Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
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 STAPHYLOCOCCUS AUREUS AGRA LYTTR DOMAIN BOUND TO DNA REVEALS A BETA FOLD WITH A NOVEL MODE OF BINDING
 
Authors :  D. J. Sidote, C. Barbieri, T. Wu, A. M. Stock
Date :  21 Dec 07  (Deposition) - 08 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Lyttr, Agra, Response Regulator, Dna Binding Domain, Activator, Cytoplasm, Dna-Binding, Phosphoprotein, Transcription, Transcription Regulation, Two-Component Regulatory System, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. J. Sidote, C. M. Barbieri, T. Wu, A. M. Stock
Structure Of The Staphylococcus Aureus Agra Lyttr Domain Bound To Dna Reveals A Beta Fold With An Unusual Mode Of Binding.
Structure V. 16 727 2008
PubMed-ID: 18462677  |  Reference-DOI: 10.1016/J.STR.2008.02.011
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ACCESSORY GENE REGULATOR PROTEIN A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET9A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN, RESIDUES 137-238
    Gene: AGRA, AGR
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Strain: DB
 
Molecule 2 - DNA (5'- D(*DTP*DTP*DTP*DAP*DAP*DCP*DAP*DGP*DTP*DTP*DAP*DAP*DGP*(BRU )P*DAP*DT)-3')
    Chains: B
    Engineered: YES
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN STAPHYLOCOCCUS AUREUS
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*DAP*DAP*(BRU) P*DAP*DCP*DTP*DTP*DAP*DAP*DCP*DTP*DGP*DTP*DTP*DAP*DA)-3')
    Chains: C
    Engineered: YES
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN STAPHYLOCOCCUS AUREUS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1BRU2Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:248 , HOH A:307 , HOH A:321 , HOH A:345 , HOH A:346 , HOH A:347BINDING SITE FOR RESIDUE MG A 1
2AC2SOFTWARESER A:190 , ASP A:193 , PHE A:196 , HOH A:264 , HOH A:314 , HOH A:348BINDING SITE FOR RESIDUE MG A 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BS1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3BS1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BS1)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LYTTRPS50930 LytTR-type HTH domain profile.AGRA_STAAU143-238  1A:143-238

(-) Exons   (0, 0)

(no "Exon" information available for 3BS1)

(-) 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:103
 aligned with AGRA_STAAU | P0A0I7 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:103
                                   145       155       165       175       185       195       205       215       225       235   
           AGRA_STAAU   136 KDNSVETIELKRGSNSVYVQYDDIMFFESSTKSHRLIAHLDNRQIEFYGNLKELSQLDDRFFRCHNSFVVNRHNIESIDSKERIVYFKNKEHCYASVRNVKKI 238
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee..eeeeee...eeeeee.....eeeeee...eeeee.hhhhhhhhh..eeeee..eeee...eeeee....eeee....eee....hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------HTH_LYTTR  PDB: A:143-238 UniProt: 143-238                                                       PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 3bs1 A 136 MDNSVETIELKRGSNSVYVQYDDIMFFESSTKSHRLIAHLDNRQIEFYGNLKELSQLDDRFFRCHNSFVVNRHNIESIDSKERIVYFKNKEHCYASVRNVKKI 238
                                   145       155       165       175       185       195       205       215       225       235   


Chain B from PDB  Type:DNA  Length:16
                                                
                 3bs1 B   1 TTTAACAGTTAAGuAT  16
                                    10   |  
                                        14-BRU


Chain C from PDB  Type:DNA  Length:16
                                                
                 3bs1 C   1 AAuACTTAACTGTTAA  16
                              |     10      
                              |             
                              3-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  (0, 0)

(no "SCOP Domain" information available for 3BS1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3BS1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BS1)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AGRA_STAAU | P0A0I7)
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:0000160    phosphorelay signal transduction system    A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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
    BRU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3bs1)
 

(-) 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
  3bs1
    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
  AGRA_STAAU | P0A0I7
    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
  AGRA_STAAU | P0A0I7
    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
        AGRA_STAAU | P0A0I7: 4g4k

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3BS1)