Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  STRUCTURAL AND FUNCTIONAL CHARACTERISATION OF PARTNER SWITCHING REGULATING THE ENVIRONMENTAL STRESS RESPONSE IN BACILLUS SUBTILIS
 
Authors :  S. W. Hardwick, J. Pane-Farre, O. Delumeau, J. Marles-Wright, J. W. Mur M. Hecker, R. J. Lewis
Date :  05 Oct 06  (Deposition) - 13 Feb 07  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E  (2x)
Keywords :  Hydrolase, Partner Switching, Protein Phosphatase, Rsbt, Rsbu, Stress, Bacillus Subtilis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. W. Hardwick, J. Pane-Farre, O. Delumeau, J. Marles-Wright, J. W. Murray, M. Hecker, R. J. Lewis
Structural And Functional Characterization Of Partner Switching Regulating The Environmental Stress Response In Bacillus Subtilis.
J. Biol. Chem. V. 282 11562 2007
PubMed-ID: 17303566  |  Reference-DOI: 10.1074/JBC.M609733200

(-) Compounds

Molecule 1 - PHOSPHOSERINE PHOSPHATASE RSBU
    Chains: A, B, C, D, E
    EC Number: 3.1.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: DE3
    Fragment: RSBT BINDING DOMAIN, RESIDUES 1-111
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: SIGMA FACTOR SIGB REGULATION PROTEIN RSBU, N-RSBU

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): AB   
Biological Unit 2 (1x):   CD 
Biological Unit 3 (2x):     E

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2J6Y)

(-) Sites  (0, 0)

(no "Site" information available for 2J6Y)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J6Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2J6Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J6Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2J6Y)

(-) Exons   (0, 0)

(no "Exon" information available for 2J6Y)

(-) Sequences/Alignments

Asymmetric 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:85
 aligned with RSBU_BACSU | P40399 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:85
                                    10        20        30        40        50        60        70        80     
            RSBU_BACSU    1 MDFREVIEQRYHQLLSRYIAELTETSLYQAQKFSRKTIEHQIPPEEIISIHRKVLKELYPSLPEDVFHSLDFLIEVMIGYGMAYQ 85
               SCOP domains d2j6ya_ A: automated matches                                                          SCOP domains
               CATH domains 2j6yA00 A:1-85 KaiA/RbsU domain                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                  2j6y A  1 MDFREVIEQRYHQLLSRYIAELTKTSLYQAQKFSRKTIEHQIPPEEIISIHRKVLKELYPSLPEDVFHSLDFLIEVMIGYGMAYQ 85
                                    10        20        30        40        50        60        70        80     


Chain B from PDB  Type:PROTEIN  Length:81
 aligned with RSBU_BACSU | P40399 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:81
                                    14        24        34        44        54        64        74        84 
            RSBU_BACSU    5 EVIEQRYHQLLSRYIAELTETSLYQAQKFSRKTIEHQIPPEEIISIHRKVLKELYPSLPEDVFHSLDFLIEVMIGYGMAYQ 85
               SCOP domains d2j6yb_ B: automated matches                                                      SCOP domains
               CATH domains 2j6yB00 B:5-85 KaiA/RbsU domain                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                  2j6y B  5 EVIEQRYHQLLSRYIAELTKTSLYQAQKFSRKTIEHQIPPEEIISIHRKVLKELYPSLPEDVFHSLDFLIEVMIGYGMAYQ 85
                                    14        24        34        44        54        64        74        84 


Chain C from PDB  Type:PROTEIN  Length:85
 aligned with RSBU_BACSU | P40399 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:85
                                    12        22        32        42        52        62        72        82     
            RSBU_BACSU    3 FREVIEQRYHQLLSRYIAELTETSLYQAQKFSRKTIEHQIPPEEIISIHRKVLKELYPSLPEDVFHSLDFLIEVMIGYGMAYQEH 87
               SCOP domains d2j6yc_ C: automated matches                                                          SCOP domains
               CATH domains 2j6yC00 C:3-87 KaiA/RbsU domain                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                  2j6y C  3 FREVIEQRYHQLLSRYIAELTKTSLYQAQKFSRKTIEHQIPPEEIISIHRKVLKELYPSLPEDVFHSLDFLIEVMIGYGMAYQEH 87
                                    12        22        32        42        52        62        72        82     


Chain D from PDB  Type:PROTEIN  Length:84
 aligned with RSBU_BACSU | P40399 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:84
                                    11        21        31        41        51        61        71        81    
            RSBU_BACSU    2 DFREVIEQRYHQLLSRYIAELTETSLYQAQKFSRKTIEHQIPPEEIISIHRKVLKELYPSLPEDVFHSLDFLIEVMIGYGMAYQ 85
               SCOP domains d2j6yd_ D: automated matches                                                         SCOP domains
               CATH domains 2j6yD00 D:2-85 KaiA/RbsU domain                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  2j6y D  2 DFREVIEQRYHQLLSRYIAELTKTSLYQAQKFSRKTIEHQIPPEEIISIHRKVLKELYPSLPEDVFHSLDFLIEVMIGYGMAYQ 85
                                    11        21        31        41        51        61        71        81    


Chain E from PDB  Type:PROTEIN  Length:81
 aligned with RSBU_BACSU | P40399 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:81
                                    11        21        31        41        51        61        71        81 
            RSBU_BACSU    2 DFREVIEQRYHQLLSRYIAELTETSLYQAQKFSRKTIEHQIPPEEIISIHRKVLKELYPSLPEDVFHSLDFLIEVMIGYGM 82
               SCOP domains d2j6ye_ E: automated matches                                                      SCOP domains
               CATH domains 2j6yE00 E:2-82 KaiA/RbsU domain                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                  2j6y E  2 DFREVIEQRYHQLLSRYIAELTKTSLYQAQKFSRKTIEHQIPPEEIISIHRKVLKELYPSLPEDVFHSLDFLIEVMIGYGM 82
                                    11        21        31        41        51        61        71        81
   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, 5)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 5)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J6Y)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E   (RSBU_BACSU | P40399)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    GO:0004647    phosphoserine phosphatase activity    Catalysis of the reaction: L(or D)-O-phosphoserine + H2O = L(or D)-serine + phosphate.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.

 Visualization

(-) Interactive Views

Asymmetric 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 2j6y)
 
  Sites
(no "Sites" information available for 2j6y)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2j6y)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 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
  2j6y
    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
  RSBU_BACSU | P40399
    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)
  3.1.3.3
    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
  RSBU_BACSU | P40399
    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
        RSBU_BACSU | P40399: 1w53 2j6z 2j70

(-) Related Entries Specified in the PDB File

1w53 KINASE RECRUITMENT DOMAIN OF THE STRESS PHOSPHATASE RSBU
2j6z STRUCTURAL AND FUNCTIONAL CHARACTERISATION OF PARTNER-SWITCHING REGULATING THE ENVIRONMENTAL STRESS RESPONSE IN B. SUBTILIS
2j70 STRUCTURAL AND FUNCTIONAL CHARACTERISATION OF PARTNER-SWITCHING REGULATING THE ENVIRONMENTAL STRESS RESPONSE IN B. SUBTILIS