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(-) Description

Title :  STRUCTURE OF A TOXIN-ANTITOXIN SYSTEM BOUND TO ITS SUBSTRATE
 
Authors :  H. Mutschler, M. Gebhardt, R. L. Shoeman, A. Meinhart
Date :  07 Jan 11  (Deposition) - 09 Mar 11  (Release) - 02 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Polynucleotide Kinase Fold, Epsilon: Antidote Zeta: Bacterial Toxin, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Mutschler, M. Gebhardt, R. L. Shoeman, A. Meinhart
A Novel Mechanism Of Programmed Cell Death In Bacteria By Toxin-Antitoxin Systems Corrupts Peptidoglycan Synthesis.
Plos Biol. V. 9 01033 2011
PubMed-ID: 21445328  |  Reference-DOI: 10.1371/JOURNAL.PBIO.1001033

(-) Compounds

Molecule 1 - ANTIDOTE OF EPSILON-ZETA POSTSEGREGATIONAL KILLING SYSTEM
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: EPSILON
    Organism Scientific: STREPTOCOCCUS PYOGENES
    Organism Taxid: 1314
 
Molecule 2 - ZETA-TOXIN
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: STREPTOCOCCUS PYOGENES
    Organism Taxid: 1314

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2UD11Ligand/IonURIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:12 , GLN B:41 , PRO B:42 , GLY B:43 , SER B:44 , GLY B:45 , LYS B:46BINDING SITE FOR RESIDUE SO4 B 602
2AC2SOFTWAREGLU C:12 , GLY D:43 , SER D:44 , GLY D:45 , LYS D:46BINDING SITE FOR RESIDUE SO4 D 603
3AC3SOFTWAREASP D:65 , ASN D:66 , ASP D:67 , GLU D:100 , ILE D:103 , ILE D:115 , GLU D:116 , GLY D:117 , THR D:118 , ARG D:120 , VAL D:124 , THR D:128BINDING SITE FOR RESIDUE UD1 D 288

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q8X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3Q8X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q8X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3Q8X)

(-) Exons   (0, 0)

(no "Exon" information available for 3Q8X)

(-) 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:85
 aligned with EATX_STRPY | Q57231 from UniProtKB/Swiss-Prot  Length:90

    Alignment length:85
                                    12        22        32        42        52        62        72        82     
           EATX_STRPY     3 VTYEKTFEIEIINELSASVYNRVLNYVLNHELNKNDSQLLEVNLLNQLKLAKRVNLFDYSLEELQAVHEYWRSMNRYSKQVLNKE  87
               SCOP domains d3q8xa_ A: automated matches                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 3q8x A   3 VTYEKTFEIEIINELSASVYNRVLNYVLNHELNKNDSQLLEVNLLNQLKLAKRVNLFDYSLEELQAVHEYWRSMNRYSKQVLNKE  87
                                    12        22        32        42        52        62        72        82     


Chain B from PDB  Type:PROTEIN  Length:272
 aligned with ZTOX_STRPY | Q54944 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:272
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272  
           ZTOX_STRPY     3 NIVNFTDKQFENRLNDNLEELIQGKKAVESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDNDTFKQQHPNFDELVKLYEKDVVKHVTPYSNRMTEAIISRLSDQGYNLVIEGTGRTTDVPIQTATMLQAKGYETKMYVMAVPKINSYLGTIERYETMYADDPMTARATPKQAHDIVVKNLPTNLETLHKTGLFSDIRLYNREGVKLYSSLETPSISPKETLEKELNRKVSGKEIQPTLERIEQKMVLNKHQETPEFKAIQQKLESLQPP 274
               SCOP domains d3q8xb_ B: automated matches                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhh........eeeeee......hhhhhhhhhhhh....eeehhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh....eeee.....eeee........hhhhhhhhhh...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q8x B   3 NIVNFTDKQFENRLNDNLEELIQGKKAVESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDNDTFKQQHPNFDELVKLYEKDVVKHVTPYSNRMTEAIISRLSDQGYNLVIEGTGRTTDVPIQTATMLQAKGYETKMYVMAVPKINSYLGTIERYETMYADDPMTARATPKQAHDIVVKNLPTNLETLHKTGLFSDIRLYNREGVKLYSSLETPSISPKETLEKELNRKVSGKEIQPTLERIEQKMVLNKHQETPEFKAIQQKLESLQPP 274
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272  


Chain C from PDB  Type:PROTEIN  Length:85
 aligned with EATX_STRPY | Q57231 from UniProtKB/Swiss-Prot  Length:90

    Alignment length:85
                                    11        21        31        41        51        61        71        81     
           EATX_STRPY     2 AVTYEKTFEIEIINELSASVYNRVLNYVLNHELNKNDSQLLEVNLLNQLKLAKRVNLFDYSLEELQAVHEYWRSMNRYSKQVLNK  86
               SCOP domains d3q8xc_ C: automated matches                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 3q8x C   2 AVTYEKTFEIEIINELSASVYNRVLNYVLNHELNKNDSQLLEVNLLNQLKLAKRVNLFDYSLEELQAVHEYWRSMNRYSKQVLNK  86
                                    11        21        31        41        51        61        71        81     


Chain D from PDB  Type:PROTEIN  Length:271
 aligned with ZTOX_STRPY | Q54944 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:271
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271 
           ZTOX_STRPY     2 ANIVNFTDKQFENRLNDNLEELIQGKKAVESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDNDTFKQQHPNFDELVKLYEKDVVKHVTPYSNRMTEAIISRLSDQGYNLVIEGTGRTTDVPIQTATMLQAKGYETKMYVMAVPKINSYLGTIERYETMYADDPMTARATPKQAHDIVVKNLPTNLETLHKTGLFSDIRLYNREGVKLYSSLETPSISPKETLEKELNRKVSGKEIQPTLERIEQKMVLNKHQETPEFKAIQQKLESLQ 272
               SCOP domains d3q8xd_ D: automated matches                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------Zeta_toxin-3q8xD01 D:19-217                                                                                                                                                                            ------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------Zeta_toxin-3q8xD02 D:19-217                                                                                                                                                                            ------------------------------------------------------- Pfam domains (2)
         Sec.struct. author hhhhh.hhhhhhhhhhhhhhhhhh........eeeeee......hhhhhhhhhhhh....eeehhhhhhhhh.....hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh....eeee.....eeee.......hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q8x D   2 ANIVNFTDKQFENRLNDNLEELIQGKKAVESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDNDTFKQQHPNFDELVKLYEKDVVKHVTPYSNRMTEAIISRLSDQGYNLVIEGTGRTTDVPIQTATMLQAKGYETKMYVMAVPKINSYLGTIERYETMYADDPMTARATPKQAHDIVVKNLPTNLETLHKTGLFSDIRLYNREGVKLYSSLETPSISPKETLEKELNRKVSGKEIQPTLERIEQKMVLNKHQETPEFKAIQQKLESLQ 272
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271
   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, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q8X)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (9, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (EATX_STRPY | Q57231)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0015643    toxic substance binding    Interacting selectively and non-covalently with a toxic substance, a poisonous substance that causes damage to biological systems.
biological process
    GO:0031342    negative regulation of cell killing    Any process that stops, prevents, or reduces the frequency, rate or extent of cell killing.
    GO:0009636    response to toxic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.

Chain B,D   (ZTOX_STRPY | Q54944)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.

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  3q8x
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  ZTOX_STRPY | Q54944
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 Related Entries

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

UniProtKB/Swiss-Prot
        EATX_STRPY | Q57231: 1gvn
        ZTOX_STRPY | Q54944: 1gvn

(-) Related Entries Specified in the PDB File

1gvn 2p5t