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(-) Description

Title :  NMR STRUCTURE OF LAC REPRESSOR HP62-DNA COMPLEX
 
Authors :  C. A. E. M. Spronk, A. M. J. J. Bonvin, P. K. Radha, G. Melacini, R. Boelens, R. Kaptein
Date :  14 Apr 99  (Deposition) - 01 Jan 00  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C,D  (11x)
Keywords :  Transcription Regulation, Lac Operon, Lac Repressor, Headpiece, Lac Operator, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. A. Spronk, A. M. Bonvin, P. K. Radha, G. Melacini, R. Boelens, R. Kaptein
The Solution Structure Of Lac Repressor Headpiece 62 Complexed To A Symmetrical Lac Operator.
Structure Fold. Des. V. 7 1483 1999
PubMed-ID: 10647179  |  Reference-DOI: 10.1016/S0969-2126(00)88339-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (LAC REPRESSOR)
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGP1-2;PET-HP62
    Expression System Strain: DH9
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: HEADPIECE, RESIDUES 1 - 62
    Gene: LAC I, THE PART ENCODING THE 62 N-TERMINAL AMINOACIDS
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: THE PROTEIN CONTAINS THE 62 N-TERMINAL RESIDUES (I.E., THE DNA BINDING REGION) OF THE COMPLETE LAC REPRESSOR PROTEIN
    Synonym: LAC HP62
 
Molecule 2 - DNA (5'- D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP *TP*TP*C)-3')
    Chains: C, D
    Engineered: YES
    Fragment: SYMMETRIC LAC OPERATOR
    Other Details: THE OPERATOR IS A PALINDROME OF THE LEFT HALF OF THE WILD-TYPE OPERATOR AND LACKS THE CENTRAL BASE- PAIR
    Other Details - Source: THE FRAGMENT IS A VARIANT OF THE WILD-TYPE OPERATOR SEQUENCE OF THE LAC OPERON OF ESCHERICHIA COLI
    Synonym: SYML OPERATOR
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (11x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1CJG)

(-) Sites  (0, 0)

(no "Site" information available for 1CJG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 1CJG)

(-) 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 d1cjga_ A: Lac repressor (LacR), N-terminal domain             SCOP domains
               CATH domains 1cjgA00 A:1-62 lambda repressor-like DNA-binding domains       CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhh...hhhhhhhh.......hhhhhhhhhhhhhh.....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
                  1cjg A  1 MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSL 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 d1cjgb_ B: Lac repressor (LacR), N-terminal domain             SCOP domains
               CATH domains 1cjgB00 B:1-62 lambda repressor-like DNA-binding domains       CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhh...hhhhhhhh.......hhhhhhhhhhhhh......hhhhhh...... 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
                  1cjg B  1 MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSL 62
                                    10        20        30        40        50        60  


Chain C from PDB  Type:DNA  Length:22
                                                     
                  1cjg C  1 GAATTGTGAGCGCTCACAATTC 22
                                    10        20  


Chain D from PDB  Type:DNA  Length:22
                                                     
                  1cjg D  1 GAATTGTGAGCGCTCACAATTC 22
                                    10        20
   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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CJG)

(-) 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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  1cjg
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  LACI_ECOLI | P03023
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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