhhh.....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
                  2kek B  1 MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRCAQQLAGKQSL 62
                                    10        20        30        40        50        60  


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


Chain D from PDB  Type:DNA  Length:23
                                                      
                  2kek D -1 GAATTGCGTTGCGCTCACTGCCG 22
                            ||       9        19   
                           -1|                     
                             1
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

NMR Structure
(-)
Clan: HTH (544)

(-) 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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LACI_ECOLI | P03023: 1cjg 1efa 1jwl 1jye 1jyf 1l1m 1lbg 1lbh 1lbi 1lcc 1lcd 1lqc 1ltp 1osl 1tlf 1z04 2bjc 2kei 2kej 2p9h 2paf 2pe5 3edc 4rzs 4rzt

(-) Related Entries Specified in the PDB File

1l1m
2kei SAME PROTEIN BOUND TO ITS NATURAL OPERATOR O1
2kej SAME PROTEIN BOUND TO ITS NATURAL OPERATOR O2