Summary: Zeta toxin
This is the Wikipedia entry entitled "Zeta toxin protein domain". More...
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Zeta toxin protein domain Edit Wikipedia article
structure and mechanism of t4 polynucleotide kinase
In molecular biology, the protein domain Zeta (ζ) toxin refers to a protein domain found in prokaryotes, which acts as a UDP-N-acetylglucosamine kinase. 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).
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.
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.
- Mutschler, H., Gebhardt, M., Shoeman, R.L. and Meinhart, A. (2011). "A novel mechanism of programmed cell death in bacteria by toxin-antitoxin systems corrupts peptidoglycan synthesis". PLoS Biol. 9: #e1001033–e1001033. doi:10.1371/journal.pbio.1001033. PMC . PMID 21445328.
- 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 . PMID 22295078.
- 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 . PMID 12571357.
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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 .
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
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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].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||ATP binding (GO:0005524)|
|kinase activity (GO:0016301)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
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AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes .
The clan contains the following 217 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_5 AAA_6 AAA_7 AAA_8 AAA_9 AAA_PrkA ABC_ATPase ABC_tran ABC_tran_Xtn Adeno_IVa2 Adenylsucc_synt ADK AFG1_ATPase AIG1 APS_kinase Arf ArgK ArsA_ATPase ATP-synt_ab ATP_bind_1 ATP_bind_2 ATPase ATPase_2 Bac_DnaA BCA_ABC_TP_C Beta-Casp Cas_Csn2 Cas_St_Csn2 CbiA CBP_BcsQ CDC73_C CENP-M CFTR_R CLP1_P CMS1 CoaE CobA_CobO_BtuR CobU cobW CPT CSM2 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 DUF1611 DUF1726 DUF2075 DUF2326 DUF2478 DUF257 DUF2791 DUF2813 DUF3584 DUF463 DUF815 DUF853 DUF87 DUF927 Dynamin_N Dynein_heavy ERCC3_RAD25_C Exonuc_V_gamma FeoB_N Fer4_NifH Flavi_DEAD FTHFS FtsK_SpoIIIE G-alpha Gal-3-0_sulfotr GBP GBP_C GTP_EFTU Gtr1_RagA Guanylate_kin GvpD HDA2-3 Helicase_C Helicase_C_2 Helicase_C_4 Helicase_RecD Herpes_Helicase Herpes_ori_bp Herpes_TK Hydin_ADK IIGP IPPT IPT IstB_IS21 KAP_NTPase KdpD Kinesin KTI12 LAP1C Lon_2 LpxK MCM MEDS Mg_chelatase Microtub_bd MipZ MMR_HSR1 MMR_HSR1_C MobB MukB MutS_V Myosin_head NACHT NB-ARC NOG1 NTPase_1 NTPase_P4 ORC3_N ParA Parvo_NS1 PAXNEB PduV-EutP PhoH PIF1 Podovirus_Gp16 Polyoma_lg_T_C Pox_A32 PPK2 PPV_E1_C PRK PSY3 Rad17 Rad51 Ras RecA ResIII RHD3 RHSP RNA12 RNA_helicase Roc RsgA_GTPase RuvB_N SbcCD_C SecA_DEAD Septin Sigma54_activ_2 Sigma54_activat SKI SMC_N SNF2_N Spore_IV_A SRP54 SRPRB SulA Sulfotransfer_1 Sulfotransfer_2 Sulfotransfer_3 Sulphotransf T2SSE 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 TsaE UvrB UvrD-helicase UvrD_C UvrD_C_2 Viral_helicase1 VirC1 VirE Zeta_toxin Zot
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
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Curation and family details
|Seed source:||Pfam-B_12374 (release 9.0)|
|Number in seed:||18|
|Number in full:||1037|
|Average length of the domain:||159.40 aa|
|Average identity of full alignment:||18 %|
|Average coverage of the sequence by the domain:||46.62 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||11|
|Download:||download the raw HMM for this family|
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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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