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(-) Description

Title :  STRUCTURE OF THE GLOBAL TRANSCRIPTION REGULATOR FAPR FROM STAPHYLOCOCCUS AUREUS IN COMPLEX WITH DNA OPERATOR
 
Authors :  D. Albanesi, M. E. Guerin, A. Buschiazzo, D. De Mendoza, P. M. Alzari
Date :  13 Sep 11  (Deposition) - 26 Sep 12  (Release) - 23 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.15
Chains :  Asym./Biol. Unit :  A,B,C,D,F,G
Keywords :  Transcription, Lipid Homeostasis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Albanesi, G. Reh, M. E. Guerin, F. Schaeffer, M. Debarbouille, A. Buschiazzo, G. E. Schujman, D. De Mendoza, P. M. Alzari
Structural Basis For Feed-Forward Transcriptional Regulation Of Membrane Lipid Homeostasis In Staphylococcus Aureus.
Plos Pathog. V. 9 3108 2013
PubMed-ID: 23300457  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1003108

(-) Compounds

Molecule 1 - TRANSCRIPTION FACTOR FAPR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: PLYSS
    Expression System Vector: PET15B
    Expression System Vector Type: PLASMID
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Synonym: FATTY ACID AND PHOSPHOLIPID BIOSYNTHESIS REGULATOR, REPRESSOR FACTOR FAPR
 
Molecule 2 - FAPR PROMOTER
    Chains: F
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synthetic: YES
 
Molecule 3 - FAPR PROMOTER
    Chains: G
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDFG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 4A12)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4A12)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4A12)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4A12)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4A12)

(-) Exons   (0, 0)

(no "Exon" information available for 4A12)

(-) 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:184
 aligned with Q2FZ56_STAA8 | Q2FZ56 from UniProtKB/TrEMBL  Length:190

    Alignment length:184
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186    
         Q2FZ56_STAA8     7 KLKKDKRREAIRQQIDSNPFITDHELSDLFQVSIQTIRLDRTYLNIPELRKRIKLVAEKNYDQISSIEEQEFIGDLIQVNPNVKAQSILDITSDSVFHKTGIARGHVLFAQANSLCVALIKQPTVLTHESSIQFIEKVKLNDTVRAEARVVNQTAKHYYVEVKSYVKHTLVFKGNFKMFYDKRG 190
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhh.....hhhhh....eeeeee...eeeeeee.............hhhhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeeee...eeeeeeeee....eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a12 A   7 KLKKDKRREAIRQQIDSNPFITDHELSDLFQVSIQTIRLDRTYLNIPELRKRIKLVAEKNYDQISSIEEQEFIGDLIQVNPNVKAQSILDITSDSVFHKTGIARGHVLFAQANSLCVALIKQPTVLTHESSIQFIEKVKLNDTVRAEARVVNQTAKHYYVEVKSYVKHTLVFKGNFKmFYDKRG 190
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186    
                                                                                                                                                                                                           184-MSE  


Chain B from PDB  Type:PROTEIN  Length:187
 aligned with Q2FZ56_STAA8 | Q2FZ56 from UniProtKB/TrEMBL  Length:190

    Alignment length:187
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       
         Q2FZ56_STAA8     4 ETLKLKKDKRREAIRQQIDSNPFITDHELSDLFQVSIQTIRLDRTYLNIPELRKRIKLVAEKNYDQISSIEEQEFIGDLIQVNPNVKAQSILDITSDSVFHKTGIARGHVLFAQANSLCVALIKQPTVLTHESSIQFIEKVKLNDTVRAEARVVNQTAKHYYVEVKSYVKHTLVFKGNFKMFYDKRG 190
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhh...eeeeee...eeeeeee.............hhhhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeeee...eeeeeeeee....eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a12 B   4 ETLKLKKDKRREAIRQQIDSNPFITDHELSDLFQVSIQTIRLDRTYLNIPELRKRIKLVAEKNYDQISSIEEQEFIGDLIQVNPNVKAQSILDITSDSVFHKTGIARGHVLFAQANSLCVALIKQPTVLTHESSIQFIEKVKLNDTVRAEARVVNQTAKHYYVEVKSYVKHTLVFKGNFKmFYDKRG 190
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183|      
                                                                                                                                                                                                              184-MSE  


Chain C from PDB  Type:PROTEIN  Length:187
 aligned with Q2FZ56_STAA8 | Q2FZ56 from UniProtKB/TrEMBL  Length:190

    Alignment length:187
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       
         Q2FZ56_STAA8     4 ETLKLKKDKRREAIRQQIDSNPFITDHELSDLFQVSIQTIRLDRTYLNIPELRKRIKLVAEKNYDQISSIEEQEFIGDLIQVNPNVKAQSILDITSDSVFHKTGIARGHVLFAQANSLCVALIKQPTVLTHESSIQFIEKVKLNDTVRAEARVVNQTAKHYYVEVKSYVKHTLVFKGNFKMFYDKRG 190
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhh...eeeeee...eeeeeee.............hhhhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeeee...eeeeeeeee....eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a12 C   4 ETLKLKKDKRREAIRQQIDSNPFITDHELSDLFQVSIQTIRLDRTYLNIPELRKRIKLVAEKNYDQISSIEEQEFIGDLIQVNPNVKAQSILDITSDSVFHKTGIARGHVLFAQANSLCVALIKQPTVLTHESSIQFIEKVKLNDTVRAEARVVNQTAKHYYVEVKSYVKHTLVFKGNFKmFYDKRG 190
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183|      
                                                                                                                                                                                                              184-MSE  


Chain D from PDB  Type:PROTEIN  Length:184
 aligned with Q2FZ56_STAA8 | Q2FZ56 from UniProtKB/TrEMBL  Length:190

    Alignment length:184
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186    
         Q2FZ56_STAA8     7 KLKKDKRREAIRQQIDSNPFITDHELSDLFQVSIQTIRLDRTYLNIPELRKRIKLVAEKNYDQISSIEEQEFIGDLIQVNPNVKAQSILDITSDSVFHKTGIARGHVLFAQANSLCVALIKQPTVLTHESSIQFIEKVKLNDTVRAEARVVNQTAKHYYVEVKSYVKHTLVFKGNFKMFYDKRG 190
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhh.....hhhhh....eeeeee...eeeeeee.............hhhhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeeee...eeeeeeeee....eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a12 D   7 KLKKDKRREAIRQQIDSNPFITDHELSDLFQVSIQTIRLDRTYLNIPELRKRIKLVAEKNYDQISSIEEQEFIGDLIQVNPNVKAQSILDITSDSVFHKTGIARGHVLFAQANSLCVALIKQPTVLTHESSIQFIEKVKLNDTVRAEARVVNQTAKHYYVEVKSYVKHTLVFKGNFKmFYDKRG 190
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186    
                                                                                                                                                                                                           184-MSE  


Chain F from PDB  Type:DNA  Length:40
                                                                        
                 4a12 F   1 GCCAATTATATACTACTATTAGTACCTAGTCTTAATTCCG  40
                                    10        20        30        40


Chain G from PDB  Type:DNA  Length:40
                                                                        
                 4a12 G   1 CGGAATTAAGACTAGGTACTAATAGTAGTATATAATTGGC  40
                                    10        20        30        40
   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 4A12)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4A12)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4A12)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q2FZ56_STAA8 | Q2FZ56)
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: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:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0045717    negative regulation of fatty acid biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of fatty acids.
    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:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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 Related Entries

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

UniProtKB/TrEMBL
        Q2FZ56_STAA8 | Q2FZ56: 4a0x 4a0y 4a0z

(-) Related Entries Specified in the PDB File

4a0x STRUCTURE OF THE GLOBAL TRANSCRIPTION REGULATOR FAPR FROM STAPHYLOCOCCUS AUREUS
4a0y STRUCTURE OF THE GLOBAL TRANSCRIPTION REGULATOR FAPR FROM STAPHYLOCOCCUS AUREUS
4a0z STRUCTURE OF THE GLOBAL TRANSCRIPTION REGULATOR FAPR FROM STAPHYLOCOCCUS AUREUS IN COMPLEX WITH MALONYL-COA