Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF THE E. COLI ANTITOXIN MQSA (YGIT/B3021) IN COMPLEX WITH ITS GENE PROMOTER
 
Authors :  B. L. Brown, W. Peti, R. Page
Date :  04 Aug 10  (Deposition) - 10 Nov 10  (Release) - 02 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,E,F
Keywords :  Hth-Xre Dna Binding Motif, Transcriptional Regulator, Bacterial Antitoxin, Zn Binding Protein, Transcription Regulator-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. L. Brown, T. K. Wood, W. Peti, R. Page
Structure Of The Escherichia Coli Antitoxin Mqsa (Ygit/B3021) Bound To Its Gene Promoter Reveals Extensive Domain Rearrangements And The Specificity Of Transcriptiona Regulation.
J. Biol. Chem. V. 286 2285 2011
PubMed-ID: 21068382  |  Reference-DOI: 10.1074/JBC.M110.172643

(-) Compounds

Molecule 1 - UNCHARACTERIZED HTH-TYPE TRANSCRIPTIONAL REGULATOR YGIT
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: RP1B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: B3021, JW2989, YGIT
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
 
Molecule 2 - DNA (26-MER)
    Chains: F
    Engineered: YES
    Other Details: MQSRA PROMOTER
    Other Details - Source: MQSRA PROMOTER PALINDROME DNA STRAND
    Synthetic: YES
 
Molecule 3 - DNA (26-MER)
    Chains: E
    Engineered: YES
    Other Details: MQSRA PROMOTER
    Other Details - Source: MQSRA PROMOTER PALINDROME REVERSE COMPLEMENT DNA STRAND
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS B:3 , CYS B:6 , CYS B:37 , CYS B:40BINDING SITE FOR RESIDUE ZN B 132
2AC2SOFTWARECYS A:3 , CYS A:6 , CYS A:37 , CYS A:40BINDING SITE FOR RESIDUE ZN A 132
3AC3SOFTWARESER A:100 , LYS A:104 , ASN A:106 , DT E:6 , DA E:7 , HOH E:154 , HOH E:308BINDING SITE FOR RESIDUE GOL E 27
4AC4SOFTWAREARG B:23 , HOH B:149 , HOH B:180 , HOH B:190 , HOH B:211 , DG F:17BINDING SITE FOR RESIDUE GOL B 133

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O9X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3O9X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O9X)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_CROC1PS50943 Cro/C1-type HTH domain profile.MQSA_ECOLI74-127
 		  2A:74-127
B:74-127

(-) Exons   (0, 0)

(no "Exon" information available for 3O9X)

(-) 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:132
 aligned with MQSA_ECOLI | Q46864 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:132
                             1                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129  
           MQSA_ECOLI     - -MKCPVCHQGEMVSGIKDIPYTFRGRKTVLKGIHGLYCVHCEESIMNKEESDAFMAQVKAFRASVNAETVAPEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAQPHPSTIKLLRVLDKHPELLNEIR 131
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeeeeeeeeeee..eeeeeeeeeeeee.....ee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhh.....hhhhhhhhhhhhhh..hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------HTH_CROC1  PDB: A:74-127 UniProt: 74-127              ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3o9x A   0 HMKCPVCHQGEMVSGIKDIPYTFRGRKTVLKGIHGLYCVHCEESIMNKEESDAFMAQVKAFRASVNAETVAPEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAQPHPSTIKLLRVLDKHPELLNEIR 131
                                     9        19        29        39        49        59        69        79        89        99       109       119       129  


Chain B from PDB  Type:PROTEIN  Length:132
 aligned with MQSA_ECOLI | Q46864 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:132
                             1                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129  
           MQSA_ECOLI     - -MKCPVCHQGEMVSGIKDIPYTFRGRKTVLKGIHGLYCVHCEESIMNKEESDAFMAQVKAFRASVNAETVAPEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAQPHPSTIKLLRVLDKHPELLNEIR 131
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeeeeeeeeeee..eeeeeeeeeeeee.....ee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhh.....hhhhhhhhhhhhhh..hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------HTH_CROC1  PDB: B:74-127 UniProt: 74-127              ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3o9x B   0 HMKCPVCHQGEMVSGIKDIPYTFRGRKTVLKGIHGLYCVHCEESIMNKEESDAFMAQVKAFRASVNAETVAPEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAQPHPSTIKLLRVLDKHPELLNEIR 131
                                     9        19        29        39        49        59        69        79        89        99       109       119       129  


Chain E from PDB  Type:DNA  Length:26
                                                          
                 3o9x E   1 AGTTATAACCTAAAAGGTTAATTACA  26
                                    10        20      


Chain F from PDB  Type:DNA  Length:26
                                                          
                 3o9x F   1 TGTAATTAACCTTTTAGGTTATAACT  26
                                    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  (0, 0)

(no "SCOP Domain" information available for 3O9X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O9X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3O9X)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MQSA_ECOLI | Q46864)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3o9x)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3o9x
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MQSA_ECOLI | Q46864
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  MQSA_ECOLI | Q46864
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        MQSA_ECOLI | Q46864: 2kz8 3fmy 3ga8 3gn5 3hi2

(-) Related Entries Specified in the PDB File

3fmy STRUCTURE OF THE C-TERMINAL DOMAIN OF THE E. COLI ANTITOXIN MQSA (YGIT/B3021)
3ga8 STRUCTURE OF THE N-TERMINAL DOMAIN OF THE E. COLI ANTITOXIN MQSA (YGIT/B3021)
3gn5 STRUCTURE OF THE E. COLI ANTITOXIN MQSA (YGIT/B3021)
3hi2 STRUCTURE OF THE E. COLI ANTITOXIN MQSA (YGIT/B3021) COMPLEXED WITH THE E. COLI TOXIN MQSR (YGIU/B3022)