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(-) Description

Title :  CRYSTAL STRUCTURES OF SARA: A PLEIOTROPIC REGULATOR OF VIRULENCE GENES IN S. AUREUS
 
Authors :  M. A. Schumacher, B. Hurlburt, R. G. Brennan
Date :  03 Oct 00  (Deposition) - 22 Jan 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym./Biol. Unit :  B,D,K,W
Keywords :  Protein-Dna Complex, Indirect Readout, D-Dna, Conformational Changes, Coil To Helix, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. A. Schumacher, B. K. Hurlburt, R. G. Brennan
Crystal Structures Of Sara, A Pleiotropic Regulator Of Virulence Genes In S. Aureus.
Nature V. 409 215 2001
PubMed-ID: 11196648  |  Reference-DOI: 10.1038/35051623
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(P*AP*TP*AP*TP*AP*TP*A)-3'
    ChainsW, K
    EngineeredYES
    SyntheticYES
 
Molecule 2 - STAPHYLOCOCCAL ACCESSORY REGULATOR A
    ChainsD, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET9
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificSTAPHYLOCOCCUS AUREUS
    Organism Taxid1280
    StrainDB
    SynonymSARA

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit BDKW

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:84 , GLU D:11 , DA W:9BINDING SITE FOR RESIDUE CA D 200
2AC2SOFTWAREGLU B:11 , DA K:9 , DT W:6BINDING SITE FOR RESIDUE CA B 200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1FZP)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp B:8 -Cys B:9

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1FZP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1FZP)

(-) Exons   (0, 0)

(no "Exon" information available for 1FZP)

(-) 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 B from PDB  Type:PROTEIN  Length:105
 aligned with SARA_STAA8 | Q2G2U9 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:115
                                    11        21        31        41        51        61        71        81        91       101       111     
           SARA_STAA8     2 AITKINDCFELLSMVTYADKLKSLIKKEFSISFEEFAVLTYISENKEKEYYLKDIINHLNYKQPQVVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQRKKIESLLSRVNKRIT 116
               SCOP domains d1fzpb_ B: Pleiotropic regulator of virulence genes, Sa          rA                                                 SCOP domains
               CATH domains 1fzpB00 B:2-116 'winged helix' repressor DNA binding do          main                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh....hhhhhhhhh..----------hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1fzp B   2 AITKINDCFELLSMVTYADKLKSLIKKEFSISFEEFAVLTYISENKEKEYYLKDI----------VVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQRKKIESLLSRVNKRIT 116
                                    11        21        31        41        51    |    -     |  71        81        91       101       111     
                                                                                 56         67                                                 

Chain B from PDB  Type:PROTEIN  Length:105
 aligned with SARA_STAAU | P0C1U6 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:115
                                    11        21        31        41        51        61        71        81        91       101       111     
           SARA_STAAU     2 AITKINDCFELLSMVTYADKLKSLIKKEFSISFEEFAVLTYISENKEKEYYLKDIINHLNYKQPQVVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQRKKIESLLSRVNKRIT 116
               SCOP domains d1fzpb_ B: Pleiotropic regulator of virulence genes, Sa          rA                                                 SCOP domains
               CATH domains 1fzpB00 B:2-116 'winged helix' repressor DNA binding do          main                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh....hhhhhhhhh..----------hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1fzp B   2 AITKINDCFELLSMVTYADKLKSLIKKEFSISFEEFAVLTYISENKEKEYYLKDI----------VVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQRKKIESLLSRVNKRIT 116
                                    11        21        31        41        51    |    -     |  71        81        91       101       111     
                                                                                 56         67                                                 

Chain D from PDB  Type:PROTEIN  Length:100
 aligned with SARA_STAA8 | Q2G2U9 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:110
                                    11        21        31        41        51        61        71        81        91       101       111
           SARA_STAA8     2 AITKINDCFELLSMVTYADKLKSLIKKEFSISFEEFAVLTYISENKEKEYYLKDIINHLNYKQPQVVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQRKKIESLLSRV 111
               SCOP domains d1fzpd_ D: Pleiotropic regulator of virulence genes, Sa          rA                                            SCOP domains
               CATH domains 1fzpD00 D:2-111 'winged helix' repressor DNA binding do          main                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.----------hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1fzp D   2 AITKINDCFELLSMVTYADKLKSLIKKEFSISFEEFAVLTYISENKEKEYYLKDI----------VVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQRKKIESLLSRV 111
                                    11        21        31        41        51    |    -     |  71        81        91       101       111
                                                                                 56         67                                            

Chain D from PDB  Type:PROTEIN  Length:100
 aligned with SARA_STAAU | P0C1U6 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:110
                                    11        21        31        41        51        61        71        81        91       101       111
           SARA_STAAU     2 AITKINDCFELLSMVTYADKLKSLIKKEFSISFEEFAVLTYISENKEKEYYLKDIINHLNYKQPQVVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQRKKIESLLSRV 111
               SCOP domains d1fzpd_ D: Pleiotropic regulator of virulence genes, Sa          rA                                            SCOP domains
               CATH domains 1fzpD00 D:2-111 'winged helix' repressor DNA binding do          main                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.----------hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1fzp D   2 AITKINDCFELLSMVTYADKLKSLIKKEFSISFEEFAVLTYISENKEKEYYLKDI----------VVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQRKKIESLLSRV 111
                                    11        21        31        41        51    |    -     |  71        81        91       101       111
                                                                                 56         67                                            

Chain K from PDB  Type:DNA  Length:7
                                       
                 1fzp K   3 ATATATA   9

Chain W from PDB  Type:DNA  Length:7
                                       
                 1fzp W   3 ATATATA   9

   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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1FZP)

(-) Gene Ontology  (7, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain B,D   (SARA_STAAU | P0C1U6)
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.
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0090609    single-species submerged biofilm formation    A process in which planktonically growing microorganisms of the same species aggregate and grow on solid substrates under the flow of a liquid and produce extracellular polymers that facilitate attachment and matrix formation, resulting in a change in the organisms' growth rate and gene 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.

Chain B,D   (SARA_STAA8 | Q2G2U9)
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.
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    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.

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 Related Entries

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(-) Related Entries Specified in the PDB File

1fzn CRYSTAL STRUCTURE OF SARA