1FZP | PD0185 - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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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)

*Molecule 1 - 5'-D(PAPTPAPTPAPTPA)-3'**
	Chains	:	W, K
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - STAPHYLOCOCCAL ACCESSORY REGULATOR A
	Chains	:	D, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET9
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Strain	:	DB
	Synonym	:	SARA

		1	2	3	4
Asymmetric/Biological Unit	:	B	D	K	W

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG B:84 , GLU D:11 , DA W:9	BINDING SITE FOR RESIDUE CA D 200
2	AC2	SOFTWARE	GLU B:11 , DA K:9 , DT W:6	BINDING SITE FOR RESIDUE CA B 200

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

Asymmetric/Biological Unit

No.	Residues
1	Asp B:8	-	Cys B:9

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

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

(no "Exon" information available for 1FZP)

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: Winged helix DNA-binding domain (576)

Family: MarR-like transcriptional regulators (34)

Protein domain: Pleiotropic regulator of virulence genes, SarA (3)

Staphylococcus aureus [TaxId: 1280] (3)

1a	d1fzpb_	B:
1b	d1fzpd_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: 'winged helix' repressor DNA binding domain (507)

[unclassified] (77)

1a	1fzpD00	D:2-111
1b	1fzpB00	B:2-116

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

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asp B:8 - Cys B:9	[ RasMol ]

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	1fzp
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1fzn	CRYSTAL STRUCTURE OF SARA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

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