5ugw: Difference between revisions

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 <StructureSection load='5ugw' size='340' side='right'caption='[[5ugw]], [[Resolution|resolution]] 2.31&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ugw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UGW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UGW FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ugw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UGW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UGW FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GSH:GLUTATHIONE'>GSH</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.31&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3du6|3du6]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GSH:GLUTATHIONE'>GSH</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TERT, EST2, TCS1, TRT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5ugw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ugw OCA], [https://pdbe.org/5ugw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ugw RCSB], [https://www.ebi.ac.uk/pdbsum/5ugw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ugw ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA-directed_DNA_polymerase RNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.49 2.7.7.49] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ugw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ugw OCA], [http://pdbe.org/5ugw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ugw RCSB], [http://www.ebi.ac.uk/pdbsum/5ugw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ugw ProSAT]</span></td></tr>
 </table>
 == Disease ==
-[[http://www.uniprot.org/uniprot/TERT_HUMAN TERT_HUMAN]] Note=Activation of telomerase has been implicated in cell immortalization and cancer cell pathogenesis.  Defects in TERT are associated with susceptibilty to aplastic anemia (AA) [MIM:[http://omim.org/entry/609135 609135]]. AA is a rare disease in which the reduction of the circulating blood cells results from damage to the stem cell pool in bone marrow. In most patients, the stem cell lesion is caused by an autoimmune attack. T-lymphocytes, activated by an endogenous or exogenous, and most often unknown antigenic stimulus, secrete cytokines, including IFN-gamma, which would in turn be able to suppress hematopoiesis.<ref>PMID:15885610</ref> <ref>PMID:16627250</ref> <ref>PMID:16990594</ref> <ref>PMID:19760749</ref>   Note=Genetic variations in TERT are associated with coronary artery disease (CAD).<ref>PMID:16890917</ref>   Defects in TERT are the cause of dyskeratosis congenita autosomal dominant type 2 (DKCA2) [MIM:[http://omim.org/entry/613989 613989]]. A rare multisystem disorder caused by defective telomere maintenance. It is characterized by progressive bone marrow failure, and the clinical triad of reticulated skin hyperpigmentation, nail dystrophy, and mucosal leukoplakia. Common but variable features include premature graying, aplastic anemia, low platelets, osteoporosis, pulmonary fibrosis, and liver fibrosis among others. Early mortality is often associated with bone marrow failure, infections, fatal pulmonary complications, or malignancy.<ref>PMID:15885610</ref> <ref>PMID:16247010</ref>   Defects in TERT are the cause of pulmonary fibrosis, and/or bone marrow failure, telomere-related, type 1 (PFBMFT1) [MIM:[http://omim.org/entry/614742 614742]]. A disease associated with shortened telomeres. Pulmonary fibrosis is the most common manifestation. Other manifestations include aplastic anemia due to bone marrow failure, hepatic fibrosis, and increased cancer risk, particularly myelodysplastic syndrome and acute myeloid leukemia. Phenotype, age at onset, and severity are determined by telomere length. infections, fatal pulmonary complications, or malignancy.<ref>PMID:15814878</ref> <ref>PMID:17460043</ref> <ref>PMID:21436073</ref> <ref>PMID:21483807</ref> <ref>PMID:22512499</ref>   Defects in TERT are the cause of dyskeratosis congenita autosomal recessive type 4 (DKCB4) [MIM:[http://omim.org/entry/613989 613989]]. A rare multisystem disorder caused by defective telomere maintenance. It is characterized by progressive bone marrow failure, and the clinical triad of reticulated skin hyperpigmentation, nail dystrophy, and mucosal leukoplakia. Common but variable features include premature graying, aplastic anemia, low platelets, osteoporosis, pulmonary fibrosis, and liver fibrosis among others. Early mortality is often associated with bone marrow failure, infections, fatal pulmonary complications, or malignancy.  Defects in TERT are a cause of susceptibility to pulmonary fibrosis idiopathic (IPF) [MIM:[http://omim.org/entry/178500 178500]]. Pulmonary fibrosis is a lung disease characterized by shortness of breath, radiographically evident diffuse pulmonary infiltrates, and varying degrees of inflammation and fibrosis on biopsy. It results in acute lung injury with subsequent scarring and endstage lung disease.
+[https://www.uniprot.org/uniprot/TERT_HUMAN TERT_HUMAN] Note=Activation of telomerase has been implicated in cell immortalization and cancer cell pathogenesis.  Defects in TERT are associated with susceptibilty to aplastic anemia (AA) [MIM:[https://omim.org/entry/609135 609135]. AA is a rare disease in which the reduction of the circulating blood cells results from damage to the stem cell pool in bone marrow. In most patients, the stem cell lesion is caused by an autoimmune attack. T-lymphocytes, activated by an endogenous or exogenous, and most often unknown antigenic stimulus, secrete cytokines, including IFN-gamma, which would in turn be able to suppress hematopoiesis.<ref>PMID:15885610</ref> <ref>PMID:16627250</ref> <ref>PMID:16990594</ref> <ref>PMID:19760749</ref>   Note=Genetic variations in TERT are associated with coronary artery disease (CAD).<ref>PMID:16890917</ref>   Defects in TERT are the cause of dyskeratosis congenita autosomal dominant type 2 (DKCA2) [MIM:[https://omim.org/entry/613989 613989]. A rare multisystem disorder caused by defective telomere maintenance. It is characterized by progressive bone marrow failure, and the clinical triad of reticulated skin hyperpigmentation, nail dystrophy, and mucosal leukoplakia. Common but variable features include premature graying, aplastic anemia, low platelets, osteoporosis, pulmonary fibrosis, and liver fibrosis among others. Early mortality is often associated with bone marrow failure, infections, fatal pulmonary complications, or malignancy.<ref>PMID:15885610</ref> <ref>PMID:16247010</ref>   Defects in TERT are the cause of pulmonary fibrosis, and/or bone marrow failure, telomere-related, type 1 (PFBMFT1) [MIM:[https://omim.org/entry/614742 614742]. A disease associated with shortened telomeres. Pulmonary fibrosis is the most common manifestation. Other manifestations include aplastic anemia due to bone marrow failure, hepatic fibrosis, and increased cancer risk, particularly myelodysplastic syndrome and acute myeloid leukemia. Phenotype, age at onset, and severity are determined by telomere length. infections, fatal pulmonary complications, or malignancy.<ref>PMID:15814878</ref> <ref>PMID:17460043</ref> <ref>PMID:21436073</ref> <ref>PMID:21483807</ref> <ref>PMID:22512499</ref>   Defects in TERT are the cause of dyskeratosis congenita autosomal recessive type 4 (DKCB4) [MIM:[https://omim.org/entry/613989 613989]. A rare multisystem disorder caused by defective telomere maintenance. It is characterized by progressive bone marrow failure, and the clinical triad of reticulated skin hyperpigmentation, nail dystrophy, and mucosal leukoplakia. Common but variable features include premature graying, aplastic anemia, low platelets, osteoporosis, pulmonary fibrosis, and liver fibrosis among others. Early mortality is often associated with bone marrow failure, infections, fatal pulmonary complications, or malignancy.  Defects in TERT are a cause of susceptibility to pulmonary fibrosis idiopathic (IPF) [MIM:[https://omim.org/entry/178500 178500]. Pulmonary fibrosis is a lung disease characterized by shortness of breath, radiographically evident diffuse pulmonary infiltrates, and varying degrees of inflammation and fibrosis on biopsy. It results in acute lung injury with subsequent scarring and endstage lung disease.
 == Function ==
-[[http://www.uniprot.org/uniprot/TERT_HUMAN TERT_HUMAN]] Telomerase is a ribonucleoprotein enzyme essential for the replication of chromosome termini in most eukaryotes. Active in progenitor and cancer cells. Inactive, or very low activity, in normal somatic cells. Catalytic component of the teleromerase holoenzyme complex whose main activity is the elongation of telomeres by acting as a reverse transcriptase that adds simple sequence repeats to chromosome ends by copying a template sequence within the RNA component of the enzyme. Catalyzes the RNA-dependent extension of 3'-chromosomal termini with the 6-nucleotide telomeric repeat unit, 5'-TTAGGG-3'. The catalytic cycle involves primer binding, primer extension and release of product once the template boundary has been reached or nascent product translocation followed by further extension. More active on substrates containing 2 or 3 telomeric repeats. Telomerase activity is regulated by a number of factors including telomerase complex-associated proteins, chaperones and polypeptide modifiers. Modulates Wnt signaling. Plays important roles in aging and antiapoptosis.<ref>PMID:9389643</ref> <ref>PMID:14963003</ref> <ref>PMID:15082768</ref> <ref>PMID:15857955</ref> <ref>PMID:17026956</ref> <ref>PMID:17548608</ref> <ref>PMID:17296728</ref> <ref>PMID:17264120</ref> <ref>PMID:19188162</ref> <ref>PMID:19567472</ref> <ref>PMID:19571879</ref> <ref>PMID:19777057</ref>
+[https://www.uniprot.org/uniprot/TERT_HUMAN TERT_HUMAN] Telomerase is a ribonucleoprotein enzyme essential for the replication of chromosome termini in most eukaryotes. Active in progenitor and cancer cells. Inactive, or very low activity, in normal somatic cells. Catalytic component of the teleromerase holoenzyme complex whose main activity is the elongation of telomeres by acting as a reverse transcriptase that adds simple sequence repeats to chromosome ends by copying a template sequence within the RNA component of the enzyme. Catalyzes the RNA-dependent extension of 3'-chromosomal termini with the 6-nucleotide telomeric repeat unit, 5'-TTAGGG-3'. The catalytic cycle involves primer binding, primer extension and release of product once the template boundary has been reached or nascent product translocation followed by further extension. More active on substrates containing 2 or 3 telomeric repeats. Telomerase activity is regulated by a number of factors including telomerase complex-associated proteins, chaperones and polypeptide modifiers. Modulates Wnt signaling. Plays important roles in aging and antiapoptosis.<ref>PMID:9389643</ref> <ref>PMID:14963003</ref> <ref>PMID:15082768</ref> <ref>PMID:15857955</ref> <ref>PMID:17026956</ref> <ref>PMID:17548608</ref> <ref>PMID:17296728</ref> <ref>PMID:17264120</ref> <ref>PMID:19188162</ref> <ref>PMID:19567472</ref> <ref>PMID:19571879</ref> <ref>PMID:19777057</ref>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Naturally occurring mutations in the ribonucleoprotein reverse transcriptase, telomerase, are associated with the bone marrow failure syndromes dyskeratosis congenita (DKC), aplastic anemia (AA), and idiopathic pulmonary fibrosis (IPF). However, the mechanism by which these mutations impact telomerase function remains unknown. Here we present the structure of the human telomerase c-terminal extension (CTE or thumb domain) determined by the method of single-wavelength anomalous diffraction (SAD) to 2.31 A resolution. We also used direct telomerase activity and nucleic acid binding assays to explain how naturally occurring mutations within this portion of telomerase contribute to human disease. The single mutations localize within three highly conserved regions of the telomerase thumb domain referred to as motifs E-I, (thumb loop and helix) E-II and E-III (the FVYL pocket, comprising the hydrophobic residues F1012, V1025, Y1089 and L1092). Biochemical data shows that the mutations associated with DKC, AA and IFP disrupt the binding between telomerases protein subunit reverse transcriptase (TERT) and its nucleic acid substrates leading to loss of telomerase activity and processivity. Collectively our data shows that although these mutations do not alter the overall stability or expression of TERT, these rare genetic disorders are associated with an impaired telomerase holoenzyme that is unable to correctly assemble with its nucleic acid substrates, leading to incomplete telomere extension and telomere attrition, which are hallmarks of these diseases.
-Structural Analysis Reveals the Deleterious Effects of Telomerase Mutations in Telomerase-Associated Bone Marrow Failure Syndromes.,Hoffman H, Rice C, Skordalakes E J Biol Chem. 2017 Feb 1. pii: jbc.M116.771204. doi: 10.1074/jbc.M116.771204. PMID:28154186<ref>PMID:28154186</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 5ugw" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Telomerase|Telomerase]]
+*[[Telomerase 3D structures|Telomerase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: RNA-directed DNA polymerase]]
+[[Category: Hoffman H]]
-[[Category: Hoffman, H]]
+[[Category: Skordalakes E]]
-[[Category: Skordalakes, E]]
-[[Category: Reverse transcriptase]]
-[[Category: Telomerase]]
-[[Category: Thumb domain]]
-[[Category: Transferase]]