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(-) Description

Title :  CRYSTAL STRUCTURE OF THE LAC REPRESSOR BOUND TO ONPG IN REPRESSED STATE
 
Authors :  R. Daber, S. E. Stayrook, A. Rosenberg, M. Lewis
Date :  02 Apr 07  (Deposition) - 18 Mar 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,D,E  (1x)
Biol. Unit 2:  C,F  (2x)
Keywords :  Lac Repressor, Allosteric Effectors, Gene Regulation, Dna- Binding, Transcription, Transcription Regulation, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Daber, S. Stayrook, A. Rosenberg, M. Lewis
Structural Analysis Of Lac Repressor Bound To Allosteric Effectors
J. Mol. Biol. V. 370 609 2007
PubMed-ID: 17543986  |  Reference-DOI: 10.1016/J.JMB.2007.04.028
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LACTOSE OPERON REPRESSOR
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidHTUA
    Expression System StrainBL21 DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentSEQUENCE DATABASE RESIDUES 2-331
    GeneLACI
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
 
Molecule 2 - DNA (5'- D(*DAP*DAP*DTP*DTP*DGP*DTP*DGP*DAP*DGP*DCP*DGP*DCP*DTP*DCP* DAP*DCP*DAP*DAP*DTP*DT)-3')
    ChainsD, E, F
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)AB DE 
Biological Unit 2 (2x)  C  F

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
11453Ligand/Ion1-O-[O-NITROPHENYL]-BETA-D-GALACTOPYRANOSE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
11452Ligand/Ion1-O-[O-NITROPHENYL]-BETA-D-GALACTOPYRANOSE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
11452Ligand/Ion1-O-[O-NITROPHENYL]-BETA-D-GALACTOPYRANOSE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:73 , ALA A:75 , PRO A:76 , ASN A:125 , LEU A:148 , ASP A:149 , PHE A:161 , SER A:193 , ARG A:197 , TRP A:220 , ASN A:246 , ASP A:274 , GLN A:291 , PHE A:293BINDING SITE FOR RESIDUE 145 A 901
2AC2SOFTWARELEU B:73 , ALA B:75 , ASN B:125 , LEU B:148 , ASP B:149 , PHE B:161 , SER B:193 , ARG B:197 , TRP B:220 , ASN B:246 , ASP B:274 , GLN B:291 , PHE B:293 , LEU B:296BINDING SITE FOR RESIDUE 145 B 902
3AC3SOFTWAREHIS C:74 , ALA C:75 , ASN C:125 , LEU C:148 , ASP C:149 , PHE C:161 , SER C:193 , ARG C:197 , TRP C:220 , ASN C:246 , ASP C:274 , GLN C:291 , PHE C:293 , LEU C:296BINDING SITE FOR RESIDUE 145 C 903

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PE5)

(-) 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, 6)

Asymmetric Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LACI_2PS50932 LacI-type HTH domain profile.LACI_ECOLI4-58
 
 
  3A:4-58
B:4-58
C:4-58
2HTH_LACI_1PS00356 LacI-type HTH domain signature.LACI_ECOLI6-24
 
 
  3A:6-24
B:6-24
C: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 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LACI_2PS50932 LacI-type HTH domain profile.LACI_ECOLI4-58
 
 
  2-
-
C:4-58
2HTH_LACI_1PS00356 LacI-type HTH domain signature.LACI_ECOLI6-24
 
 
  2-
-
C:6-24

(-) Exons   (0, 0)

(no "Exon" information available for 2PE5)

(-) 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:328
 aligned with LACI_ECOLI | P03023 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:328
                                    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 KPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTT 329
               SCOP domains d2pe5a1 A:2-61 Lac repressor (LacR), N-terminal domain      d2pe5a2 A:62-329 Lac-repressor (lacR) core (C-terminal domain)                                                                                                                                                                                                               SCOP domains
               CATH domains 2pe5A01 A:2-60 lambda repressor-like DNA-binding domains   2pe5A02 A:61-160,A:293-318  [code=3.40.50.2300, no name defined]                                    2pe5A03 A:161-292,A:319-329  [code=3.40.50.2300, no name defined]                                                                   2pe5A02 A:61-160,A:293-3182pe5A03     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhhhhhhhh....hhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhh....eee..........eeeehhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhhh.......eee....hhhhhhh.....eee.hhhhhhhhhhhhhhhhhhh.....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
                 2pe5 A   2 KPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQLLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTT 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        

Chain B from PDB  Type:PROTEIN  Length:330
 aligned with LACI_ECOLI | P03023 from UniProtKB/Swiss-Prot  Length:360

    Alignment length: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       331
           LACI_ECOLI     2 KPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLA 331
               SCOP domains d2pe5b1 B:2-61 Lac repressor (LacR), N-terminal domain      d2pe5b2 B:62-329 Lac-repressor (lacR) core (C-terminal domain)                                                                                                                                                                                                              -- SCOP domains
               CATH domains 2pe5B01 B:2-60 lambda repressor-like DNA-binding domains   2pe5B02 B:61-160,B:293-318  [code=3.40.50.2300, no name defined]                                    2pe5B03 B:161-292,B:319-331  [code=3.40.50.2300, no name defined]                                                                   2pe5B02 B:61-160,B:293-3182pe5B03       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhh.hhhhhhhhhh......hhhhhhhhhhhh......hhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh....eee..........eeeehhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh.......eee...hhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhh........eee....hhhhhhh.....ee..hhhhhhhhhhhhhhhhhhh.....eeee...ee....... 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
                 2pe5 B   2 KPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQLLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLA 331
                                    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       331

Chain C from PDB  Type:PROTEIN  Length:328
 aligned with LACI_ECOLI | P03023 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:328
                                    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 KPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTT 329
               SCOP domains d2pe5c1 C:2-61 Lac repressor (LacR), N-terminal domain      d2pe5c2 C:62-329 Lac-repressor (lacR) core (C-terminal domain)                                                                                                                                                                                                               SCOP domains
               CATH domains 2pe5C01 C:2-60 lambda repressor-like DNA-binding domains   2pe5C02 C:61-160,C:293-318  [code=3.40.50.2300, no name defined]                                    2pe5C03 C:161-292,C:319-329  [code=3.40.50.2300, no name defined]                                                                   2pe5C02 C:61-160,C:293-3182pe5C03     CATH domains
           Pfam domains (1) ---LacI-2pe5C01 C:5-50                           ------------------------------------------------------------------------------------------------------------------------Peripla_BP_3-2pe5C04 C:171-329                                                                                                                                  Pfam domains (1)
           Pfam domains (2) ---LacI-2pe5C02 C:5-50                           ------------------------------------------------------------------------------------------------------------------------Peripla_BP_3-2pe5C05 C:171-329                                                                                                                                  Pfam domains (2)
           Pfam domains (3) ---LacI-2pe5C03 C:5-50                           ------------------------------------------------------------------------------------------------------------------------Peripla_BP_3-2pe5C06 C:171-329                                                                                                                                  Pfam domains (3)
         Sec.struct. author .......hhhhhh.hhhhhhhhh..........hhhhhhhhhhh....hhhhhhhh.....eeeeeee...hhhhhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh....eee..........eeeehhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh.......eee...hhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhh........eee.....hhhhhh.....ee..hhhhhhhhhhhhhhhhhhh.....eeee...ee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D----------------------------------------------- SAPs(SNPs)
                PROSITE (1) --HTH_LACI_2  PDB: C:4-58 UniProt: 4-58                  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----HTH_LACI_1         ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pe5 C   2 KPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQLLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTT 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        

Chain D from PDB  Type:DNA  Length:17
                                                 
                 2pe5 D   5 TGTGAGCGCTCACAATT  21
                                    14       

Chain E from PDB  Type:DNA  Length:17
                                                 
                 2pe5 E   2 AATTGTGAGCGCTCACA  18
                                    11       

Chain F from PDB  Type:DNA  Length:17
                                                 
                 2pe5 F   2 AATTGTGAGCGCTCACA  18
                                    11       

   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, 6)

Asymmetric Unit

(-) CATH Domains  (2, 9)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
1a2pe5A03A:161-292,A:319-329
1b2pe5C03C:161-292,C:319-329
1c2pe5B03B:161-292,B:319-331
1d2pe5A02A:61-160,A:293-318
1e2pe5B02B:61-160,B:293-318
1f2pe5C02C:61-160,C:293-318

(-) Pfam Domains  (2, 6)

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 1jwl 1jye 1jyf 1l1m 1lbg 1lbh 1lbi 1lcc 1lcd 1lqc 1ltp 1osl 1tlf 1z04 2bjc 2kei 2kej 2kek 2p9h 2paf 3edc 4rzs 4rzt

(-) Related Entries Specified in the PDB File

2p9h 2paf