InterPro : IPR010663

Name  Zinc finger, DNA glycosylase/AP lyase/isoleucyl tRNA synthetase Short Name  Znf_DNA_glyclase/IsotRNA_synth
Type  Domain Description  Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis(African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc.DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity () and AP lyase activity () []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; ) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; ). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase () [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) [].
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Sequence Features

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Proteins

InterPro protein domain ID --> Contigs

 

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0 Child Features

1 Contains

Id Name Short Name Type
IPR015887 DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site DNA_glyclase_Znf_dom_DNA_BS Binding_site

3 Found In

Id Name Short Name Type
IPR009080 Aminoacyl-tRNA synthetase, class 1a, anticodon-binding tRNAsynth_1a_anticodon-bd Domain
IPR000191 DNA glycosylase/AP lyase DNA_glycosylase/AP_lyase Family
IPR020629 Formamidopyrimidine-DNA glycosylase Formamido-pyr_DNA_Glyclase Family

0 Parent Features

14 Publications

First Author Title Year Journal Volume Pages
Matthews JM Zinc fingers--folds for many occasions. 2002 IUBMB Life 54 351-5
Gamsjaeger R Sticky fingers: zinc-fingers as protein-recognition motifs. 2007 Trends Biochem Sci 32 63-70
Hall TM Multiple modes of RNA recognition by zinc finger proteins. 2005 Curr Opin Struct Biol 15 367-73
Brown RS Zinc finger proteins: getting a grip on RNA. 2005 Curr Opin Struct Biol 15 94-8
Klug A Zinc finger peptides for the regulation of gene expression. 1999 J Mol Biol 293 215-8
Laity JH Zinc finger proteins: new insights into structural and functional diversity. 2001 Curr Opin Struct Biol 11 39-46
O'Connor TR Fpg protein of Escherichia coli is a zinc finger protein whose cysteine residues have a structural and/or functional role. 1993 J Biol Chem 268 9063-70
Sugahara M Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile, Thermus thermophilus HB8. 2000 EMBO J 19 3857-69
Doublié S The crystal structure of human endonuclease VIII-like 1 (NEIL1) reveals a zincless finger motif required for glycosylase activity. 2004 Proc Natl Acad Sci U S A 101 10284-9
Silvian LF Insights into editing from an ile-tRNA synthetase structure with tRNAile and mupirocin. 1999 Science 285 1074-7
Fukunaga R Structural basis for substrate recognition by the editing domain of isoleucyl-tRNA synthetase. 2006 J Mol Biol 359 901-12
Gilboa R Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA. 2002 J Biol Chem 277 19811-6
Zharkov DO Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate. 2002 EMBO J 21 789-800
Zhou L Mutation of the carboxy terminal zinc finger of E. coli isoleucyl-tRNA synthetase alters zinc binding and aminoacylation activity. 1995 Biochem Biophys Res Commun 216 648-54



To cite PlanMine, please refer to the following publication:

Rozanski, A., Moon, H., Brandl, H., Martín-Durán, J. M., Grohme, M., Hüttner, K., Bartscherer, K., Henry, I., & Rink, J. C.
PlanMine 3.0—improvements to a mineable resource of flatworm biology and biodiversity
Nucleic Acids Research, gky1070. doi:10.1093/nar/gky1070 (2018)