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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DNA BINDING DOMAIN OF KORB IN COMPLEX WITH THE OPERATOR DNA
 
Authors :  D. Khare, G. Ziegelin, E. Lanka, U. Heinemann
Date :  17 Oct 03  (Deposition) - 01 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B,E,F,I,J  (1x)
Biol. Unit 2:  C,D,G,H,K,L  (1x)
Keywords :  Incp, Plasmid Partitioning, Protein-Dna Complex, Heilx-Turn- Helix Motif, Transcription Factor, Parb Homologue, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Khare, G. Ziegelin, E. Lanka, U. Heinemann
Sequence-Specific Dna Binding Determined By Contacts Outside The Helix-Turn-Helix Motif Of The Parb Homolog Korb.
Nat. Struct. Mol. Biol. V. 11 656 2004
PubMed-ID: 15170177  |  Reference-DOI: 10.1038/NSMB773
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*AP*(BRU) P*TP*TP*TP*AP*GP*CP*GP*GP*CP*TP*AP*AP*AP*AP*G)-3'
    Chains: E, J, G, K
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-D(*CP*(BRU) P*TP*TP*TP*AP*GP*CP*CP*GP*CP*TP*AP*AP*AP*AP*(BRU))-3'
    Chains: I, F, L, H
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - TRANSCRIPTIONAL REPRESSOR PROTEIN KORB
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMS51-12
    Expression System Strain: SCS1, SUPE44, RELA1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: OPERATOR BINDING DOMAIN (RESIDUES 117-294)
    Gene: KORB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): AB  EF  IJ  
Biological Unit 2 (1x):   CD  GH  KL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric Unit (1, 12)
No.NameCountTypeFull Name
1BRU12Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1BRU6Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1BRU6Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 1R71)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R71)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Glu A:139 -Ala A:140
2Asp A:251 -Glu A:252
3Arg D:149 -Asn D:150

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R71)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R71)

(-) Exons   (0, 0)

(no "Exon" information available for 1R71)

(-) 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:114
 aligned with KORB2_ECOLX | P07674 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:114
                                   148       158       168       178       188       198       208       218       228       238       248    
          KORB2_ECOLX   139 EADQVIENLQRNELTPREIADFIGRELAKGKKKGDIAKEIGKSPAFITQHVTLLDLPEKIADAFNTGRVRDVTVVNELVTAFKKRPEEVEAWLDDDTQEITRGTVKLLREFLDE 252
               SCOP domains d1r71a_ A: Transcriptional repressor protein KorB DNA-binding domain                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1r71 A 139 EADQVIENLQRNELTPREIADFIGRELAKGKKKGDIAKEIGKSPAFITQHVTLLDLPEKIADAFNTGRVRDVTVVNELVTAFKKRPEEVEAWLDDDTQEITRGTVKLLREFLDE 252
                                   148       158       168       178       188       198       208       218       228       238       248    


Chain B from PDB  Type:PROTEIN  Length:116
 aligned with KORB2_ECOLX | P07674 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:116
                                   146       156       166       176       186       196       206       216       226       236       246      
          KORB2_ECOLX   137 YNEADQVIENLQRNELTPREIADFIGRELAKGKKKGDIAKEIGKSPAFITQHVTLLDLPEKIADAFNTGRVRDVTVVNELVTAFKKRPEEVEAWLDDDTQEITRGTVKLLREFLDE 252
               SCOP domains d1r71b_ B: Transcriptional repressor protein KorB DNA-binding domain                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1r71 B 137 YNEADQVIENLQRNELTPREIADFIGRELAKGKKKGDIAKEIGKSPAFITQHVTLLDLPEKIADAFNTGRVRDVTVVNELVTAFKKRPEEVEAWLDDDTQEITRGTVKLLREFLDE 252
                                   146       156       166       176       186       196       206       216       226       236       246      


Chain C from PDB  Type:PROTEIN  Length:112
 aligned with KORB2_ECOLX | P07674 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:112
                                   149       159       169       179       189       199       209       219       229       239       249  
          KORB2_ECOLX   140 ADQVIENLQRNELTPREIADFIGRELAKGKKKGDIAKEIGKSPAFITQHVTLLDLPEKIADAFNTGRVRDVTVVNELVTAFKKRPEEVEAWLDDDTQEITRGTVKLLREFLD 251
               SCOP domains d1r71c_ C: Transcriptional repressor protein KorB DNA-binding domain                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1r71 C 140 ADQVIENLQRNELTPREIADFIGRELAKGKKKGDIAKEIGKSPAFITQHVTLLDLPEKIADAFNTGRVRDVTVVNELVTAFKKRPEEVEAWLDDDTQEITRGTVKLLREFLD 251
                                   149       159       169       179       189       199       209       219       229       239       249  


Chain D from PDB  Type:PROTEIN  Length:115
 aligned with KORB2_ECOLX | P07674 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:115
                                   147       157       167       177       187       197       207       217       227       237       247     
          KORB2_ECOLX   138 NEADQVIENLQRNELTPREIADFIGRELAKGKKKGDIAKEIGKSPAFITQHVTLLDLPEKIADAFNTGRVRDVTVVNELVTAFKKRPEEVEAWLDDDTQEITRGTVKLLREFLDE 252
               SCOP domains d1r71d_ D: Transcriptional repressor protein KorB DNA-binding domain                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ParBc-1r71D05---------------KorB-1r71D01 D:166-252                                                                  Pfam domains (1)
           Pfam domains (2) ParBc-1r71D06---------------KorB-1r71D02 D:166-252                                                                  Pfam domains (2)
           Pfam domains (3) ParBc-1r71D07---------------KorB-1r71D03 D:166-252                                                                  Pfam domains (3)
           Pfam domains (4) ParBc-1r71D08---------------KorB-1r71D04 D:166-252                                                                  Pfam domains (4)
         Sec.struct. author hhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1r71 D 138 NEADQVIENLQRNELTPREIADFIGRELAKGKKKGDIAKEIGKSPAFITQHVTLLDLPEKIADAFNTGRVRDVTVVNELVTAFKKRPEEVEAWLDDDTQEITRGTVKLLREFLDE 252
                                   147       157       167       177       187       197       207       217       227       237       247     


Chain E from PDB  Type:DNA  Length:17
                                                 
                 1r71 E   1 AuTTTAGCGGCTAAAAG  17
                             |      10       
                             2-BRU           


Chain F from PDB  Type:DNA  Length:17
                                                 
                 1r71 F   1 CuTTTAGCCGCTAAAAu  17
                             |      10      |
                             2-BRU         17-BRU


Chain G from PDB  Type:DNA  Length:17
                                                 
                 1r71 G   1 AuTTTAGCGGCTAAAAG  17
                             |      10       
                             |               
                             2-BRU           


Chain H from PDB  Type:DNA  Length:17
                                                 
                 1r71 H   1 CuTTTAGCCGCTAAAAu  17
                             |      10      |
                             2-BRU         17-BRU


Chain I from PDB  Type:DNA  Length:17
                                                 
                 1r71 I   1 CuTTTAGCCGCTAAAAu  17
                             |      10      |
                             |             17-BRU
                             2-BRU           


Chain J from PDB  Type:DNA  Length:17
                                                 
                 1r71 J   1 AuTTTAGCGGCTAAAAG  17
                             |      10       
                             |               
                             2-BRU           


Chain K from PDB  Type:DNA  Length:17
                                                 
                 1r71 K   1 AuTTTAGCGGCTAAAAG  17
                             |      10       
                             2-BRU           


Chain L from PDB  Type:DNA  Length:17
                                                 
                 1r71 L   1 CuTTTAGCCGCTAAAAu  17
                             |      10      |
                             2-BRU         17-BRU
   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, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1R71)

(-) Pfam Domains  (2, 8)

Asymmetric Unit
(-)
Clan: HTH (544)
(-)
Family: KorB (1)
(-)
Escherichia coli (1)
1aKorB-1r71D01D:166-252
1bKorB-1r71D02D:166-252
1cKorB-1r71D03D:166-252
1dKorB-1r71D04D:166-252
(-)
Clan: ParBc (6)
(-)
Family: ParBc (6)
(-)
Escherichia coli (1)
2aParBc-1r71D05D:138-150
2bParBc-1r71D06D:138-150
2cParBc-1r71D07D:138-150
2dParBc-1r71D08D:138-150

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (KORB2_ECOLX | P07674)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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.

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  Cis Peptide Bonds
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    Glu A:139 - Ala A:140   [ RasMol ]  
 
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  1r71
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 Related Entries

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

UniProtKB/Swiss-Prot
        KORB2_ECOLX | P07674: 1igq 1igu

(-) Related Entries Specified in the PDB File

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