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

(-) Description

Title :  CRYSTAL STRUCTURE OF AHRC, THE ARGININE REPRESSOR/ACTIVATOR PROTEIN FROM BACILLUS SUBTILIS
 
Authors :  C. A. Dennis, N. M. Glykos, M. R. Parsons, S. E. V. Phillips
Date :  11 Jul 00  (Deposition) - 27 Feb 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Winged-Helix-Turn-Helix, Arginine Repressor, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. A. Dennis C, N. M. Glykos, M. R. Parsons, S. E. Phillips
The Structure Of Ahrc, The Arginine Repressor/Activator Protein From Bacillus Subtilis.
Acta Crystallogr. , Sect. D V. 58 421 2002
PubMed-ID: 11856827  |  Reference-DOI: 10.1107/S0907444901021692
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ARGININE REPRESSOR/ACTIVATOR PROTEIN
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: AHRC

 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 1F9N)

(-) Sites  (0, 0)

(no "Site" information available for 1F9N)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F9N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1F9N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F9N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1F9N)

(-) Exons   (0, 0)

(no "Exon" information available for 1F9N)

(-) 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:147
 aligned with ARGR_BACSU | P17893 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:147
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       
           ARGR_BACSU     3 KGQRHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIKELHLVKVPTNNGSYKYSLPADQRFNPLSKLKRALMDAFVKIDSASHMIVLKTMPGNAQAIGALMDNLDWDEMMGTICGDDTILIICRTPEDTEGVKNRLLELL 149
               SCOP domains d1f9na1 A:3-78 Arginine repressor (ArgR), N-terminal DNA-binding domain     d1f9na2 A:79-149 C-terminal domain of arginine repressor                SCOP domains
               CATH domains ------1f9nA01 A:9-67 'winged helix' repressor DNA binding domain -----------1f9nA02 A:79-148  [code=3.30.1360.40, no name defined]                - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhh.eeee.....eeee.......hhhhhhhhhhhhheeeeee...eeeeee...hhhhhhhhhhh.....eeeeee...eeeeee.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f9n A   3 KGQRHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIKELHLVKVPTNNGSYKYSLPADQRFNPLSKLKRALMDAFVKIDSASHMIVLKTMPGNAQAIGALMDNLDWDEMMGTICGDDTILIICRTPEDTEGVKNRLLELL 149
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       


Chain B from PDB  Type:PROTEIN  Length:149
 aligned with ARGR_BACSU | P17893 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         
           ARGR_BACSU     1 MNKGQRHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIKELHLVKVPTNNGSYKYSLPADQRFNPLSKLKRALMDAFVKIDSASHMIVLKTMPGNAQAIGALMDNLDWDEMMGTICGDDTILIICRTPEDTEGVKNRLLELL 149
               SCOP domains d1f9nb1 B:1-78 Arginine repressor (ArgR), N-terminal DNA-binding domain       d1f9nb2 B:79-149 C-terminal domain of arginine repressor                SCOP domains
               CATH domains -------1f9nB01 B:8-67 'winged helix' repressor DNA binding domain  -----------1f9nB02 B:79-148  [code=3.30.1360.40, no name defined]                - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhhhh.eeee.....eeee.......hhhhhhhhhhhhheeeeee...eeeeee...hhhhhhhhhh......eeeeee...eeeeee.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f9n B   1 MNKGQRHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIKELHLVKVPTNNGSYKYSLPADQRFNPLSKLKRALMDAFVKIDSASHMIVLKTMPGNAQAIGALMDNLDWDEMMGTICGDDTILIICRTPEDTEGVKNRLLELL 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         


Chain C from PDB  Type:PROTEIN  Length:148
 aligned with ARGR_BACSU | P17893 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141        
           ARGR_BACSU     2 NKGQRHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIKELHLVKVPTNNGSYKYSLPADQRFNPLSKLKRALMDAFVKIDSASHMIVLKTMPGNAQAIGALMDNLDWDEMMGTICGDDTILIICRTPEDTEGVKNRLLELL 149
               SCOP domains d1f9nc1 C:2-78 Arginine repressor (ArgR), N-terminal DNA-binding domain      d1f9nc2 C:79-149 C-terminal domain of arginine repressor                SCOP domains
               CATH domains ------1f9nC01 C:8-67 'winged helix' repressor DNA binding domain  -----------1f9nC02 C:79-148  [code=3.30.1360.40, no name defined]                - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhhhh..eee.....eee..........hhhhhhhhhhheeeeee...eeeeee...hhhhhhhhhh......eeeeeee..eeeeee.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f9n C   2 NKGQRHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIKELHLVKVPTNNGSYKYSLPADQRFNPLSKLKRALMDAFVKIDSASHMIVLKTMPGNAQAIGALMDNLDWDEMMGTICGDDTILIICRTPEDTEGVKNRLLELL 149
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141        


Chain D from PDB  Type:PROTEIN  Length:146
 aligned with ARGR_BACSU | P17893 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:146
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143      
           ARGR_BACSU     4 GQRHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIKELHLVKVPTNNGSYKYSLPADQRFNPLSKLKRALMDAFVKIDSASHMIVLKTMPGNAQAIGALMDNLDWDEMMGTICGDDTILIICRTPEDTEGVKNRLLELL 149
               SCOP domains d1f9nd1 D:4-78 Arginine repressor (ArgR), N-terminal DNA-binding domain    d1f9nd2 D:79-149 C-terminal domain of arginine repressor                SCOP domains
               CATH domains -----1f9nD01 D:9-67 'winged helix' repressor DNA binding domain -----------1f9nD02 D:79-148  [code=3.30.1360.40, no name defined]                - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.......hhhhhhhhhh....hhhhhhhhhhhh..eee.......eee.......hhhhhhhhhhhhheeeeee...eeeeee...hhhhhhhhhhhhh...eeeeee...eeeeee.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f9n D   4 GQRHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIKELHLVKVPTNNGSYKYSLPADQRFNPLSKLKRALMDAFVKIDSASHMIVLKTMPGNAQAIGALMDNLDWDEMMGTICGDDTILIICRTPEDTEGVKNRLLELL 149
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143      


Chain E from PDB  Type:PROTEIN  Length:148
 aligned with ARGR_BACSU | P17893 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141        
           ARGR_BACSU     2 NKGQRHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIKELHLVKVPTNNGSYKYSLPADQRFNPLSKLKRALMDAFVKIDSASHMIVLKTMPGNAQAIGALMDNLDWDEMMGTICGDDTILIICRTPEDTEGVKNRLLELL 149
               SCOP domains d1f9ne1 E:2-78 Arginine repressor (ArgR), N-terminal DNA-binding domain      d1f9ne2 E:79-149 C-terminal domain of arginine repressor                SCOP domains
               CATH domains ------1f9nE01 E:8-67 'winged helix' repressor DNA binding domain  -----------1f9nE02 E:79-148  [code=3.30.1360.40, no name defined]                - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh...hhhhhhhhhhh.....hhhhhhhhhhhh..eeee.....eeee.......hhhhhhhhhhhhheeeeee...eeeeee...hhhhhhhhhh......eeeeee...eeeeee.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f9n E   2 NKGQRHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIKELHLVKVPTNNGSYKYSLPADQRFNPLSKLKRALMDAFVKIDSASHMIVLKTMPGNAQAIGALMDNLDWDEMMGTICGDDTILIICRTPEDTEGVKNRLLELL 149
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141        


Chain F from PDB  Type:PROTEIN  Length:149
 aligned with ARGR_BACSU | P17893 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         
           ARGR_BACSU     1 MNKGQRHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIKELHLVKVPTNNGSYKYSLPADQRFNPLSKLKRALMDAFVKIDSASHMIVLKTMPGNAQAIGALMDNLDWDEMMGTICGDDTILIICRTPEDTEGVKNRLLELL 149
               SCOP domains d1f9nf1 F:1-78 Arginine repressor (ArgR), N-terminal DNA-binding domain       d1f9nf2 F:79-149 C-terminal domain of arginine repressor                SCOP domains
               CATH domains --------1f9nF01 F:9-67 'winged helix' repressor DNA binding domain -----------1f9nF02 F:79-148  [code=3.30.1360.40, no name defined]                - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhhhh.eeee.....eeee...hhhhhhhhhhhhhhhhheeeeee...eeeeee...hhhhhhhhhh......eeeeee...eeeeee.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f9n F   1 MNKGQRHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIKELHLVKVPTNNGSYKYSLPADQRFNPLSKLKRALMDAFVKIDSASHMIVLKTMPGNAQAIGALMDNLDWDEMMGTICGDDTILIICRTPEDTEGVKNRLLELL 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
   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 1F9N)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (ARGR_BACSU | P17893)
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:0019547    arginine catabolic process to ornithine    The chemical reactions and pathways resulting in the breakdown of arginine into other compounds, including ornithine.
    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
(no "Ligands, Modified Residues, Ions" information available for 1f9n)
 
  Sites
(no "Sites" information available for 1f9n)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1f9n)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit 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
  1f9n
    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
  ARGR_BACSU | P17893
    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
  ARGR_BACSU | P17893
    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
        ARGR_BACSU | P17893: 2p5k 2p5l 2p5m

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1F9N)