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PubMed:12207025 JSONTXT

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Test-Species-PubTator

Id Subject Object Predicate Lexical cue resolved_to
2 99-103 Chemical denotes Mn2+ -
3 108-118 Chemical denotes isocitrate MESH:C034219
32 251-254 Gene denotes IDH 3417
33 271-275 Chemical denotes Mn2+ -
34 280-290 Chemical denotes isocitrate MESH:C034219
35 357-373 Species denotes Escherichia coli 562
36 451-459 Gene denotes thrombin 2147
37 573-581 Chemical denotes selenium MESH:D012643
38 610-626 Chemical denotes selenomethionine MESH:D012645
39 667-676 Gene denotes NADP+-IDH 3417
40 750-753 Gene denotes IDH 3417
41 759-766 Species denotes E. coli 562
42 771-788 Species denotes Bacillus subtilis 1423
43 844-853 Species denotes mammalian 9606
44 925-928 Gene denotes IDH 3417
45 1050-1059 Species denotes mammalian 9606
46 1069-1072 Gene denotes IDH 3417
47 1189-1196 Species denotes E. coli 562
48 1202-1213 Species denotes B. subtilis 1423
49 1214-1217 Gene denotes IDH 3417
50 1279-1288 Species denotes mammalian 9606
51 1334-1338 Chemical denotes Mn2+ -
52 1339-1349 Chemical denotes isocitrate MESH:C034219
53 1436-1439 Gene denotes IDH 3417
54 1468-1472 Chemical denotes Mn2+ -
55 1479-1487 Chemical denotes hydroxyl MESH:D017665
56 1491-1501 Chemical denotes isocitrate MESH:C034219
57 1531-1536 Chemical denotes NADP+ MESH:D009249
58 1607-1612 Chemical denotes water MESH:D014867
59 1732-1737 Chemical denotes water MESH:D014867

Test-Species-PubDictionaries

Id Subject Object Predicate Lexical cue db_id
T1 357-373 OrganismTaxon denotes Escherichia coli 562
T2 759-766 OrganismTaxon denotes E. coli 562
T3 771-788 OrganismTaxon denotes Bacillus subtilis 1423
T4 844-853 OrganismTaxon denotes mammalian 40674
T5 1050-1059 OrganismTaxon denotes mammalian 40674
T6 1189-1196 OrganismTaxon denotes E. coli 562
T7 1279-1288 OrganismTaxon denotes mammalian 40674

Test-Species-PubDictionaries-PubMedBERT

Id Subject Object Predicate Lexical cue db_id
T1 21-28 Species denotes porcine 9823
T2 181-188 Species denotes porcine 9823
T3 357-373 Species denotes Escherichia coli 562
T4 659-666 Species denotes porcine 9823
T5 759-766 Species denotes E. coli 562
T6 771-788 Species denotes Bacillus subtilis 1423
T7 844-853 Species denotes mammalian 40674
T8 866-873 Species denotes porcine 9823
T9 1050-1059 Species denotes mammalian 40674
T10 1180-1187 Species denotes porcine 9823
T11 1189-1196 Species denotes E. coli 562
T12 1205-1213 Species denotes subtilis 1423
T13 1279-1288 Species denotes mammalian 40674

sentences

Id Subject Object Predicate Lexical cue
T1 0-119 Sentence denotes Crystal structure of porcine mitochondrial NADP+-dependent isocitrate dehydrogenase complexed with Mn2+ and isocitrate.
T2 120-155 Sentence denotes Insights into the enzyme mechanism.
T3 156-328 Sentence denotes The crystal structure of porcine heart mitochondrial NADP+-dependent isocitrate dehydrogenase (IDH) complexed with Mn2+ and isocitrate was solved to a resolution of 1.85 A.
T4 329-488 Sentence denotes The enzyme was expressed in Escherichia coli, purified as a fusion protein with maltose binding protein, and cleaved with thrombin to yield homogeneous enzyme.
T5 489-654 Sentence denotes The structure was determined by multiwavelength anomalous diffraction phasing using selenium substitution in the form of selenomethionine as the anomalous scatterer.
T6 655-861 Sentence denotes The porcine NADP+-IDH enzyme is structurally compared with the previously solved structures of IDH from E. coli and Bacillus subtilis that share 16 and 17% identity, respectively, with the mammalian enzyme.
T7 862-983 Sentence denotes The porcine enzyme has a protein fold similar to the bacterial IDH structures with each monomer folding into two domains.
T8 984-1120 Sentence denotes However, considerable differences exist between the bacterial and mammalian forms of IDH in regions connecting core secondary structure.
T9 1121-1296 Sentence denotes Based on the alignment of sequence and structure among the porcine, E. coli, and B. subtilis IDH, a putative phosphorylation site has been identified for the mammalian enzyme.
T10 1297-1421 Sentence denotes The active site, including the bound Mn2+-isocitrate complex, is highly ordered and, therefore, mechanistically informative.
T11 1422-1557 Sentence denotes The consensus IDH mechanism predicts that the Mn2+-bound hydroxyl of isocitrate is deprotonated prior to its NADP+-dependent oxidation.
T12 1558-1738 Sentence denotes The present crystal structure has an active site water that is well positioned to accept the proton and ultimately transfer the proton to solvent through an additional bound water.

Glycosmos6-MAT

Id Subject Object Predicate Lexical cue
T1 189-194 http://purl.obolibrary.org/obo/MAT_0000036 denotes heart

GlyCosmos15-Glycan

Id Subject Object Predicate Lexical cue image
T1 409-416 Glycan denotes maltose https://api.glycosmos.org/wurcs2image/latest/png/binary/G44653LT

mondo_disease

Id Subject Object Predicate Lexical cue mondo_id
T1 251-254 Disease denotes IDH http://purl.obolibrary.org/obo/MONDO_0017326
T2 673-676 Disease denotes IDH http://purl.obolibrary.org/obo/MONDO_0017326
T3 750-753 Disease denotes IDH http://purl.obolibrary.org/obo/MONDO_0017326
T4 925-928 Disease denotes IDH http://purl.obolibrary.org/obo/MONDO_0017326
T5 1069-1072 Disease denotes IDH http://purl.obolibrary.org/obo/MONDO_0017326
T6 1214-1217 Disease denotes IDH http://purl.obolibrary.org/obo/MONDO_0017326
T7 1436-1439 Disease denotes IDH http://purl.obolibrary.org/obo/MONDO_0017326

Glycan-GlyCosmos

Id Subject Object Predicate Lexical cue image
T1 409-416 Glycan denotes maltose https://api.glycosmos.org/wurcs2image/latest/png/binary/G44653LT

Organism-PubDic

Id Subject Object Predicate Lexical cue db_id
T1 357-373 Species denotes Escherichia coli 562
T2 759-766 Species denotes E. coli 562
T3 771-788 Species denotes Bacillus subtilis 1423
T4 844-853 Species denotes mammalian 40674
T5 1050-1059 Species denotes mammalian 40674
T6 1189-1196 Species denotes E. coli 562
T7 1279-1288 Species denotes mammalian 40674

Organism-PubTator

Id Subject Object Predicate Lexical cue db_id
35 357-373 Species denotes Escherichia coli 562
41 759-766 Species denotes E. coli 562
42 771-788 Species denotes Bacillus subtilis 1423
43 844-853 Species denotes mammalian 9606
45 1050-1059 Species denotes mammalian 9606
47 1189-1196 Species denotes E. coli 562
48 1202-1213 Species denotes B. subtilis 1423
50 1279-1288 Species denotes mammalian 9606

Organism-PubDic-Bert-9

Id Subject Object Predicate Lexical cue db_id
T1 357-373 Species denotes Escherichia coli 562
T2 759-766 Species denotes E. coli 562
T3 771-788 Species denotes Bacillus subtilis 1423
T4 844-853 Species denotes mammalian 40674
T5 1050-1059 Species denotes mammalian 40674
T6 1189-1196 Species denotes E. coli 562
T7 1279-1288 Species denotes mammalian 40674

Organism-PubDic-Bert-8

Id Subject Object Predicate Lexical cue db_id
T1 21-28 Species denotes porcine 9823
T2 181-188 Species denotes porcine 9823
T3 357-373 Species denotes Escherichia coli 562
T4 659-666 Species denotes porcine 9823
T5 759-766 Species denotes E. coli 562
T6 771-788 Species denotes Bacillus subtilis 1423
T7 844-853 Species denotes mammalian 40674
T8 866-873 Species denotes porcine 9823
T9 1050-1059 Species denotes mammalian 40674
T10 1180-1187 Species denotes porcine 9823
T11 1189-1196 Species denotes E. coli 562
T12 1205-1213 Species denotes subtilis 1423
T13 1279-1288 Species denotes mammalian 40674

Organism-Gold

Id Subject Object Predicate Lexical cue db_id
T1 357-373 Species denotes Escherichia coli 562
T2 759-766 Species denotes E. coli 562
T3 771-788 Species denotes Bacillus subtilis 1423
T4 844-853 Species denotes mammalian 40674
T5 1050-1059 Species denotes mammalian 40674
T6 1189-1196 Species denotes E. coli 562
T7 1279-1288 Species denotes mammalian 40674
T8 1202-1213 Species denotes B. subtilis 1423

GlyCosmos15-Taxon

Id Subject Object Predicate Lexical cue db_id
T1 357-373 Organism denotes Escherichia coli 562
T2 759-766 Organism denotes E. coli 562
T3 771-788 Organism denotes Bacillus subtilis 1423
T4 844-853 Organism denotes mammalian 40674
T5 1050-1059 Organism denotes mammalian 40674
T6 1189-1196 Organism denotes E. coli 562
T7 1279-1288 Organism denotes mammalian 40674

GlyCosmos15-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 189-194 Body_part denotes heart http://purl.obolibrary.org/obo/UBERON_0000948|http://purl.obolibrary.org/obo/UBERON_0007100|http://purl.obolibrary.org/obo/UBERON_0015228|http://purl.obolibrary.org/obo/UBERON_0015230

GlyCosmos15-Sentences

Id Subject Object Predicate Lexical cue
T1 0-119 Sentence denotes Crystal structure of porcine mitochondrial NADP+-dependent isocitrate dehydrogenase complexed with Mn2+ and isocitrate.
T2 120-155 Sentence denotes Insights into the enzyme mechanism.
T3 156-488 Sentence denotes The crystal structure of porcine heart mitochondrial NADP+-dependent isocitrate dehydrogenase (IDH) complexed with Mn2+ and isocitrate was solved to a resolution of 1.85 A. The enzyme was expressed in Escherichia coli, purified as a fusion protein with maltose binding protein, and cleaved with thrombin to yield homogeneous enzyme.
T4 489-654 Sentence denotes The structure was determined by multiwavelength anomalous diffraction phasing using selenium substitution in the form of selenomethionine as the anomalous scatterer.
T5 655-861 Sentence denotes The porcine NADP+-IDH enzyme is structurally compared with the previously solved structures of IDH from E. coli and Bacillus subtilis that share 16 and 17% identity, respectively, with the mammalian enzyme.
T6 862-983 Sentence denotes The porcine enzyme has a protein fold similar to the bacterial IDH structures with each monomer folding into two domains.
T7 984-1120 Sentence denotes However, considerable differences exist between the bacterial and mammalian forms of IDH in regions connecting core secondary structure.
T8 1121-1296 Sentence denotes Based on the alignment of sequence and structure among the porcine, E. coli, and B. subtilis IDH, a putative phosphorylation site has been identified for the mammalian enzyme.
T9 1297-1421 Sentence denotes The active site, including the bound Mn2+-isocitrate complex, is highly ordered and, therefore, mechanistically informative.
T10 1422-1557 Sentence denotes The consensus IDH mechanism predicts that the Mn2+-bound hydroxyl of isocitrate is deprotonated prior to its NADP+-dependent oxidation.
T11 1558-1738 Sentence denotes The present crystal structure has an active site water that is well positioned to accept the proton and ultimately transfer the proton to solvent through an additional bound water.

GlyCosmos15-FMA

Id Subject Object Predicate Lexical cue db_id
T1 189-194 Body_part denotes heart FMA:7088

GlyCosmos15-MAT

Id Subject Object Predicate Lexical cue mat_id
T1 189-194 Body_part denotes heart http://purl.obolibrary.org/obo/MAT_0000036

NCBITAXON

Id Subject Object Predicate Lexical cue db_id
T1 357-373 OrganismTaxon denotes Escherichia coli 562
T2 759-766 OrganismTaxon denotes E. coli 562
T3 771-788 OrganismTaxon denotes Bacillus subtilis 1423
T4 1189-1196 OrganismTaxon denotes E. coli 562

Anatomy-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 189-194 Body_part denotes heart http://purl.obolibrary.org/obo/UBERON_0000948|http://purl.obolibrary.org/obo/UBERON_0007100|http://purl.obolibrary.org/obo/UBERON_0015228|http://purl.obolibrary.org/obo/UBERON_0015230

Anatomy-MAT

Id Subject Object Predicate Lexical cue mat_id
T1 189-194 Body_part denotes heart http://purl.obolibrary.org/obo/MAT_0000036