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(-)Asym./Biol. Unit
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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CLASSIC PROTEIN WITH A NEW TWIST: CRYSTAL STRUCTURE OF A LEXA REPRESSOR DNA COMPLEX
 
Authors :  A. P. P. Zhang, Y. Z. Pigli, P. A. Rice
Date :  10 Sep 09  (Deposition) - 18 Aug 10  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Protein-Dna Complex, Winged Helix-Turn-Helix, Double Helix, Repressor, Lexa, Sos System, Autocatalytic Cleavage, Dna Damage, Dna Repair, Dna Replication, Dna-Binding, Hydrolase, Sos Response, Transcription, Transcription Regulation, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. P. Zhang, Y. Z. Pigli, P. A. Rice
Structure Of The Lexa-Dna Complex And Implications For Sos Box Measurement.
Nature V. 466 883 2010
PubMed-ID: 20703307  |  Reference-DOI: 10.1038/NATURE09200

(-) Compounds

Molecule 1 - LEXA REPRESSOR
    Chains: A, B
    EC Number: 3.4.21.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LEXA, EXRA, SPR, TSL, UMUA, B4043, JW4003
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333
    Strain: K12
 
Molecule 2 - DNA (5'- D(*TP*AP*TP*AP*CP*TP*GP*TP*AP*TP*GP*CP*GP*CP*AP*TP*AP*CP*AP*GP*TP*A)- 3')
    Chains: C, D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3JSP)

(-) Sites  (0, 0)

(no "Site" information available for 3JSP)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3JSP)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Leu A:88 -Leu A:89
2Lys A:106 -Pro A:107
3Gln B:92 -His B:93
4Ile B:94 -Glu B:95
5Lys B:106 -Pro B:107

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_LEXA_ECOLI_001 *G85DLEXA_ECOLI  ---  ---AG85D
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3JSP)

(-) Exons   (0, 0)

(no "Exon" information available for 3JSP)

(-) Sequences/Alignments

Asymmetric/Biological 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:194
 aligned with LEXA_ECOLI | P0A7C2 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:198
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191        
           LEXA_ECOLI     2 KALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEIVSGASRGIRLLQEEEEGLPLVGRVAAGEPLLAQQHIEGHYQVDPSLFKPNADFLLRVSGMSMKDIGIMDGDLLAVHKTQDVRNGQVVVARIDDEVTVKRLKKQGNKVELLPENSEFKPIVVDLRQQSFTIEGLAVGVIRNG 199
               SCOP domains d3jspa1 A:2-70 automated matches                                     ----d3jspa2 A:75-199 automated matches                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhh..eee.......eee..----.eeee.................ee..hhhhh.....eeee.....hhhhh.....eeeee.........eeeeee..eeeeeeeeee..eeeee........eeee.....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------D------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3jsp A   2 KALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEIVSGASRGIRLLQ----GLPLVGRVAAGEPLLAQQHIEGHYQVDPSLFKPNADFLLRVSGMSMKDIGIMDGDLLAVHKTQDVRNGQVVVARIDDEVTVARLKKQGNKVELLPENSEFKPIVVDLRQQSFTIEGLAVGVIRNG 199
                                    11        21        31        41        51        61        |-   |    81        91       101       111       121       131       141       151       161       171       181       191        
                                                                                               70   75                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:192
 aligned with LEXA_ECOLI | P0A7C2 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:201
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201 
           LEXA_ECOLI     2 KALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEIVSGASRGIRLLQEEEEGLPLVGRVAAGEPLLAQQHIEGHYQVDPSLFKPNADFLLRVSGMSMKDIGIMDGDLLAVHKTQDVRNGQVVVARIDDEVTVKRLKKQGNKVELLPENSEFKPIVVDLRQQSFTIEGLAVGVIRNGDWL 202
               SCOP domains d3jspb1 B:2-71 automated matches                                         d3jspb2       B:75-202 automated matches                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) LexA_DNA_bind-3jspB01 B:2-65                                    ------------------------------------------------Peptidase_S24-3jspB03 B:114-182                                      -------------------- Pfam domains (1)
           Pfam domains (2) LexA_DNA_bind-3jspB02 B:2-65                                    ------------------------------------------------Peptidase_S24-3jspB04 B:114-182                                      -------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhh..eee.......eee...---..ee....------.......ee.............eeee.....hhhhh.....eeeee.........eeeeee..eeeeeeeeee..eeeee........eeee.....eeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jsp B   2 KALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEIVSGASRGIRLLQE---GLPLVGRV------LAQQHIEGHYQVDPSLFKPNADFLLRVSGMSMKDIGIMDGDLLAVHKTQDVRNGQVVVARIDDEVTVARLKKQGNKVELLPENSEFKPIVVDLRQQSFTIEGLAVGVIRNGDWL 202
                                    11        21        31        41        51        61        71   |    81|      |91       101       111       121       131       141       151       161       171       181       191       201 
                                                                                                71  75     82     89                                                                                                                 


Chain C from PDB  Type:DNA  Length:22
                                                      
                 3jsp C   1 TATACTGTATGCGCATACAGTA  22
                                    10        20  


Chain D from PDB  Type:DNA  Length:22
                                                      
                 3jsp D   1 TATACTGTATGCGCATACAGTA  22
                                    10        20
   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, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3JSP)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)
(-)
Clan: Peptidase_SF (8)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (LEXA_ECOLI | P0A7C2)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0009432    SOS response    An error-prone process for repairing damaged microbial DNA.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    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
    Gln B:92 - His B:93   [ RasMol ]  
    Ile B:94 - Glu B:95   [ RasMol ]  
    Leu A:88 - Leu A:89   [ RasMol ]  
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  3jsp
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 Related Entries

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

UniProtKB/Swiss-Prot
        LEXA_ECOLI | P0A7C2: 1jhc 1jhe 1jhf 1jhh 1lea 1leb 1mvd 1qaa 3jso 3k3r

(-) Related Entries Specified in the PDB File

3jso THE SAME PROTEIN COMPLEXED WITH A DIFFERENT DNA SUBSTRATE