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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  MODEL OF LACTOSE REPRESSOR CORE BASED ON ALIGNMENT WITH SUGAR BINDING PROTEINS IS CONCORDANT WITH GENETIC AND CHEMICAL DATA
 
Authors :  J. C. Nichols, N. K. Vyas, F. A. Quiocho, K. S. Matthews
Date :  10 May 93  (Deposition) - 31 Oct 93  (Release) - 31 Oct 93  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  L
Keywords :  Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. C. Nichols, N. K. Vyas, F. A. Quiocho, K. S. Matthews
Model Of Lactose Repressor Core Based On Alignment With Sugar-Binding Proteins Is Concordant With Genetic And Chemical Data.
J. Biol. Chem. V. 268 17602 1993
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LACTOSE REPRESSOR
    Chains: L
    Engineered: YES
    Expression System Vector Type: LAC
    Organism Scientific: ESCHERICHIA COLI

 Structural Features

(-) Chains, Units

  
Theoretical Model : 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1LTP)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Theoretical Model
No.Residues
1Glu L:100 -Arg L:101
2Arg L:101 -Ser L:102
3Pro L:155 -Ile L:156
4His L:179 -Gln L:180
5Val L:264 -Gly L:265
6Ile L:283 -Pro L:284
7Pro L:285 -Leu L:286
8Arg L:294 -Leu L:295

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Theoretical Model (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_LACI_ECOLI_001 *Y282DLACI_ECOLI  ---  ---LY282D
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1LTP)

(-) Exons   (0, 0)

(no "Exon" information available for 1LTP)

(-) Sequences/Alignments

Theoretical Model
   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 L from PDB  Type:PROTEIN  Length:262
 aligned with LACI_ECOLI | P03023 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:262
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321  
           LACI_ECOLI    62 LLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSL 323
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......hhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh..eeeeee.......ee...hhhhhhhhhhhhhh.....ee......hhhhhhhhhhhhhhhh..............hhhhhhhhhhhhh......eeee...hhhhhhhhhhhhhh.......eeee..............hhhhh................hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D----------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ltp L  62 LLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSL 323
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321
   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  (0, 0)

(no "SCOP Domain" information available for 1LTP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1LTP)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Theoretical Model(hide GO term definitions)
Chain L   (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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  Cis Peptide Bonds
    Arg L:101 - Ser L:102   [ RasMol ]  
    Arg L:294 - Leu L:295   [ RasMol ]  
    Glu L:100 - Arg L:101   [ RasMol ]  
    His L:179 - Gln L:180   [ RasMol ]  
    Ile L:283 - Pro L:284   [ RasMol ]  
    Pro L:155 - Ile L:156   [ RasMol ]  
    Pro L:285 - Leu L:286   [ RasMol ]  
    Val L:264 - Gly L:265   [ RasMol ]  
 

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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 1osl 1tlf 1z04 2bjc 2kei 2kej 2kek 2p9h 2paf 2pe5 3edc 4rzs 4rzt

(-) Related Entries Specified in the PDB File

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