PubMed:11877432 JSONTXT

{"project":"PMID_GLOBAL","denotations":[{"id":"T1","span":{"begin":0,"end":98},"obj":"Sentence"},{"id":"T2","span":{"begin":99,"end":254},"obj":"Sentence"},{"id":"T3","span":{"begin":255,"end":359},"obj":"Sentence"},{"id":"T4","span":{"begin":360,"end":476},"obj":"Sentence"},{"id":"T5","span":{"begin":477,"end":680},"obj":"Sentence"},{"id":"T6","span":{"begin":681,"end":745},"obj":"Sentence"},{"id":"T7","span":{"begin":746,"end":833},"obj":"Sentence"},{"id":"T8","span":{"begin":834,"end":978},"obj":"Sentence"},{"id":"T9","span":{"begin":979,"end":1106},"obj":"Sentence"},{"id":"T10","span":{"begin":1107,"end":1335},"obj":"Sentence"}],"text":"Crystal structure of Thermotoga maritima 0065, a member of the IclR transcriptional factor family.\nMembers of the IclR family of transcription regulators modulate signal-dependent expression of genes involved in carbon metabolism in bacteria and archaea. The Thermotoga maritima TM0065 gene codes for a protein (TM-IclR) that is homologous to the IclR family. We have determined the crystal structure of TM-IclR at 2.2 A resolution using MAD phasing and synchrotron radiation. The protein is composed of two domains: the N-terminal DNA-binding domain contains the winged helix-turn-helix motif, and the C-terminal presumed regulatory domain is involved in binding signal molecule. In a proposed signal-binding site, a bound Zn(2+) ion was found. In the crystal, TM-IclR forms a dimer through interactions between DNA-binding domains. In the dimer, the DNA-binding domains are 2-fold related, but the dimer is asymmetric with respect to the orientation of signal-binding domains. Crystal packing analysis showed that TM-IclR dimers form a tetramer through interactions exclusively by signal-binding domains. A model is proposed for binding of IclR-like factors to DNA, and it suggests that signal-dependent transcription regulation is accomplished by affecting an oligomerization state of IclR and therefore its affinity for DNA target."}

{"project":"sentences","denotations":[{"id":"T1","span":{"begin":0,"end":98},"obj":"Sentence"},{"id":"T2","span":{"begin":99,"end":254},"obj":"Sentence"},{"id":"T3","span":{"begin":255,"end":359},"obj":"Sentence"},{"id":"T4","span":{"begin":360,"end":476},"obj":"Sentence"},{"id":"T5","span":{"begin":477,"end":680},"obj":"Sentence"},{"id":"T6","span":{"begin":681,"end":745},"obj":"Sentence"},{"id":"T7","span":{"begin":746,"end":833},"obj":"Sentence"},{"id":"T8","span":{"begin":834,"end":978},"obj":"Sentence"},{"id":"T9","span":{"begin":979,"end":1106},"obj":"Sentence"},{"id":"T10","span":{"begin":1107,"end":1335},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Crystal structure of Thermotoga maritima 0065, a member of the IclR transcriptional factor family.\nMembers of the IclR family of transcription regulators modulate signal-dependent expression of genes involved in carbon metabolism in bacteria and archaea. The Thermotoga maritima TM0065 gene codes for a protein (TM-IclR) that is homologous to the IclR family. We have determined the crystal structure of TM-IclR at 2.2 A resolution using MAD phasing and synchrotron radiation. The protein is composed of two domains: the N-terminal DNA-binding domain contains the winged helix-turn-helix motif, and the C-terminal presumed regulatory domain is involved in binding signal molecule. In a proposed signal-binding site, a bound Zn(2+) ion was found. In the crystal, TM-IclR forms a dimer through interactions between DNA-binding domains. In the dimer, the DNA-binding domains are 2-fold related, but the dimer is asymmetric with respect to the orientation of signal-binding domains. Crystal packing analysis showed that TM-IclR dimers form a tetramer through interactions exclusively by signal-binding domains. A model is proposed for binding of IclR-like factors to DNA, and it suggests that signal-dependent transcription regulation is accomplished by affecting an oligomerization state of IclR and therefore its affinity for DNA target."}

{"project":"mondo_disease","denotations":[{"id":"T1","span":{"begin":438,"end":441},"obj":"Disease"}],"attributes":[{"id":"A1","pred":"mondo_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/MONDO_0015177"},{"id":"A2","pred":"mondo_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/MONDO_0016584"}],"text":"Crystal structure of Thermotoga maritima 0065, a member of the IclR transcriptional factor family.\nMembers of the IclR family of transcription regulators modulate signal-dependent expression of genes involved in carbon metabolism in bacteria and archaea. The Thermotoga maritima TM0065 gene codes for a protein (TM-IclR) that is homologous to the IclR family. We have determined the crystal structure of TM-IclR at 2.2 A resolution using MAD phasing and synchrotron radiation. The protein is composed of two domains: the N-terminal DNA-binding domain contains the winged helix-turn-helix motif, and the C-terminal presumed regulatory domain is involved in binding signal molecule. In a proposed signal-binding site, a bound Zn(2+) ion was found. In the crystal, TM-IclR forms a dimer through interactions between DNA-binding domains. In the dimer, the DNA-binding domains are 2-fold related, but the dimer is asymmetric with respect to the orientation of signal-binding domains. Crystal packing analysis showed that TM-IclR dimers form a tetramer through interactions exclusively by signal-binding domains. A model is proposed for binding of IclR-like factors to DNA, and it suggests that signal-dependent transcription regulation is accomplished by affecting an oligomerization state of IclR and therefore its affinity for DNA target."}

{"project":"NCBITAXON","denotations":[{"id":"T1","span":{"begin":21,"end":40},"obj":"OrganismTaxon"},{"id":"T2","span":{"begin":233,"end":241},"obj":"OrganismTaxon"},{"id":"T4","span":{"begin":246,"end":253},"obj":"OrganismTaxon"},{"id":"T5","span":{"begin":259,"end":278},"obj":"OrganismTaxon"}],"attributes":[{"id":"A1","pred":"db_id","subj":"T1","obj":"2336"},{"id":"A2","pred":"db_id","subj":"T2","obj":"2"},{"id":"A3","pred":"db_id","subj":"T2","obj":"629395"},{"id":"A4","pred":"db_id","subj":"T4","obj":"2157"},{"id":"A5","pred":"db_id","subj":"T5","obj":"2336"}],"text":"Crystal structure of Thermotoga maritima 0065, a member of the IclR transcriptional factor family.\nMembers of the IclR family of transcription regulators modulate signal-dependent expression of genes involved in carbon metabolism in bacteria and archaea. The Thermotoga maritima TM0065 gene codes for a protein (TM-IclR) that is homologous to the IclR family. We have determined the crystal structure of TM-IclR at 2.2 A resolution using MAD phasing and synchrotron radiation. The protein is composed of two domains: the N-terminal DNA-binding domain contains the winged helix-turn-helix motif, and the C-terminal presumed regulatory domain is involved in binding signal molecule. In a proposed signal-binding site, a bound Zn(2+) ion was found. In the crystal, TM-IclR forms a dimer through interactions between DNA-binding domains. In the dimer, the DNA-binding domains are 2-fold related, but the dimer is asymmetric with respect to the orientation of signal-binding domains. Crystal packing analysis showed that TM-IclR dimers form a tetramer through interactions exclusively by signal-binding domains. A model is proposed for binding of IclR-like factors to DNA, and it suggests that signal-dependent transcription regulation is accomplished by affecting an oligomerization state of IclR and therefore its affinity for DNA target."}

{"project":"Anatomy-UBERON","denotations":[{"id":"T1","span":{"begin":571,"end":576},"obj":"Body_part"},{"id":"T2","span":{"begin":582,"end":587},"obj":"Body_part"}],"attributes":[{"id":"A1","pred":"uberon_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/UBERON_0002488"},{"id":"A2","pred":"uberon_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/UBERON_0002488"}],"text":"Crystal structure of Thermotoga maritima 0065, a member of the IclR transcriptional factor family.\nMembers of the IclR family of transcription regulators modulate signal-dependent expression of genes involved in carbon metabolism in bacteria and archaea. The Thermotoga maritima TM0065 gene codes for a protein (TM-IclR) that is homologous to the IclR family. We have determined the crystal structure of TM-IclR at 2.2 A resolution using MAD phasing and synchrotron radiation. The protein is composed of two domains: the N-terminal DNA-binding domain contains the winged helix-turn-helix motif, and the C-terminal presumed regulatory domain is involved in binding signal molecule. In a proposed signal-binding site, a bound Zn(2+) ion was found. In the crystal, TM-IclR forms a dimer through interactions between DNA-binding domains. In the dimer, the DNA-binding domains are 2-fold related, but the dimer is asymmetric with respect to the orientation of signal-binding domains. Crystal packing analysis showed that TM-IclR dimers form a tetramer through interactions exclusively by signal-binding domains. A model is proposed for binding of IclR-like factors to DNA, and it suggests that signal-dependent transcription regulation is accomplished by affecting an oligomerization state of IclR and therefore its affinity for DNA target."}