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(-) Description

Title :  STRUCTURE OF THE ARGININE REPRESSOR FROM BACILLUS STEAROTHERMOPHILUS
 
Authors :  J. Ni, V. Sakanyan, D. Charlier, N. Glansdorff, G. D. Van Duyne
Date :  18 Dec 98  (Deposition) - 15 Jun 99  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Repressor, Arginine, Helix Turn Helix (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Ni, V. Sakanyan, D. Charlier, N. Glansdorff, G. D. Van Duyne
Structure Of The Arginine Repressor From Bacillus Stearothermophilus.
Nat. Struct. Biol. V. 6 427 1999
PubMed-ID: 10331868  |  Reference-DOI: 10.1038/8229
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ARGININE REPRESSOR
    Chains: A, B, C, D, E, F
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1B4A)

(-) Sites  (0, 0)

(no "Site" information available for 1B4A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1B4A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1B4A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1B4A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1B4A)

(-) Exons   (0, 0)

(no "Exon" information available for 1B4A)

(-) 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:146
 aligned with ARGR_GEOSE | O31408 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:146
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143      
           ARGR_GEOSE     4 GQRHIKIREIIMSNDIETQDELVDRLREAGFNVTQATVSRDIKEMQLVKVPMANGRYKYSLPSDQRFNPLQKLKRALVDVFIKLDGTGNLLVLRTLPGNAHAIGVLLDNLDWDEIVGTICGDDTCLIICRTPKDAKKVSNQLLSML 149
               SCOP domains d1b4aa1 A:4-78 Arginine repressor (ArgR), N-terminal DNA-binding domain    d1b4aa2 A:79-149 C-terminal domain of arginine repressor                SCOP domains
               CATH domains -----1b4aA01 A:9-67 'winged helix' repressor DNA binding domain -----------1b4aA02 A:79-148  [code=3.30.1360.40, no name defined]                - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.....hhhhhhhhhh......hhhhhhhhhh...eeee.....eeee........hhhhhhhhhhhheeeeeee..eeeeee....hhhhhhhhhhh....eeeeee...eeeeee..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b4a A   4 GQRHIKIREIIMSNDIETQDELVDRLREAGFNVTQATVSRDIKEMQLVKVPMANGRYKYSLPSDQRFNPLQKLKRALVDVFIKLDGTGNLLVLRTLPGNAHAIGVLLDNLDWDEIVGTICGDDTCLIICRTPKDAKKVSNQLLSML 149
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143      


Chain B from PDB  Type:PROTEIN  Length:146
 aligned with ARGR_GEOSE | O31408 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:146
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143      
           ARGR_GEOSE     4 GQRHIKIREIIMSNDIETQDELVDRLREAGFNVTQATVSRDIKEMQLVKVPMANGRYKYSLPSDQRFNPLQKLKRALVDVFIKLDGTGNLLVLRTLPGNAHAIGVLLDNLDWDEIVGTICGDDTCLIICRTPKDAKKVSNQLLSML 149
               SCOP domains d1b4ab1 B:4-78 Arginine repressor (ArgR), N-terminal DNA-binding domain    d1b4ab2 B:79-149 C-terminal domain of arginine repressor                SCOP domains
               CATH domains -----1b4aB01 B:9-67 'winged helix' repressor DNA binding domain -----------1b4aB02 B:79-148  [code=3.30.1360.40, no name defined]                - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.....hhhhhhhhhh......hhhhhhhhhh...eeee.....eeee........hhhhhhhhhhhheeeeeee..eeeeee....hhhhhhhhhhh....eeeeee...eeeeee..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b4a B   4 GQRHIKIREIIMSNDIETQDELVDRLREAGFNVTQATVSRDIKEMQLVKVPMANGRYKYSLPSDQRFNPLQKLKRALVDVFIKLDGTGNLLVLRTLPGNAHAIGVLLDNLDWDEIVGTICGDDTCLIICRTPKDAKKVSNQLLSML 149
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143      


Chain C from PDB  Type:PROTEIN  Length:146
 aligned with ARGR_GEOSE | O31408 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:146
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143      
           ARGR_GEOSE     4 GQRHIKIREIIMSNDIETQDELVDRLREAGFNVTQATVSRDIKEMQLVKVPMANGRYKYSLPSDQRFNPLQKLKRALVDVFIKLDGTGNLLVLRTLPGNAHAIGVLLDNLDWDEIVGTICGDDTCLIICRTPKDAKKVSNQLLSML 149
               SCOP domains d1b4ac1 C:4-78 Arginine repressor (ArgR), N-terminal DNA-binding domain    d1b4ac2 C:79-149 C-terminal domain of arginine repressor                SCOP domains
               CATH domains ------1b4aC01 C:10-67                                           -----------1b4aC02 C:79-148  [code=3.30.1360.40, no name defined]                - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.....hhhhhhhhh.......hhhhhhhhhhh.eeeee.....eeeee.......hhhhhhhhhhhheeeeeee..eeeeee....hhhhhhhhhhh....eeeeee...eeeeee..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b4a C   4 GQRHIKIREIIMSNDIETQDELVDRLREAGFNVTQATVSRDIKEMQLVKVPMANGRYKYSLPSDQRFNPLQKLKRALVDVFIKLDGTGNLLVLRTLPGNAHAIGVLLDNLDWDEIVGTICGDDTCLIICRTPKDAKKVSNQLLSML 149
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143      


Chain D from PDB  Type:PROTEIN  Length:146
 aligned with ARGR_GEOSE | O31408 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:146
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143      
           ARGR_GEOSE     4 GQRHIKIREIIMSNDIETQDELVDRLREAGFNVTQATVSRDIKEMQLVKVPMANGRYKYSLPSDQRFNPLQKLKRALVDVFIKLDGTGNLLVLRTLPGNAHAIGVLLDNLDWDEIVGTICGDDTCLIICRTPKDAKKVSNQLLSML 149
               SCOP domains d1b4ad1 D:4-78 Arginine repressor (ArgR), N-terminal DNA-binding domain    d1b4ad2 D:79-149 C-terminal domain of arginine repressor                SCOP domains
               CATH domains -----1b4aD01 D:9-67 'winged helix' repressor DNA binding domain -----------1b4aD02 D:79-148  [code=3.30.1360.40, no name defined]                - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.....hhhhhhhhhh......hhhhhhhhhh...eeee.....eeee........hhhhhhhhhhhheeeeeee..eeeeee....hhhhhhhhhhh....eeeeee...eeeeee..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b4a D   4 GQRHIKIREIIMSNDIETQDELVDRLREAGFNVTQATVSRDIKEMQLVKVPMANGRYKYSLPSDQRFNPLQKLKRALVDVFIKLDGTGNLLVLRTLPGNAHAIGVLLDNLDWDEIVGTICGDDTCLIICRTPKDAKKVSNQLLSML 149
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143      


Chain E from PDB  Type:PROTEIN  Length:146
 aligned with ARGR_GEOSE | O31408 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:146
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143      
           ARGR_GEOSE     4 GQRHIKIREIIMSNDIETQDELVDRLREAGFNVTQATVSRDIKEMQLVKVPMANGRYKYSLPSDQRFNPLQKLKRALVDVFIKLDGTGNLLVLRTLPGNAHAIGVLLDNLDWDEIVGTICGDDTCLIICRTPKDAKKVSNQLLSML 149
               SCOP domains d1b4ae1 E:4-78 Arginine repressor (ArgR), N-terminal DNA-binding domain    d1b4ae2 E:79-149 C-terminal domain of arginine repressor                SCOP domains
               CATH domains -----1b4aE01 E:9-67 'winged helix' repressor DNA binding domain -----------1b4aE02 E:79-148  [code=3.30.1360.40, no name defined]                - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.....hhhhhhhhhh......hhhhhhhhhh...eeee.....eeee........hhhhhhhhhhhheeeeeee..eeeeee....hhhhhhhhhhh....eeeeee...eeeeee..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b4a E   4 GQRHIKIREIIMSNDIETQDELVDRLREAGFNVTQATVSRDIKEMQLVKVPMANGRYKYSLPSDQRFNPLQKLKRALVDVFIKLDGTGNLLVLRTLPGNAHAIGVLLDNLDWDEIVGTICGDDTCLIICRTPKDAKKVSNQLLSML 149
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143      


Chain F from PDB  Type:PROTEIN  Length:146
 aligned with ARGR_GEOSE | O31408 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:146
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143      
           ARGR_GEOSE     4 GQRHIKIREIIMSNDIETQDELVDRLREAGFNVTQATVSRDIKEMQLVKVPMANGRYKYSLPSDQRFNPLQKLKRALVDVFIKLDGTGNLLVLRTLPGNAHAIGVLLDNLDWDEIVGTICGDDTCLIICRTPKDAKKVSNQLLSML 149
               SCOP domains d1b4af1 F:4-78 Arginine repressor (ArgR), N-terminal DNA-binding domain    d1b4af2 F:79-149 C-terminal domain of arginine repressor                SCOP domains
               CATH domains -----1b4aF01 F:9-67 'winged helix' repressor DNA binding domain -----------1b4aF02 F:79-148  [code=3.30.1360.40, no name defined]                - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.....hhhhhhhhhh......hhhhhhhhhh...eeee.....eeee........hhhhhhhhhhhheeeeeee..eeeeee....hhhhhhhhhhh....eeeeee...eeeeee..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b4a F   4 GQRHIKIREIIMSNDIETQDELVDRLREAGFNVTQATVSRDIKEMQLVKVPMANGRYKYSLPSDQRFNPLQKLKRALVDVFIKLDGTGNLLVLRTLPGNAHAIGVLLDNLDWDEIVGTICGDDTCLIICRTPKDAKKVSNQLLSML 149
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143
   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  (2, 12)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 12)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1B4A)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (ARGR_GEOSE | O31408)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0034618    arginine binding    Interacting selectively and non-covalently with 2-amino-5-(carbamimidamido)pentanoic acid.
    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:0006526    arginine biosynthetic process    The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
    GO:0006525    arginine metabolic process    The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0051259    protein oligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    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

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

UniProtKB/Swiss-Prot
        ARGR_GEOSE | O31408: 1b4b

(-) Related Entries Specified in the PDB File

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