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(-) Description

Title :  STRUCTURE OF THE DNA COMPLEX OF THE C-TERMINAL DOMAIN OF LER
 
Authors :  T. N. Cordeiro, H. Schimdt, C. Madrid, A. Juarez, P. Bernado, C. Grisien J. Garcia, M. Pons
Date :  23 Jun 11  (Deposition) - 07 Dec 11  (Release) - 07 Dec 11  (Revision)
Method :  SOLUTION NMR; SOLUTION SCATTERING
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C  (20x)
NMR Structure *:  A,B,C  (1x)
Keywords :  Transcription Regulator-Dna Complex, Arginine-Minor-Groove Recognition, Horizontal Gene Transfer, Indirect Readout, Nucleoid Associated Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. N. Cordeiro, H. Schmidt, C. Madrid, A. Juarez, P. Bernado, C. Griesinger, J. Garcia, M. Pons
Indirect Dna Readout By An H-Ns Related Protein: Structure Of The Dna Complex Of The C-Terminal Domain Of Ler.
Plos Pathog. V. 7 02380 2011
PubMed-ID: 22114557  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1002380

(-) Compounds

Molecule 1 - LER
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PHAT2
    Fragment: SEQUENCE DATABASE RESIDUES 56-102
    Gene: LER
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 2 - DNA (5'-D(*GP*CP*GP*AP*TP*AP*AP*TP*TP*GP*AP*TP*AP*GP*G)- 3')
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*CP*CP*TP*AP*TP*CP*AP*AP*TP*TP*AP*TP*CP*GP*C)- 3')
    Chains: C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
NMR Structure (20x): ABC
NMR Structure * (1x): ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2LEV)

(-) Sites  (0, 0)

(no "Site" information available for 2LEV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2LEV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2LEV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2LEV)

(-) Exons   (0, 0)

(no "Exon" information available for 2LEV)

(-) 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:57
 aligned with E9N650_ECOLX | E9N650 from UniProtKB/TrEMBL  Length:105

    Alignment length:69
                                    43        53        63        73        83        93         
         E9N650_ECOLX    34 YYNITLQELGYTNVPDDGLARRNSSKGVYYRNEEGQTWSGVGRQPRWLKEALLNGMKKEDFLVKDTEEE 102
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........------------.....eeee.....ee......hhhhhhhhhh..hhhh.eee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 2lev A  -9 SHHHHHHSMG------------NSSKGVYYRNEEGQTWSGVGRQPRWLKEALLNGMKKEDFLVKDTEEE  47
                                     0         -  |      8        18        28        38         
                                     0            1                                              


Chain A from PDB  Type:PROTEIN  Length:57
 aligned with Q7DB51_ECO57 | Q7DB51 from UniProtKB/TrEMBL  Length:129

    Alignment length:113
                                    19        29        39        49        59        69        79        89        99       109       119   
         Q7DB51_ECO57    10 ENNSHTTSPYIQLIEQIAVLQQEAKRLREQEVQSVIESIQKQITYYNITLQELGYTNVPDDGLARRNSSKGVYYRNEEGQTWSGVGRQPRWLKEALLNGMKKEDFLVKDTEEE 122
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........--------------------------------------------..------------.....eeee.....ee......hhhhhhhhhh..hhhh.eee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 2lev A  -9 SHHHHHHS--------------------------------------------MG------------NSSKGVYYRNEEGQTWSGVGRQPRWLKEALLNGMKKEDFLVKDTEEE  47
                                   | -         -         -         -         -  ||     -      |  4        14        24        34        44   
                                  -2                                           -1|            1                                              
                                                                                 0                                                           


Chain B from PDB  Type:DNA  Length:15
                                               
                 2lev B   1 GCGATAATTGATAGG  15
                                    10     


Chain C from PDB  Type:DNA  Length:15
                                               
                 2lev C  16 CCTATCAATTATCGC  30
                                    25
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 2LEV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2LEV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2LEV)

(-) Gene Ontology  (3, 6)

NMR Structure(hide GO term definitions)
Chain A   (Q7DB51_ECO57 | Q7DB51)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

Chain A   (E9N650_ECOLX | E9N650)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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