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(-) Description

Title :  SHEWANELLA ONEIDENSIS MR-1 TOXIN ANTITOXIN SYSTEM HIPA, HIPB AND ITS OPERATOR DNA COMPLEX (SPACE GROUP P212121)
 
Authors :  Y. Wen, E. Behiels, J. Felix, J. Elegheert, B. Vergauwen, B. Devreese, S
Date :  12 Mar 14  (Deposition) - 06 Aug 14  (Release) - 17 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.39
Chains :  Asym./Biol. Unit :  A,B,C,D,P,Q
Keywords :  Toxin Antitoxin System, Toxin-Antitoxin-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Wen, E. Behiels, J. Felix, J. Elegheert, B. Vergauwen, B. Devreese, S. N. Savvides
The Bacterial Antitoxin Hipb Establishes A Ternary Complex With Operator Dna And Phosphorylated Toxin Hipa To Regulate Bacterial Persistence.
Nucleic Acids Res. V. 42 10134 2014
PubMed-ID: 25056321  |  Reference-DOI: 10.1093/NAR/GKU665

(-) Compounds

Molecule 1 - TOXIN-ANTITOXIN SYSTEM TOXIN HIPA FAMILY
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: SO_0706
    Organism Scientific: SHEWANELLA ONEIDENSIS
    Organism Taxid: 211586
    Strain: MR-1
 
Molecule 2 - TOXIN-ANTITOXIN SYSTEM ANTIDOTE TRANSCRIPTIONAL REPRESSOR XRE FAMILY
    Chains: D, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SO_0705
    Organism Scientific: SHEWANELLA ONEIDENSIS
    Organism Taxid: 211586
    Strain: MR-1
    Synonym: HIPB
 
Molecule 3 - OPERATOR DNA
    Chains: Q
    Engineered: YES
    Organism Scientific: SHEWANELLA ONEIDENSIS
    Organism Taxid: 70863
    Other Details: STRAND 1
    Synthetic: YES
 
Molecule 4 - OPERATOR DNA
    Chains: P
    Engineered: YES
    Organism Scientific: SHEWANELLA ONEIDENSIS
    Organism Taxid: 70863
    Other Details: STRAND 2
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDPQ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SEP2Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (0, 0)

(no "Site" information available for 4PU3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PU3)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1Pro A:132 -Thr A:133
2Pro A:136 -Met A:137
3Glu A:138 -Ile A:139
4Trp A:140 -Asp A:141
5Asp A:141 -Gly A:142
6Trp B:135 -Pro B:136
7Asp B:141 -Gly B:142
8Leu B:146 -Sep B:147
9Ala B:149 -Gly B:150
10Gly D:95 -Trp D:96

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PU3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PU3)

(-) Exons   (0, 0)

(no "Exon" information available for 4PU3)

(-) 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:426
                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..eeeeeeeee....eeeeeehhhhhhhh.............hhhhhhhhhhhh....hhhhhhhhhhh....hhhhhhhhhh......eeee...........ee.hhhhhhhhhh.......................eeeeee....eee........eeeee....hhhhhhhhhhhhhhhh......eeeeee..eeeeeee...eee......eee..eeehhhhhh.hhhhhh.................hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhh.eeeee..eeee...........................hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4pu3 A   8 TLEMHLGDLMIGELSFDATADTFAVHYTKDWQQSGFPLSPTIPLDGTGTSNQISMFLVNLLPENKGLDYLIESLGVSKGNTFALIRAIGLDTAGAIAFVPKGALLPETQLRPIKAEEVIQRIEDPTMWPMEIWDGKPRLsVAGVQPKLNLFYNGKEFAFAEGTLSSTHIVKFEKYHHLVINEFITMRLAKVLGMNVANVDIVHFGRYKALCVERFDRRNIPGEQRVLRRHIVDSCQALGFSVSKKYERNFGTGRDVKDIREGVSFNRLFSLAAKCRNPVAAKQDMLQWALFNLLTGNADAHGKNYSFFMTPSGMEPTPWYDLVSVDMYEDFEQQLAMAIDDEFDPNSIYAYQLAAFMDGLGLPRNLLISNLTRIARRIPQAIAEVILMLPPLDEDEASFVAHYKTQLLARCERYLGFVDEVRDVEV 433
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427      
                                                                                                                                                                     147-SEP                                                                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:426
                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..eeeeeeeee....eeeeeehhhhhhhh.............hhhhhhhhhhhh....hhhhhhhhhh......hhhhhhhhh......eeee...........eeehhhhhhhhhh.......................eeeeee....eee........eeeee....hhhhhhhhhhhhhhhh......eeeeee..eeeeeee...eee......eee..eeehhhhhh.hhhhhh.................hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhh.eeeee..eeee...........................hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4pu3 B   8 TLEMHLGDLMIGELSFDATADTFAVHYTKDWQQSGFPLSPTIPLDGTGTSNQISMFLVNLLPENKGLDYLIESLGVSKGNTFALIRAIGLDTAGAIAFVPKGALLPETQLRPIKAEEVIQRIEDPTMWPMEIWDGKPRLsVAGVQPKLNLFYNGKEFAFAEGTLSSTHIVKFEKYHHLVINEFITMRLAKVLGMNVANVDIVHFGRYKALCVERFDRRNIPGEQRVLRRHIVDSCQALGFSVSKKYERNFGTGRDVKDIREGVSFNRLFSLAAKCRNPVAAKQDMLQWALFNLLTGNADAHGKNYSFFMTPSGMEPTPWYDLVSVDMYEDFEQQLAMAIDDEFDPNSIYAYQLAAFMDGLGLPRNLLISNLTRIARRIPQAIAEVILMLPPLDEDEASFVAHYKTQLLARCERYLGFVDEVRDVEV 433
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427      
                                                                                                                                                                     147-SEP                                                                                                                                                                                                                                                                                          


Chain C from PDB  Type:PROTEIN  Length:71
                                                                                                       
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhh....hhhhhhhhhhhh...eee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 4pu3 C  19 IMASPLNQQSLGLLIKERRKSAALTQDVAAMLCGVTKKTLIRVEKGEDVYISTVFKILDGLGIDIVSAGWY  97
                                    28        38        48        58        68        78       |96 
                                                                                              86|  
                                                                                               95  


Chain D from PDB  Type:PROTEIN  Length:71
                                                                                                       
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhh....hhhhhhhhhhhh...eee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 4pu3 D  19 IMASPLNQQSLGLLIKERRKSAALTQDVAAMLCGVTKKTLIRVEKGEDVYISTVFKILDGLGIDIVSAGWY  97
                                    28        38        48        58        68        78       |96 
                                                                                              86|  
                                                                                               95  


Chain P from PDB  Type:DNA  Length:24
                                                        
                 4pu3 P   1 ATTAGGTGTACTTATCTACACTTT  24
                                    10        20    


Chain Q from PDB  Type:DNA  Length:25
                                                         
                 4pu3 Q   1 AAAAGTGTAGATAAGTACACCTAAT  25
                                    10        20
   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 4PU3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PU3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PU3)

(-) Gene Ontology  (14, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala B:149 - Gly B:150   [ RasMol ]  
    Asp A:141 - Gly A:142   [ RasMol ]  
    Asp B:141 - Gly B:142   [ RasMol ]  
    Glu A:138 - Ile A:139   [ RasMol ]  
    Gly D:95 - Trp D:96   [ RasMol ]  
    Leu B:146 - Sep B:147   [ RasMol ]  
    Pro A:132 - Thr A:133   [ RasMol ]  
    Pro A:136 - Met A:137   [ RasMol ]  
    Trp A:140 - Asp A:141   [ RasMol ]  
    Trp B:135 - Pro B:136   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        HIPA_SHEON | Q8EIX3: 4pu4 4pu5
        HIPB_SHEON | Q8EIX4: 4pu4 4pu7 4pu8

(-) Related Entries Specified in the PDB File

4pu4 4pu5