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(-) Description

Title :  STRUCTURE OF THE DIMERIC LAC REPRESSOR/OPERATOR O1/ONPF COMPLEX
 
Authors :  C. E. Bell, M. Lewis
Date :  04 Sep 01  (Deposition) - 05 Oct 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.00
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B,D,E  (1x)
Biol. Unit 2:  C  (2x)
Keywords :  Lac Repressor, Gene Regulation, Dna-Bending, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. E. Bell, M. Lewis
Crystallographic Analysis Of Lac Repressor Bound To Natural Operator O1.
J. Mol. Biol. V. 312 921 2001
PubMed-ID: 11580238  |  Reference-DOI: 10.1006/JMBI.2001.5024
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- D(*AP*GP*AP*AP*T*TP*GP*TP*GP*AP*GP*CP*GP*GP*AP*TP*AP*AP*CP* AP*AP*TP*T)-3'
    ChainsD
    EngineeredYES
    Other DetailsO1 TOP STRAND
    SyntheticYES
 
Molecule 2 - 5'- D(*TP*AP*AP*TP*TP*GP*TP*TP*AP*TP*CP*CP*GP*CP*TP*CP*AP*CP*AP *AP*TP*TP*C)-3'
    ChainsE
    EngineeredYES
    Other DetailsO1 BOTTOM STRAND
    SyntheticYES
 
Molecule 3 - LACTOSE OPERON REPRESSOR
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL DELETION MUTANT
    GeneLACI
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit ABCDE
Biological Unit 1 (1x)AB DE
Biological Unit 2 (2x)  C  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1NPF3Ligand/IonORTHONITROPHENYL-BETA-D-FUCOPYRANOSIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NPF2Ligand/IonORTHONITROPHENYL-BETA-D-FUCOPYRANOSIDE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NPF2Ligand/IonORTHONITROPHENYL-BETA-D-FUCOPYRANOSIDE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA B:75 , ILE B:79 , LEU B:148 , ASP B:149 , PHE B:161 , ARG B:197 , ASN B:246 , ASP B:274 , GLN B:291 , PHE B:293BINDING SITE FOR RESIDUE NPF B 334
2AC2SOFTWAREALA C:75 , ILE C:79 , LEU C:148 , PHE C:161 , ARG C:197 , ASN C:246 , ASP C:274 , GLN C:291 , PHE C:293 , LEU C:296BINDING SITE FOR RESIDUE NPF C 334
3AC3SOFTWAREALA A:75 , ILE A:79 , ASN A:125 , PHE A:161 , ARG A:197 , TRP A:220 , ASN A:246 , ASP A:274 , PHE A:293BINDING SITE FOR RESIDUE NPF A 334

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ile A:283 -Pro A:284
2Ile B:283 -Pro B:284
3Ile C:283 -Pro C:284

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 3)

Asymmetric Unit (1, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_LACI_ECOLI_001 *Y282DLACI_ECOLI  ---  ---A/B/CY282D
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_LACI_ECOLI_001 *Y282DLACI_ECOLI  ---  ---A/BY282D
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_LACI_ECOLI_001 *Y282DLACI_ECOLI  ---  ---CY282D
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (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
Biological Unit 1 (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
Biological Unit 2 (, 0)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LACI_2PS50932 LacI-type HTH domain profile.LACI_ECOLI4-58
 
  0-
-
2HTH_LACI_1PS00356 LacI-type HTH domain signature.LACI_ECOLI6-24
 
  0-
-

(-) Exons   (0, 0)

(no "Exon" information available for 1JWL)

(-) Sequences/Alignments

Asymmetric Unit
   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:329
 aligned with LACI_ECOLI | P03023 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:329
                                    11        21        31        41        51        61        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     2 KPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTL 330
               SCOP domains d1jwla1 A:2-60 Lac repressor (LacR), N-terminal domain     d1jwla2 A:61-330 Lac-repressor (lacR) core (C-terminal domain)                                                                                                                                                                                                                 SCOP domains
               CATH domains 1jwlA01 A:2-59 lambda repressor-like DNA-binding domains  1jwlA02 A:60-160,A:291-317  [code=3.40.50.2300, no name defined]                                     1jwlA03 A:161-290,A:318-330  [code=3.40.50.2300, no name defined]                                                                 1jwlA02 A:60-160,A:291-317 1jwlA03       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh...hhhhhhhhhh......hhhhhhhhhhhhhhh...hhhhhhhh.....eeeeeee...hhhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh....eee..........eeeehhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhh.........eeeeee..hhhhhh....eeee.hhhhhhhhhhhhhhhhhh......eeee..eee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D------------------------------------------------ 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
                 1jwl A   2 KPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKTAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTL 330
                                    11        21        31        41        51        61        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         

Chain B from PDB  Type:PROTEIN  Length:329
 aligned with LACI_ECOLI | P03023 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:329
                                    11        21        31        41        51        61        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     2 KPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTL 330
               SCOP domains d1jwlb1 B:2-60 Lac repressor (LacR), N-terminal domain     d1jwlb2 B:61-330 Lac-repressor (lacR) core (C-terminal domain)                                                                                                                                                                                                                 SCOP domains
               CATH domains 1jwlB01 B:2-59 lambda repressor-like DNA-binding domains  1jwlB02 B:60-160,B:291-317  [code=3.40.50.2300, no name defined]                                     1jwlB03 B:161-290,B:318-330  [code=3.40.50.2300, no name defined]                                                                 1jwlB02 B:60-160,B:291-317 1jwlB03       CATH domains
           Pfam domains (1) ---LacI-1jwlB01 B:5-50                           ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---LacI-1jwlB02 B:5-50                           ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .....hhhhhh...hhhhhhhhhh......hhhhhhhhhhhhhhh...hhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh....eee..........eeeehhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhh.........eeeeee..hhhhhh....eeee.hhhhhhhhhhhhhhhhhh......eeee..eee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D------------------------------------------------ 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
                 1jwl B   2 KPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKTAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTL 330
                                    11        21        31        41        51        61        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         

Chain C from PDB  Type:PROTEIN  Length:269
 aligned with LACI_ECOLI | P03023 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:269
                                    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 LLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTL 330
               SCOP domains d1jwlc_ C: Lac-repressor (lacR) core (C-terminal domain)                                                                                                                                                                                                                      SCOP domains
               CATH domains 1jwlC01 C:62-161,C:291-320  [code=3.40.50.2300, no name defined]                                    1jwlC02 C:162-290,C:321-330  [code=3.40.50.2300, no name defined]                                                                1jwlC01 C:62-161,C:291-320    1jwlC02    CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------Peripla_BP_3-1jwlC01 C:171-329                                                                                                                                 - Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------Peripla_BP_3-1jwlC02 C:171-329                                                                                                                                 - Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------Peripla_BP_3-1jwlC03 C:171-329                                                                                                                                 - Pfam domains (3)
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh....eee..........eeeehhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhh.........eeeeee..hhhhhh....eeee.hhhhhhhhhhhhhhhhhh......eeee..eee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jwl C  62 LLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKTAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTL 330
                                    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         

Chain D from PDB  Type:DNA  Length:14
                                              
                 1jwl D   6 TGTGAGCGGATAAC  19
                                    15    

Chain E from PDB  Type:DNA  Length:14
                                              
                 1jwl E   6 GTTATCCGCTCACA  19
                                    15    

   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  (2, 5)

Asymmetric Unit

(-) CATH Domains  (2, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
1a1jwlC02C:162-290,C:321-330
1b1jwlB02B:60-160,B:291-317
1c1jwlA03A:161-290,A:318-330
1d1jwlB03B:161-290,B:318-330
1e1jwlC01C:62-161,C:291-320
1f1jwlA02A:60-160,A:291-317

(-) Pfam Domains  (2, 5)

Asymmetric Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (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 | P030231cjg 1efa 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

(no "Related Entries Specified in the PDB File" available for 1JWL)