Protein Family Models

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2024-08-14

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2024-08-14

Uracil-DNA glycosylase inhibitor (UGI) found in Bacillus subtilis phage, is an inhibitor that inactivates the host uracil-DNA glycosylase (UDG), also known as (UNG) uracil-DNA N-glycosylase. UDG is a highly conserved enzyme responsible for the initiation of uracil-base excision repair (1). UGI forms a tight non-covalent bond to UDG, completely inhibiting it from binding to DNA by inserting its beta-1 strand into the conserved DNA-binding groove of the enzyme (2). In complex with UDG, UGI folds into an alpha-beta-alpha sandwich structure formed by five-stranded antiparallel beta-strands and two helices (3). [1]. 7552746. Nucleotide mimicry in the crystal structure of the uracil-DNA. glycosylase-uracil glycosylase inhibitor protein complex.. Savva R, Pearl LH;. Nat Struct Biol. 1995;2:752-757.. [2]. 25084329. Structural and biophysical analysis of interactions between cod. and human uracil-DNA N-glycosylase (UNG) and UNG inhibitor. (Ugi).. Assefa NG, Niiranen L, Johnson KA, Leiros HK, Smalas AO,. Willassen NP, Moe E;. Acta Crystallogr D Biol Crystallogr. 2014;70:2093-2100.. [3]. 12136137. Domain closure and action of uracil DNA glycosylase (UDG):. structures of new crystal forms containing the Escherichia coli. enzyme and a comparative study of the known structures involving. UDG.. Saikrishnan K, Bidya Sagar M, Ravishankar R, Roy S, Purnapatre. K, Handa P, Varshney U, Vijayan M;. Acta Crystallogr D Biol Crystallogr. 2002;58:1269-1276. (from Pfam)

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2024-08-14

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NFACT-R RNA binding family found found in bacteria fused to the ThiI domain as a variant of the canonical tRNA 4-thiouridylation pathway [1]. [1]. 24646681. A highly conserved family of domains related to the. DNA-glycosylase fold helps predict multiple novel pathways for. RNA modifications.. Burroughs AM, Aravind L;. RNA Biol. 2014;11:360-372. (from Pfam)

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2024-08-14

This is a predicted RRM-fold domain present at the C-terminus of Demeter-like glycoslyases [1]. These proteins are involved in DNA demethylation in plants where they catalyze removal of the 5mC base and subsequently cleave the backbone through lyase activity. Orthologs of Demeter are present in plants and stramenopiles. The RRM fold domain is predicted to facilitate interaction of the catalytic domain with ssDNA or regulatory RNA [1]. [1]. 21507349. Natural history of eukaryotic DNA methylation systems.. Iyer LM, Abhiman S, Aravind L;. Prog Mol Biol Transl Sci. 2011;101:25-104.. [2]. 16469697. DEMETER DNA glycosylase establishes MEDEA polycomb gene. self-imprinting by allele-specific demethylation.. Gehring M, Huh JH, Hsieh TF, Penterman J, Choi Y, Harada JJ,. Goldberg RB, Fischer RL;. Cell. 2006;124:495-506. (from Pfam)

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2024-08-14

This is the C-terminal domain of the NFACT (NEMF, FbpA, Caliban, and Tae2) proteins involved in the ribosomal quality control pathway. This context is conserved in archaea and eukaryotes, but NFACT proteins in bacteria lack the NFACT-C domain [1]. [1]. 24646681. A highly conserved family of domains related to the. DNA-glycosylase fold helps predict multiple novel pathways for. RNA modifications.. Burroughs AM, Aravind L;. RNA Biol. 2014;11:360-372. (from Pfam)

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2024-08-14

Escherichia coli endonuclease III (EC 4.2.99.18) [1] is a DNA repair enzyme that acts both as a DNA N-glycosylase, removing oxidised pyrimidines from DNA, and as an apurinic/apyrimidinic (AP) endonuclease, introducing a single-strand nick at the site from which the damaged base was removed. Endonuclease III is an iron-sulfur protein that binds a single 4Fe-4S cluster. The 4Fe-4S cluster does not seem to be important for catalytic activity, but is probably involved in the proper positioning of the enzyme along the DNA strand [2]. The 4Fe-4S cluster is bound by four cysteines which are all located in a 17 amino acid region at the C-terminal end of endonuclease III. A similar region is also present in the central section of mutY and in the C-terminus of ORF-10 and of the Micro-coccus UV endonuclease [4]. [1]. 7664751. Novel DNA binding motifs in the DNA repair enzyme endonuclease. III crystal structure.. Thayer MM, Ahern H, Xing D, Cunningham RP, Tainer JA;. EMBO J. 1995;14:4108-4120.. [2]. 9045706. Cloning and expression of the cDNA encoding the human homologue. of the DNA repair enzyme, Escherichia coli endonuclease III.. Hilbert TP, Chaung W, Boorstein RJ, Cunningham RP, Teebor GW;. J Biol Chem. 1997;272:6733-6740.. [3]. 16096281. Engineering functional changes in Escherichia coli endonuclease. III based on phylogenetic and structural analyses.. Watanabe T, Blaisdell JO, Wallace SS, Bond JP;. J Biol Chem. 2005;280:34378-34384.. [4]. 16967954. Direct electrochemistry of endonuclease III in the presence and. absence of DNA.. Gorodetsky AA, Boal AK, Barton JK;. J Am Chem Soc. 2006;128:12082-12083. (from Pfam)

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2024-08-14

Members of this family are predominantly found in Endonuclease VIII-like 1 and adopt a glucocorticoid receptor-like fold. They allow for DNA binding [1]. [1]. 15232006. The crystal structure of human endonuclease VIII-like 1 (NEIL1). reveals a zincless finger motif required for glycosylase. activity.. Doublie S, Bandaru V, Bond JP, Wallace SS;. Proc Natl Acad Sci U S A. 2004;101:10284-10289. (from Pfam)

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2024-08-14

This domain is predominantly found in the Archaeal protein N-glycosylase/DNA lyase. [1]. 15604455. Pa-AGOG, the founding member of a new family of archaeal. 8-oxoguanine DNA-glycosylases.. Sartori AA, Lingaraju GM, Hunziker P, Winkler FK, Jiricny J;. Nucleic Acids Res. 2004;32:6531-6539.. [2]. 15642264. A DNA glycosylase from Pyrobaculum aerophilum with an. 8-oxoguanine binding mode and a noncanonical helix-hairpin-helix. structure.. Lingaraju GM, Sartori AA, Kostrewa D, Prota AE, Jiricny J,. Winkler FK;. Structure. 2005;13:87-98. (from Pfam)

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2024-08-14

Members of this family are DNA glycosylases performing base excision for DNA repair. Substrates include 8-oxoguanine and 3-methyladenine.

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Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidised purines from damaged DNA. This family is the central domain containing the DNA-binding helix-two turn-helix domain [1]. [1]. 11912217. Structure of formamidopyrimidine-DNA glycosylase covalently. complexed to DNA.. Gilboa R, Zharkov DO, Golan G, Fernandes AS, Gerchman SE, Matz. E, Kycia JH, Grollman AP, Shoham G;. J Biol Chem 2002;277:19811-19816. (from Pfam)

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2024-08-14

Members of this family have two copies of a winged helix domain, suggsting DNA-binding. YcaQ from Escherichia coli was shown to be a DNA glycosylase that removes crosslinks between strands of DNA.

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2024-08-14

SAUGI (S. aureus uracil-DNA glycosylase inhibitor) is described as a DNA mimic protein that affects uracil-DNA glycosylase activity.

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2024-08-14

A winged helix-turn-helix domain present in the plant HB1, vertebrate ASXL, the H. pylori restriction endonuclease HpyAIII(HgrA), the RNA polymerase delta subunit(RpoE) of Gram positive bacteria and several restriction endonucleases [1]. The domain is distinguished by the presence of a conserved one-turn helix between helix-3 and the preceding conserved turn. Its diverse architectures in eukaryotic species with extensive gene body methylation is suggestive of a chromatin function. The genetic interaction of the HARE-HTH containing ASXL with the methyl cytosine hydroxylating Tet2 protein is suggestive of a role for the domain in discriminating sequences with DNA modifications such as hmC [1]. Bacterial versions include fusions to diverse restriction endonucleases, and a DNA glycosylase where it may play a similar role in detecting modified DNA. Certain bacterial version of the HARE-HTH domain show fusions to the helix-hairpin-helix domain of the RNA polymerase alpha subunit and the HTH domains found in regions 3 and 4 of the sigma factors [1]. These versions are predicted to function as a novel inhibitor of the binding of RNA polymerase to transcription start sites, similar to the Bacillus delta protein [2,3]. [1]. 10336502. Expression, abundance, and RNA polymerase binding properties of. the delta factor of Bacillus subtilis.. Lopez de Saro FJ, Yoshikawa N, Helmann JD;. J Biol Chem 1999;274:15953-15958.. [2]. 7545758. Structural analysis of the Bacillus subtilis delta factor: a. protein polyanion which displaces RNA from RNA polymerase.. Lopez de Saro FJ, Woody AY, Helmann JD;. J Mol Biol 1995;252:189-202.. [3]. 22. TRUNCATED at 1650 bytes (from Pfam)

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This zinc binding domain is found at the C-terminus of isoleucyl tRNA synthetase and the enzyme Formamidopyrimidine-DNA glycosylase EC:3.2.2.23. (from Pfam)

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2024-08-14

This domain occurs in proteins that have been annotated as Fibronectin/fibrinogen binding protein by similarity. This annotation comes from Swiss:O34693 where the N-terminal region is involved in this activity [1]. It is an RNA binding domain of the NFACT (NEMF, FbpA, Caliban, and Tae2) proteins. This NFACT-R family is found in two eukaryotic gene contexts: fused to the NFACT-N and NFACT-C domains in the NFACT protein involved in the ribosomal quality control pathway which contributes to CAT-tailing and as a standalone domain [2]. Additionally this domain contains a conserved motif D/E-X-W/Y-X-H that may be functionally important. [1]. 8063411. Cloning, sequencing, and expression of a. fibronectin/fibrinogen-binding protein from group A. streptococci.. Courtney HS, Li Y, Dale JB, Hasty DL;. Infect Immun 1994;62:3937-3946.. [2]. 24646681. A highly conserved family of domains related to the. DNA-glycosylase fold helps predict multiple novel pathways for. RNA modifications.. Burroughs AM, Aravind L;. RNA Biol. 2014;11:360-372. (from Pfam)

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2024-08-14

The DNA-3-methyladenine glycosylase I is constitutively expressed and is specific for the alkylated 3-methyladenine DNA. [1]. 8502545. Excision of 3-methylguanine from alkylated DNA by. 3-methyladenine DNA glycosylase I of Escherichia coli.. Bjelland S, Bjoras M, Seeberg E;. Nucleic Acids Res 1993;21:2045-2049. (from Pfam)

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2024-08-14

Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a Uracil-DNA glycosylase that is related to other cyclins [4]. Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the C-terminal domain. The cyclins include an internal duplication, which is related to. that found in TFIIB and the RB protein.. [1]. 8152925. Evidence for a protein domain superfamily shared by the cyclins,. TFIIB and RB/p107.. Gibson TJ, Thompson JD, Blocker A, Kouzarides T;. Nucleic Acids Res 1994;22:946-952.. [2]. 8591034. The crystal structure of cyclin A. Brown NR, Noble MEM, Endicott JA, Garman EF, Wakatsuki S,. Mitchell E, Rasmussen B, Hunt T, Johnson LN;. Structure. 1995;3:1235-1247.. Complex of cyclin and cyclin dependent kinase.. [3]. 8756328. Structural basis of cyclin-dependant kinase activation by. phosphorylation.. Russo AA, Jeffrey PD, Pavletich NP;. Nat Struct Biol. 1996;3:696-700.. [4]. 2001396. Isolation and characterization of a human cDNA encoding. uracil-DNA glycosylase.. Muller SJ, Caradonna S;. Biochim Biophys Acta 1991;1088:197-207. (from Pfam)

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2024-08-14