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(-) Description

Title :  STRUCTURE OF THE COMPLEX OF LAC REPRESSOR HEADPIECE AND AN 11 BASE-PAIR HALF-OPERATOR DETERMINED BY NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY AND RESTRAINED MOLECULAR DYNAMICS
 
Authors :  V. P. Chuprina, J. A. C. Rullmann, R. M. J. N. Lamerichs, J. H. Van Boom, R. Boelens, R. Kaptein
Date :  25 Mar 93  (Deposition) - 31 Jan 94  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C
Keywords :  Dna, Nmr, Half-Operator, Lac Operator, Lac Repressor, Headpiece, Gene Regulation/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. P. Chuprina, J. A. Rullmann, R. M. Lamerichs, J. H. Van Boom, R. Boelens, R. Kaptein
Structure Of The Complex Of Lac Repressor Headpiece And An 11 Base-Pair Half-Operator Determined By Nuclear Magnetic Resonance Spectroscopy And Restrained Molecular Dynamics.
J. Mol. Biol. V. 234 446 1993
PubMed-ID: 8230225  |  Reference-DOI: 10.1006/JMBI.1993.1598
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*G)-3')
    Chains: B
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED
    Synthetic: YES
 
Molecule 2 - DNA (5'-D(*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3')
    Chains: C
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED
    Synthetic: YES
 
Molecule 3 - LAC REPRESSOR
    Chains: A
    Engineered: YES
    Expression System Vector Type: LAC
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: BMH 74-12

 Structural Features

(-) Chains, Units

  
NMR Structure : 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

NMR Structure (1, 1)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:24 , HOH A:58 , HOH A:60 , DC C:3 , DT C:4 , HOH C:319BINDING SITE FOR RESIDUE NA C 12

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LCC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LCC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LCC)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LACI_2PS50932 LacI-type HTH domain profile.LACI_ECOLI4-58  1A:4-51
2HTH_LACI_1PS00356 LacI-type HTH domain signature.LACI_ECOLI6-24  1A:6-24

(-) Exons   (0, 0)

(no "Exon" information available for 1LCC)

(-) 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:51
 aligned with LACI_ECOLI | P03023 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:51
                                    10        20        30        40        50 
            LACI_ECOLI    1 MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNR 51
               SCOP domains d1lcca_ A: Lac repressor (LacR), N-terminal domain  SCOP domains
               CATH domains 1lccA00 A:1-51                                      CATH domains
               Pfam domains ----LacI-1lccA01 A:5-50                           - Pfam domains
         Sec.struct. author ....hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---HTH_LACI_2  PDB: A:4-51 UniProt: 4-58            PROSITE (1)
                PROSITE (2) -----HTH_LACI_1         --------------------------- PROSITE (2)
                 Transcript --------------------------------------------------- Transcript
                  1lcc A  1 MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNR 51
                                    10        20        30        40        50 


Chain B from PDB  Type:DNA  Length:11
                                          
                  1lcc B  1 AATTGTGAGCG 11
                                    10 


Chain C from PDB  Type:DNA  Length:11
                                          
                  1lcc C  1 CGCTCACAATT 11
                                    10
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: HTH (544)

(-) Gene Ontology  (8, 8)

NMR Structure(hide GO term definitions)
Chain A   (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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  1lcc
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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 1lcd 1lqc 1ltp 1osl 1tlf 1z04 2bjc 2kei 2kej 2kek 2p9h 2paf 2pe5 3edc 4rzs 4rzt

(-) Related Entries Specified in the PDB File

1lcd ENSEMBLE OF 3 STRUCTURES