Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF A REX-FAMILY TRANSCRIPTIONAL REGULATORY PROTEIN FROM STREPTOCOCCUS AGALACTIAE BOUND TO A PALINDROMIC OPERATOR
 
Authors :  S. Thiyagarajan, D. Logan, C. Von Wachenfeldt
Date :  26 Oct 09  (Deposition) - 10 Nov 10  (Release) - 10 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Protein-Dna Complex, Winged Helix, Rossmann Fold, Nad+, Repressor, Transcription, Transcription Regulation, Redox Sensing, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Thiyagarajan, D. Logan, C. Von Wachenfeldt
Structure And Functional Properties Of The Streptococcus Transcriptional Repressor Rex
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - REDOX-SENSING TRANSCRIPTIONAL REPRESSOR REX
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET101
    Expression System Strain: TUNER (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GBS1167, REX
    Organism Scientific: STREPTOCOCCUS AGALACTIAE SEROGROUP III
    Organism Taxid: 216495
    Strain: NEM316
 
Molecule 2 - DNA (5'-D(*AP*AP*TP*TP*GP*TP*GP*AP*AP*AP*T)-3')
    Chains: B
    Engineered: YES
    Other Details: NUCLEOTIDE SYNTHESIS
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*AP*TP*TP*TP*CP*AP*CP*AP*AP*TP*T)-3')
    Chains: C
    Engineered: YES
    Other Details: NUCLEOTIDE SYNTHESIS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:91 , CYS A:92 , GLY A:93 , ASN A:94 , ILE A:95 , ALA A:98 , LEU A:99 , TYR A:102 , ASP A:117 , LEU A:118 , ILE A:137 , THR A:155 , VAL A:156 , PRO A:157 , SER A:158 , VAL A:164 , PHE A:179 , SER A:180 , THR A:198 , HOH A:217 , HOH A:220 , HOH A:224 , HOH A:226 , HOH A:285BINDING SITE FOR RESIDUE NAD A 213
2AC2SOFTWAREARG A:20 , TYR A:102 , PRO A:181 , THR A:198BINDING SITE FOR RESIDUE MG A 214

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KET)

(-) 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:205
 aligned with REX_STRA3 | Q8E565 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:205
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205     
            REX_STRA3     6 SIPKATAKRLSLYYRIFKRFNTDGIEKASSKQIADALGIDSATVRRDFSYFGELGRRGFGYDVKKLMNFFAEILNDHSTTNVMLVGCGNIGRALLHYRFHDRNKMQISMAFDLDSNDLVGKTTEDGIPVYGISTINDHLIDSDIETAILTVPSTEAQEVADILVKAGIKGILSFSPVHLTLPKDIIVQYVDLTSELQTLLYFMNQ 210
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Put_DNA-bind_N-3ketA01 A:6-54                    ---------------------------CoA_binding-3ketA02 A:82-182                                                                         ---------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhh.hhhhhhhhhhh..........eehhhhhhhhhhhh.....eeeeee..hhhhhhhhh.hhhhh..eeeeeeee................eee..hhhhhh......eeee..hhhhhhhhhhhhhhh...eeee............eeee.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ket A   6 SIPKATAKRLSLYYRIFKRFNTDGIEKASSKQIADALGIDSATVRRDFSYFGELGRRGFGYDVKKLMNFFAEILNDHSTTNVMLVGCGNIGRALLHYRFHDRNKMQISMAFDLDSNDLVGKTTEDGIPVYGISTINDHLIDSDIETAILTVPSTEAQEVADILVKAGIKGILSFSPVHLTLPKDIIVQYVDLTSELQTLLYFMNQ 210
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205     


Chain B from PDB  Type:DNA  Length:11
                                           
                 3ket B   1 AATTGTGAAAT  11
                                    10 


Chain C from PDB  Type:DNA  Length:11
                                           
                 3ket C  34 ATTTCACAATT  44
                                    43
   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 3KET)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: HTH (544)
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (REX_STRA3 | Q8E565)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0050662    coenzyme binding    Interacting selectively and non-covalently with a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
    GO:0048037    cofactor binding    Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
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:0051775    response to redox state    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating redox state. Redox state refers to the balance of oxidized versus reduced forms of electron donors and acceptors in an organelle, cell or organ; plastoquinone, glutathione (GSH/GSSG), and nicotinamide nucleotides (NAD+/NADH and NADP+/NADPH) are among the most important.
    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 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
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ket)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  3ket
    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
  REX_STRA3 | Q8E565
    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
  REX_STRA3 | Q8E565
    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
        REX_STRA3 | Q8E565: 3keo 3keq

(-) Related Entries Specified in the PDB File

2dt5 CRYSTAL STRUCTURE OF TTHA1657 (AT-RICH DNA-BINDING PROTEIN) FROM THERMUS THERMOPHILUS HB8
2vt3 STRUCTURE AND FUNCTIONAL PROPERTIES OF THE BACILLUS SUBTILIS TRANSCRIPTIONAL REPRESSOR REX
3keo STRUCTURE AND FUNCTIONAL PROPERTIES OF THE STREPTOCOCCUS AGALACTIAE TRANSCRIPTIONAL REPRESSOR REX
3keq STRUCTURE AND FUNCTIONAL PROPERTIES OF THE STREPTOCOCCUS AGALACTIAE TRANSCRIPTIONAL REPRESSOR REX