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8  structures 949  species 1  interaction 1247  sequences 17  architectures

Family: Zeta_toxin (PF06414)

Summary: Zeta toxin

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This is the Wikipedia entry entitled "Zeta toxin protein domain". More...

Zeta toxin protein domain Edit Wikipedia article

Zeta_toxin
PDB 1ly1 EBI.jpg
structure and mechanism of t4 polynucleotide kinase
Identifiers
Symbol Zeta_toxin
Pfam PF06414
Pfam clan CL0023
InterPro IPR010488
SCOP 1gvn
SUPERFAMILY 1gvn

In molecular biology, the protein domain Zeta (ζ) toxin refers to a protein domain found in prokaryotes. Its function is to inhibit cell wall biosynthesis and it may act as a bactericide in nature. It is also thought that Zeta toxin induces reversible protective dormancy and permeation to propidium iodide (PI).[1]

Mechanism[edit]

This protein family entry consists of several bacterial zeta toxin proteins. Zeta toxin is thought to be part of a postsegregational killing (PSK) system involved in the killing of plasmid-free cells. It relies on antitoxin/toxin systems that secure stable inheritance of low and medium copy number plasmids during cell division and kill cells that have lost the plasmid.[2]

Structure[edit]

The Zeta Toxin is folded like a phosphotransferase. This domain features an α/β structure and the central twisted β-sheet contains six β-strands. The first 5 strands are parallel but β-strand 6 is antiparallel and connected by a short loop to β-strand 5. α-Helices are inserted between and flank the β-strands.[2]

References[edit]

  1. ^ Lioy VS, Machon C, Tabone M, Gonzalez-Pastor JE, Daugelavicius R, Ayora S et al. (2012). "The ζ toxin induces a set of protective responses and dormancy.". PLoS ONE 7 (1): e30282. doi:10.1371/journal.pone.0030282. PMC 3266247. PMID 22295078. 
  2. ^ a b Meinhart A, Alonso JC, Sträter N, Saenger W (February 2003). "Crystal structure of the plasmid maintenance system epsilon/zeta: functional mechanism of toxin zeta and inactivation by epsilon 2 zeta 2 complex formation". Proc. Natl. Acad. Sci. U.S.A. 100 (4): 1661–6. doi:10.1073/pnas.0434325100. PMC 149889. PMID 12571357. 

This article incorporates text from the public domain Pfam and InterPro IPR010488

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Zeta toxin Provide feedback

This family consists of several bacterial zeta toxin proteins. Zeta toxin is thought to be part of a postregulational killing system in bacteria. It relies on antitoxin/toxin systems that secure stable inheritance of low and medium copy number plasmids during cell division and kill cells that have lost the plasmid [1].

Literature references

  1. Meinhart A, Alonso JC, Strater N, Saenger W; , Proc Natl Acad Sci U S A 2003;100:1661-1666.: Crystal structure of the plasmid maintenance system epsilon/zeta: functional mechanism of toxin zeta and inactivation by epsilon 2 zeta 2 complex formation. PUBMED:12571357 EPMC:12571357


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR010488

This entry represents a domain originally identified in bacterial zeta toxin proteins, where it comprises the whole protein [PUBMED:12571357]. It has subsequently been found in a number of other proteins, such as polynucleotide kinase and 2',3'-cyclic-nucleotide 3'-phosphodiesterase. It appears to function as a kinase domain [PUBMED:12220496, PUBMED:21445328].

Gene Ontology

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Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan P-loop_NTPase (CL0023), which contains the following 198 members:

6PF2K AAA AAA-ATPase_like AAA_10 AAA_11 AAA_12 AAA_13 AAA_14 AAA_15 AAA_16 AAA_17 AAA_18 AAA_19 AAA_2 AAA_21 AAA_22 AAA_23 AAA_24 AAA_25 AAA_26 AAA_27 AAA_28 AAA_29 AAA_3 AAA_30 AAA_31 AAA_32 AAA_33 AAA_34 AAA_35 AAA_4 AAA_5 AAA_6 AAA_7 AAA_8 AAA_9 AAA_PrkA ABC_ATPase ABC_tran ABC_tran_2 Adeno_IVa2 Adenylsucc_synt ADK AFG1_ATPase AIG1 APS_kinase Arch_ATPase Arf ArgK ArsA_ATPase ATP-synt_ab ATP_bind_1 ATP_bind_2 Bac_DnaA CbiA CMS1 CoaE CobA_CobO_BtuR CobU cobW CPT CTP_synth_N Cytidylate_kin Cytidylate_kin2 DAP3 DEAD DEAD_2 DLIC DNA_pack_C DNA_pack_N DNA_pol3_delta DNA_pol3_delta2 DnaB_C dNK DUF1253 DUF1611 DUF2075 DUF2478 DUF258 DUF2791 DUF2813 DUF3584 DUF463 DUF815 DUF853 DUF87 DUF927 Dynamin_N Exonuc_V_gamma FeoB_N Fer4_NifH Flavi_DEAD FTHFS FtsK_SpoIIIE G-alpha Gal-3-0_sulfotr GBP GTP_EFTU GTP_EFTU_D2 GTP_EFTU_D4 Gtr1_RagA Guanylate_kin GvpD HDA2-3 Helicase_C Helicase_C_2 Helicase_C_4 Helicase_RecD Herpes_Helicase Herpes_ori_bp Herpes_TK IIGP IPPT IPT IstB_IS21 KaiC KAP_NTPase Kinesin Kinesin-relat_1 Kinesin-related KTI12 LpxK MCM MEDS Mg_chelatase Mg_chelatase_2 MipZ Miro MMR_HSR1 MobB MukB MutS_V Myosin_head NACHT NB-ARC NOG1 NTPase_1 ParA Parvo_NS1 PAXNEB PduV-EutP PhoH PIF1 Podovirus_Gp16 Polyoma_lg_T_C Pox_A32 PPK2 PPV_E1_C PRK Rad17 Rad51 Ras RecA ResIII RHD3 RHSP RNA12 RNA_helicase RuvB_N SbcCD_C SecA_DEAD Septin Sigma54_activ_2 Sigma54_activat SKI SMC_N SNF2_N Spore_IV_A SRP54 SRPRB Sulfotransfer_1 Sulfotransfer_2 Sulfotransfer_3 Sulphotransf T2SE T4SS-DNA_transf Terminase_1 Terminase_3 Terminase_6 Terminase_GpA Thymidylate_kin TIP49 TK TniB Torsin TraG-D_C tRNA_lig_kinase TrwB_AAD_bind UPF0079 UvrD-helicase UvrD_C UvrD_C_2 Viral_helicase1 VirC1 VirE YhjQ Zeta_toxin Zot

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(40)
Full
(1247)
Representative proteomes NCBI
(6029)
Meta
(2517)
RP15
(67)
RP35
(159)
RP55
(208)
RP75
(252)
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  Seed
(40)
Full
(1247)
Representative proteomes NCBI
(6029)
Meta
(2517)
RP15
(67)
RP35
(159)
RP55
(208)
RP75
(252)
Alignment:
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Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(40)
Full
(1247)
Representative proteomes NCBI
(6029)
Meta
(2517)
RP15
(67)
RP35
(159)
RP55
(208)
RP75
(252)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

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Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_12374 (release 9.0)
Previous IDs: none
Type: Family
Author: Moxon SJ
Number in seed: 40
Number in full: 1247
Average length of the domain: 168.70 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 56.57 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.3 22.3
Trusted cut-off 22.3 22.3
Noise cut-off 22.2 22.2
Model length: 201
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Epsilon_antitox

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Zeta_toxin domain has been found. There are 8 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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