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(-) Description

Title :  SHEWANELLA ONEIDENSIS MR-1 TOXIN ANTITOXIN SYSTEM HIPA, HIPB AND ITS OPERATOR DNA COMPLEX (SPACE GROUP P21)
 
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 :  3.79
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 Taxid: 562
    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 4PU4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PU4)

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Leu A:112 -Pro A:113
2Pro A:113 -Glu A:114
3Glu A:114 -Thr A:115
4Gly A:150 -Val A:151
5Leu B:112 -Pro B:113
6Pro B:113 -Glu B:114
7Glu B:114 -Thr B:115
8Gly B:150 -Val B:151
9Gln D:88 -Thr D:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PU4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PU4)

(-) Exons   (0, 0)

(no "Exon" information available for 4PU4)

(-) 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:420
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee..eeeeeeeee....eeeeeehhhhhhhh.............hhhhhhhhhhh....hhhhhhhhhhhh....hhhhhhhhhh......eeeee.........eee.hhhhhhhhhhh...............eeeeee....eeee.......eeeee....hhhhhhhhhhhhhhhh......eeeeee..eeeeeee...eee......eee..eeehhhhhh.hhhhh..................hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhh.eeeee..eeee...........................hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4pu4 A   7 LTLEMHLGDLMIGELSFDATADTFAVHYTKDWQQSGFPLSPTIPLDGTGTSNQISMFLVNLLPENKGLDYLIESLGVSKGNTFALIRAIGLDTAGAIAFVPKGALLPETQLRPIKAEEVIQRIEDPTMWPPRLsVAGVQPKLNLFYNGKEFAFAEGTLSSTHIVKFEKYHHLVINEFITMRLAKVLGMNVANVDIVHFGRYKALCVERFDRRNIPGEQRVLRRHIVDSCQALGFSVSKKYERNFGTGRDVKDIREGVSFNRLFSLAAKCRNPVAAKQDMLQWALFNLLTGNADAHGKNYSFFMTPSGMEPTPWYDLVSVDMYEDFEQQLAMAIDDEFDPNSIYAYQLAAFMDGLGLPRNLLISNLTRIARRIPQAIAEVILMLPPLDEDEASFVAHYKTQLLARCERYLGFVDEVRDVEV 433
                                    16        26        36        46        56        66        76        86        96       106       116       126       136|  |   153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433
                                                                                                                                                           136|  |                                                                                                                                                                                                                                                                                              
                                                                                                                                                            144  |                                                                                                                                                                                                                                                                                              
                                                                                                                                                               147-SEP                                                                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:419
                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeeeeeeee....eeeeeehhhhhhhh.............hhhhhhhhhhh....hhhhhhhhhhhh.....hhhhhhhhh......eeeee.........eee.hhhhhhh..................eeeeee....eeee.......eeeee....hhhhhhhhhhhhhhhh......eeeeee..eeeeeee...eee......eee..eeehhhhhh.hhhhhh.................hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhh.eeee....eee...........................hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pu4 B   7 LTLEMHLGDLMIGELSFDATADTFAVHYTKDWQQSGFPLSPTIPLDGTGTSNQISMFLVNLLPENKGLDYLIESLGVSKGNTFALIRAIGLDTAGAIAFVPKGALLPETQLRPIKAEEVIQRIEDPTMWPRLsVAGVQPKLNLFYNGKEFAFAEGTLSSTHIVKFEKYHHLVINEFITMRLAKVLGMNVANVDIVHFGRYKALCVERFDRRNIPGEQRVLRRHIVDSCQALGFSVSKKYERNFGTGRDVKDIREGVSFNRLFSLAAKCRNPVAAKQDMLQWALFNLLTGNADAHGKNYSFFMTPSGMEPTPWYDLVSVDMYEDFEQQLAMAIDDEFDPNSIYAYQLAAFMDGLGLPRNLLISNLTRIARRIPQAIAEVILMLPPLDEDEASFVAHYKTQLLARCERYLGFVDEVRDVEV 433
                                    16        26        36        46        56        66        76        86        96       106       116       126       136| |    154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424         
                                                                                                                                                           136| |                                                                                                                                                                                                                                                                                              
                                                                                                                                                            145 |                                                                                                                                                                                                                                                                                              
                                                                                                                                                              147-SEP                                                                                                                                                                                                                                                                                          


Chain C from PDB  Type:PROTEIN  Length:68
                                                                                                    
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhh....hhhhhhhhhhhhh...ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 4pu4 C  20 IMASPLNQQSLGLLIKERRKSAALTQDVAAMLCGVTKKTLIRVEKGEDVYISTVFKILDGLGIDIVSA  87
                                    29        39        49        59        69        79        


Chain D from PDB  Type:PROTEIN  Length:78
                                                                                                              
               SCOP domains ------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhh....hhhhhhhhhhhhh..ee.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 4pu4 D  20 IMASPLNQQSLGLLIKERRKSAALTQDVAAMLCGVTKKTLIRVEKGEDVYISTVFKILDGLGIDIVSAQTSDTETNGW  97
                                    29        39        49        59        69        79        89        


Chain P from PDB  Type:DNA  Length:24
                                                        
                 4pu4 P   1 ATTAGGTGTACTTATCTACACTTT  24
                                    10        20    


Chain Q from PDB  Type:DNA  Length:25
                                                         
                 4pu4 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 4PU4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PU4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PU4)

(-) Gene Ontology  (14, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gln D:88 - Thr D:89   [ RasMol ]  
    Glu A:114 - Thr A:115   [ RasMol ]  
    Glu B:114 - Thr B:115   [ RasMol ]  
    Gly A:150 - Val A:151   [ RasMol ]  
    Gly B:150 - Val B:151   [ RasMol ]  
    Leu A:112 - Pro A:113   [ RasMol ]  
    Leu B:112 - Pro B:113   [ RasMol ]  
    Pro A:113 - Glu A:114   [ RasMol ]  
    Pro B:113 - Glu B:114   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        HIPA_SHEON | Q8EIX3: 4pu3 4pu5
        HIPB_SHEON | Q8EIX4: 4pu3 4pu7 4pu8

(-) Related Entries Specified in the PDB File

4pu3 4pu5