Summary: Zinc finger found in FPG and IleRS
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This is the Wikipedia entry entitled "FPG IleRS zinc finger". More...
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FPG IleRS zinc finger Edit Wikipedia article
|SCOP2||1qu2 / SCOPe / SUPFAM|
The FPG IleRS zinc finger domain 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.
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 (EC) and AP lyase activity (EC). 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; EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; EC). 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 (EC). 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).
- Gilboa R, Zharkov DO, Golan G, Fernandes AS, Gerchman SE, Matz E, Kycia JH, Grollman AP, Shoham G (May 2002). "Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA". J. Biol. Chem. 277 (22): 19811â€“6. doi:10.1074/jbc.M202058200. PMIDÂ 11912217.
- Sugahara M, Mikawa T, Kumasaka T, Yamamoto M, Kato R, Fukuyama K, Inoue Y, Kuramitsu S (August 2000). "Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile, Thermus thermophilus HB8". EMBO J. 19 (15): 3857â€“69. doi:10.1093/emboj/19.15.3857. PMCÂ 306600. PMIDÂ 10921868.
- O'Connor TR, Graves RJ, de Murcia G, Castaing B, Laval J (April 1993). "Fpg protein of Escherichia coli is a zinc finger protein whose cysteine residues have a structural and/or functional role". J. Biol. Chem. 268 (12): 9063â€“70. doi:10.1016/S0021-9258(18)52978-1. PMIDÂ 8473347.
- Zharkov DO, Golan G, Gilboa R, Fernandes AS, Gerchman SE, Kycia JH, Rieger RA, Grollman AP, Shoham G (February 2002). "Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate". EMBO J. 21 (4): 789â€“800. doi:10.1093/emboj/21.4.789. PMCÂ 125349. PMIDÂ 11847126.
- DoubliÃ© S, Bandaru V, Bond JP, Wallace SS (July 2004). "The crystal structure of human endonuclease VIII-like 1 (NEIL1) reveals a zincless finger motif required for glycosylase activity". Proc. Natl. Acad. Sci. U.S.A. 101 (28): 10284â€“9. Bibcode:2004PNAS..10110284D. doi:10.1073/pnas.0402051101. PMCÂ 478564. PMIDÂ 15232006.
- Silvian LF, Wang J, Steitz TA (August 1999). "Insights into editing from an ile-tRNA synthetase structure with tRNAile and mupirocin". Science. 285 (5430): 1074â€“7. doi:10.1126/science.285.5430.1074. PMIDÂ 10446055.
- Zhou L, Rosevear PR (November 1995). "Mutation of the carboxy terminal zinc finger of E. coli isoleucyl-tRNA synthetase alters zinc binding and aminoacylation activity". Biochem. Biophys. Res. Commun. 216 (2): 648â€“54. doi:10.1006/bbrc.1995.2671. PMIDÂ 7488160.
- Fukunaga R, Yokoyama S (June 2006). "Structural basis for substrate recognition by the editing domain of isoleucyl-tRNA synthetase". J. Mol. Biol. 359 (4): 901â€“12. doi:10.1016/j.jmb.2006.04.025. PMIDÂ 16697013.
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Zinc finger found in FPG and IleRS Provide feedback
This zinc binding domain is found at the C-terminus of isoleucyl tRNA synthetase and the enzyme Formamidopyrimidine-DNA glycosylase EC:126.96.36.199.
Internal database links
|SCOOP:||Auto_anti-p27 NFACT_N zf-TFIIB zinc-ribbons_6|
|Similarity to PfamA using HHSearch:||zf-TFIIB zf-ACC HscB_4_cys|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR010663
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 ( EC ) and AP lyase activity ( EC ) [ PUBMED:11912217 ]. 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; EC ) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; EC ). 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 [ PUBMED:10921868 ]. 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 [ PUBMED:10921868 ]. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines [ PUBMED:8473347 ]. 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 [ PUBMED:11847126 , PUBMED:15232006 ].
An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase ( EC ) [ PUBMED:10446055 , PUBMED:7488160 ]. 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) [ PUBMED:16697013 ].
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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A clan of zinc-binding ribbon domains.
The clan contains the following 89 members:A2L_zn_ribbon Auto_anti-p27 Baculo_LEF5_C CpXC DNA_RNApol_7kD DUF1451 DUF1936 DUF2072 DUF2116 DUF2180 DUF2387 DUF2614 DUF35_N DUF3945 DUF4379 DUF6574 DZR DZR_2 Elf1 GATA HVO_2753_ZBP Lar_restr_allev LIM MscL Mu-like_Com NinF NOB1_Zn_bind Nudix_N_2 Ogr_Delta OrfB_Zn_ribbon PriA_CRR Prim_Zn_Ribbon RecO_C Ribosomal_L32p Ribosomal_L33 Ribosomal_L37ae Ribosomal_L37e Ribosomal_L40e Ribosomal_L44 Ribosomal_S27 Ribosomal_S27e RNA_POL_M_15KD Rubredoxin_2 Spt4 Stc1 TF_Zn_Ribbon TFIIS_C Tnp_zf-ribbon_2 Topo_Zn_Ribbon Toprim_Crpt Trm112p UPF0547 YjdM_Zn_Ribbon zf-C4 zf-C4_ClpX zf-C4_Topoisom zf-CHC2 zf-CSL zf-dskA_traR zf-FPG_IleRS zf-GRF zf-ISL3 zf-NADH-PPase zf-PARP zf-RanBP zf-ribbon_3 zf-RING_7 zf-RRN7 zf-TFIIB zf-trcl zf-ZPR1 zf_PR_Knuckle zf_Rg zinc-ribbon_6 zinc-ribbons_6 zinc_ribbon_10 zinc_ribbon_11 zinc_ribbon_12 zinc_ribbon_13 zinc_ribbon_15 zinc_ribbon_2 zinc_ribbon_4 zinc_ribbon_5 zinc_ribbon_9 Zn-ribbon_8 Zn_ribbon_recom Zn_ribbon_SprT Zn_Tnp_IS1 Zn_Tnp_IS1595
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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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.
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|Seed source:||Bateman A|
|Number in seed:||78|
|Number in full:||11667|
|Average length of the domain:||29.40 aa|
|Average identity of full alignment:||34 %|
|Average coverage of the sequence by the domain:||6.22 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||17|
|Download:||download the raw HMM for this family|
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Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
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Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
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Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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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 zf-FPG_IleRS domain has been found. There are 89 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 sequence.
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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.