Triose Phosphate Isomerase - Revision history

Michal Harel at 10:55, 8 March 2020

2020-03-08T10:55:08Z

←Older revision		Revision as of 10:55, 8 March 2020
Line 105:		Line 105:

	</StructureSection>		</StructureSection>
-	== 3D Structures of triose phosphate isomerase==

-	Updated on {{REVISIONDAY2}}-{{MONTHNAME\|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
-	{{#tree:id=OrganizedByTopic\|openlevels=0\|
-
-	*TIM
-
-	**[[1wyi]], [[1hti]], [[2jk2]], [[4br1]], [[4poc]], [[6d43]] – hTIM - human<br />
-	**[[2vom]], [[4pod]], [[4unk]], [[4unl]], [[4zvj]], [[6c2g]], [[6nlh]] – hTIM (mutant)<br />
-	**[[1r2r]], [[1r2s]], [[1r2t]] – rTIM – rabbit<br />
-	**[[8tim]], [[1tim]], [[1tpb]], [[1tpc]], [[1tpw]] – cTIM – chicken<br />
-	**[[1spq]], [[1sq7]], [[1ssd]], [[1ssg]], [[1su5]], [[1sw0]], [[1sw3]], [[1sw7]], [[1tpu]], [[1tpv]], [[4p61]] - cTIM (mutant) <br />
-	**[[4ohq]], [[4obt]] – AtTIM – ''Arabidopsis thaliana''<br />
-	**[[6nxq]], [[6nxr]], [[6nxs]], [[6nxw]], [[6nxx]], [[6nxy]] – AtTIM (mutant)<br />
-	**[[6cg9]] – TIM – maize<br />
-	**[[1ypi]], [[3ypi]] - yTIM - yeast<br />
-	**[[1i45]], [[4ff7]] – yTIM (mutant)<br />
-	**[[1tmh]] – EcTIM/cTIM – ''Escherichia coli''<br />
-	**[[1tre]], [[4k6a]], [[4iot]] - EcTIM<br />
-	**[[1amk]] – LmTIM – ''Leishmania mexicana''<br />
-	**[[1qds]] - LmTIM (mutant) <br />
-	**[[1dkw]], [[1ml1]], [[1mss]], [[1tpd]], [[1tpe]], [[1tpf]], [[1trd]], [[2v5l]], [[3tim]] - TbTIM – ''Trypanosoma brucei''<br />
-	**[[2j27]], [[1kv5]], [[2j24]], [[2v0t]], [[2v2c]], [[2v2d]], [[2v2h]], [[2y6z]], [[2y70]], [[5i3f]], [[5i3g]], [[5i3h]], [[5i3j]], [[5i3i]], [[5i3k]] - TbTIM (mutant) <br />
-	**[[1ci1]], [[1tcd]] - TcTIM – ''Trypanosoma cruzi''<br />
-	**[[4hhp]], [[4jeq]] – TcTIM (mutant)<br />
-	**[[3q37]] – TcTIM/TbTIM<br />
-	**[[1mo0]] – TIM – ''Caenorhabditis elegans''<br />
-	**[[1m6j]] – TIM – ''Entamoeba histolytica''<br />
-	**[[1ydv]] – PfTIM – ''Plasmodium falciparum''<br />
-	**[[1vga]], [[2vfd]], [[2vff]], [[3psv]], [[3psw]], [[3pwa]], [[3py2]], [[5gzp]], [[5gv4]], [[5brb]], [[5bnk]], [[5bmw]], [[5bmx]], [[4zz9]], [[4z0j]], [[4z0s]], [[4yxg]], [[4ywi]] – PfTIM (mutant) <br />
-	**[[1w0m]] – TIM – ''Thermoproteus tenax''<br />
-	**[[2btm]] – GsTIM – ''Geobacillus stearothermophilus''<br />
-	**[[2dp3]], [[3pf3]], [[4bi5]] - GiTIM (mutant) – ''Giardia intestinalis''<br />
-	**[[2h6r]]– TIM – ''Methanocaldococcus jannaschii''<br />
-	**[[2jgq]] – TIM – ''Helicobacter pylori''<br />
-	**[[3gvg]], [[3ta6]] – MtTIM – ''Mycobacterium tuberculosis''<br />
-	**[[3kxq]] – TIM – ''Bartonella henselae''<br />
-	**[[3m9y]], [[3uwy]] – SaTIM – ''Staphylococcus aureus''<br />
-	**[[4g1k]] – TIM – ''Burkholderia thailandensis''<br />
-	**[[4nvt]] – TIM – ''Brucella melitensis''<br />
-	**[[5ibx]] – TIM – ''Streptococcus pneumoniae''<br />
-	**[[5csr]] – TaTIM – ''Thermoplasma acidophilum''<br />
-	**[[4y9a]] – TIM – ''Streptomyces coelicolor''<br />
-	**[[4y96]] – TIM – ''Gemmata obscuriglobus''<br />
-	**[[4y90]] – TIM – ''Deinococcus radiodurans''<br />
-	**[[4y8f]] – TIM – ''Clostridium perfringens''<br />
-	**[[4x22]] - LiTIM – ''Leptospira interrogans''<br />
-	**[[4mkn]] - TIM – ''Chlamydomonas reinhardtii''<br />
-
-	*TIM binary complexes with phosphoglycolate
-
-	**[[6oog]] - TIM + 2-phosphoglycolate – pork tapeworm<br />
-	**[[2ypi]] - yTIM + 2-phosphoglycolate<br />
-	**[[1aw1]] – MmTIM + 2-phosphoglycolate – ''Moritella marina''<br />
-	**[[1btm]] - GsTIM + 2-phosphoglycolate<br />
-	**[[1n55]] - LmTIM (mutant) + 2-phosphoglycolate<br />
-	**[[3pvf]] - PfTIM (mutant) + 2-phosphoglycolate<br />
-	**[[1lyx]], [[1lzo]] - PfTIM + 2-phosphoglycolate<br />
-	**[[4bi7]], [[4bi6]] - GiTIM (mutant) + 2-phosphoglycolate<br />
-	**[[6ooi]] - TIM + 2-phosphoglycolate – ''Schistosoma mansoni''<br />
-	**[[6bve]] - TIM + 2-phosphoglycolate – ''Synechocystis''<br />
-
-	*TIM binary complexes with phosphoglycerate
-
-	**[[1iih]], [[4tim]], [[5tim]], [[6tim]] - TbTIM + phosphoglycerate<br />
-	**[[1o5x]], [[1woa]], [[2vfe]], [[2vfg]], [[2vfh]], [[2vfi]] - PfTIM (mutant) + 3-phosphoglycerate<br />
-	**[[1m7o]], [[1m7p]] - PfTIM + 3-phosphoglycerate<br />
-	**[[3uwu]], [[3uwv]], [[3uww]], [[3uwz]] - SaTIM + 3-phosphoglycerate<br />
-	**[[5css]] - TaTIM + 3-phosphoglycerate<br />
-
-	*TIM binary complexes with phosphoglycohydroxamate
-
-	**[[1tph]] – cTIM + phosphoglycohydroxamate<br />
-	**[[7tim]] - yTIM + phosphoglycohydroxamate<br />
-	**[[2vxn]] - LmTIM (mutant) + phosphoglycohydroxamate<br />
-	**[[3tao]] - MtTIM + phosphoglycohydroxamate<br />
-
-	*Other TIM binary complexes
-
-	**[[4owg]] – rTIM + phosphoenolpyruvate<br />
-	**[[1ney]]– yTIM + dihydroxyacetonephosphate<br />
-	**[[1nf0]] – yTIM (mutant) + dihydroxyacetonephosphate<br />
-	**[[1aw2]] – MmTIM + sulfate<br />
-	**[[1hg3]] – TIM + carboxyethylphosphonate – ''Pyrococcus woesei''<br />
-	**[[1if2]] – LmTIM + IPP<br />
-	**[[2y61]], [[2y62]] - LmTIM (mutant) + glycidol phosphate<br />
-	**[[2y63]] - LmTIM (mutant) + hydroxyacetonephosphate<br />
-	**[[1ag1]] – TbTIM + phosphate<br />
-	**[[1iig]] - TbTIM + 3-phosphonopropionate<br />
-	**[[1tsi]] – TbTIM + phosphonobutanamide<br />
-	**[[4ymz]] - LiTIM + dihydroxyacetonephosphate <br />
-	**[[5ujw]] – TIM + dihydroxyacetonephosphate – ''Francisella tularensis''<br />
-	**[[1wob]] - PfTIM (mutant) + sulfate<br />
-	**[[1sux]] – TcTIM + sulfonic acid derivative<br />
-	**[[2oma]] – TcTIM + dithiobenzylamine<br />
-	**[[4mva]] – EcTIM + acetyl phosphate<br />
-
-	*MonoTIM – stable monomeric variant of TIM
-
-	**[[2wsq]], [[2wsr]], [[1tti]], [[1ttj]], [[2vek]], [[2vel]], [[2vem]], [[2ven]], [[2x16]], [[2x1r]], [[2x1s]], [[2x1t]], [[2x1u]], [[2x2g]] – TbMonoTIM (mutant) <br />
-	**[[1tri]], [[2vei]] – TbMonoTIM<br />
-	**[[2v5b]] - TcMonoTIM
-	}}
	== Additional Resources ==		== Additional Resources ==
	*[[Carbohydrate Metabolism]]		*[[Carbohydrate Metabolism]]

Michal Harel at 10:53, 8 March 2020

2020-03-08T10:53:42Z

←Older revision		Revision as of 10:53, 8 March 2020
Line 101:		Line 101:

	One specific example of sequence homology is that of loop 6 and loop 7 residues, whose structural contributions are discussed above. In a sequence alignment of 133 TIM sequences, two highly conserved motifs are noticed. First, 114 sequences in loop 6 contain the PXW sequence family (where X is I,L or V in 112 sequences or otherwise a T or K). Secondly, loop 7 contains a highly conserved YGGS motif; however, this motif is only found when the N-terminal hinge contains tryptophan.		One specific example of sequence homology is that of loop 6 and loop 7 residues, whose structural contributions are discussed above. In a sequence alignment of 133 TIM sequences, two highly conserved motifs are noticed. First, 114 sequences in loop 6 contain the PXW sequence family (where X is I,L or V in 112 sequences or otherwise a T or K). Secondly, loop 7 contains a highly conserved YGGS motif; however, this motif is only found when the N-terminal hinge contains tryptophan.
		+	== 3D Structures of triose phosphate isomerase==
		+	[[Triose phosphate isomerase 3D structures]]
		+
	</StructureSection>		</StructureSection>
	== 3D Structures of triose phosphate isomerase==		== 3D Structures of triose phosphate isomerase==
Line 109:		Line 112:
	*TIM		*TIM

		+	**[[1wyi]], [[1hti]], [[2jk2]], [[4br1]], [[4poc]], [[6d43]] – hTIM - human<br />
		+	**[[2vom]], [[4pod]], [[4unk]], [[4unl]], [[4zvj]], [[6c2g]], [[6nlh]] – hTIM (mutant)<br />
		+	**[[1r2r]], [[1r2s]], [[1r2t]] – rTIM – rabbit<br />
	**[[8tim]], [[1tim]], [[1tpb]], [[1tpc]], [[1tpw]] – cTIM – chicken<br />		**[[8tim]], [[1tim]], [[1tpb]], [[1tpc]], [[1tpw]] – cTIM – chicken<br />
	**[[1spq]], [[1sq7]], [[1ssd]], [[1ssg]], [[1su5]], [[1sw0]], [[1sw3]], [[1sw7]], [[1tpu]], [[1tpv]], [[4p61]] - cTIM (mutant) <br />		**[[1spq]], [[1sq7]], [[1ssd]], [[1ssg]], [[1su5]], [[1sw0]], [[1sw3]], [[1sw7]], [[1tpu]], [[1tpv]], [[4p61]] - cTIM (mutant) <br />
		+	**[[4ohq]], [[4obt]] – AtTIM – ''Arabidopsis thaliana''<br />
		+	**[[6nxq]], [[6nxr]], [[6nxs]], [[6nxw]], [[6nxx]], [[6nxy]] – AtTIM (mutant)<br />
		+	**[[6cg9]] – TIM – maize<br />
		+	**[[1ypi]], [[3ypi]] - yTIM - yeast<br />
		+	**[[1i45]], [[4ff7]] – yTIM (mutant)<br />
	**[[1tmh]] – EcTIM/cTIM – ''Escherichia coli''<br />		**[[1tmh]] – EcTIM/cTIM – ''Escherichia coli''<br />
	**[[1tre]], [[4k6a]], [[4iot]] - EcTIM<br />		**[[1tre]], [[4k6a]], [[4iot]] - EcTIM<br />
	**[[1amk]] – LmTIM – ''Leishmania mexicana''<br />		**[[1amk]] – LmTIM – ''Leishmania mexicana''<br />
	**[[1qds]] - LmTIM (mutant) <br />		**[[1qds]] - LmTIM (mutant) <br />
-	**[[~~1wyi~~]], [[~~1hti~~]], [[~~2jk2~~]], [[~~4br1~~]], [[~~4poc~~]], [[~~6d43]] – hTIM - human<br />~~	+	**[[1dkw]], [[1ml1]], [[1mss]], [[1tpd]], [[1tpe]], [[1tpf]], [[1trd]], [[2v5l]], [[3tim]] - TbTIM – ''Trypanosoma brucei''<br />
-	**[[2vom]], [[~~4pod~~]], [[~~4unk~~]], [[~~4unl]], [[4zvj]], [[6c2g~~]] – ~~hTIM (mutant)~~<br />	+	**[[2j27]], [[1kv5]], [[2j24]], [[2v0t]], [[2v2c]], [[2v2d]], [[2v2h]], [[2y6z]], [[2y70]], [[5i3f]], [[5i3g]], [[5i3h]], [[5i3j]], [[5i3i]], [[5i3k]] - TbTIM (mutant) <br />
-	**[[2j27]], [[1kv5]], [[2j24]], [[2v0t]], [[2v2c]], [[2v2d]], [[2v2h]], [[2y6z]], [[2y70]], [[5i3f]], [[5i3g]], [[5i3h]], [[5i3j]], [[5i3i]], [[5i3k]] - TbTIM (mutant) ~~– ''Trypanosoma brucei''~~<br />	+
-	**[[1dkw]], [[1ml1]], [[1mss]], [[1tpd]], [[1tpe]], [[1tpf]], [[1trd]], [[2v5l]], [[3tim]] - TbTIM	+
	**[[1ci1]], [[1tcd]] - TcTIM – ''Trypanosoma cruzi''<br />		**[[1ci1]], [[1tcd]] - TcTIM – ''Trypanosoma cruzi''<br />
	**[[4hhp]], [[4jeq]] – TcTIM (mutant)<br />		**[[4hhp]], [[4jeq]] – TcTIM (mutant)<br />
	**[[3q37]] – TcTIM/TbTIM<br />		**[[3q37]] – TcTIM/TbTIM<br />
	**[[1mo0]] – TIM – ''Caenorhabditis elegans''<br />		**[[1mo0]] – TIM – ''Caenorhabditis elegans''<br />
-	**[[1i45]], [[4ff7]] – yTIM (mutant) – yeast<br />
-	**[[1ypi]], [[3ypi]] - yTIM<br />
	**[[1m6j]] – TIM – ''Entamoeba histolytica''<br />		**[[1m6j]] – TIM – ''Entamoeba histolytica''<br />
-	**[[1r2r]], [[1r2s]], [[1r2t]] – rTIM – rabbit<br />
	**[[1ydv]] – PfTIM – ''Plasmodium falciparum''<br />		**[[1ydv]] – PfTIM – ''Plasmodium falciparum''<br />
	**[[1vga]], [[2vfd]], [[2vff]], [[3psv]], [[3psw]], [[3pwa]], [[3py2]], [[5gzp]], [[5gv4]], [[5brb]], [[5bnk]], [[5bmw]], [[5bmx]], [[4zz9]], [[4z0j]], [[4z0s]], [[4yxg]], [[4ywi]] – PfTIM (mutant) <br />		**[[1vga]], [[2vfd]], [[2vff]], [[3psv]], [[3psw]], [[3pwa]], [[3py2]], [[5gzp]], [[5gv4]], [[5brb]], [[5bnk]], [[5bmw]], [[5bmx]], [[4zz9]], [[4z0j]], [[4z0s]], [[4yxg]], [[4ywi]] – PfTIM (mutant) <br />
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	**[[4g1k]] – TIM – ''Burkholderia thailandensis''<br />		**[[4g1k]] – TIM – ''Burkholderia thailandensis''<br />
	**[[4nvt]] – TIM – ''Brucella melitensis''<br />		**[[4nvt]] – TIM – ''Brucella melitensis''<br />
-	**[[4ohq]], [[4obt]] – TIM – ''Arabidopsis thaliana''<br />
	**[[5ibx]] – TIM – ''Streptococcus pneumoniae''<br />		**[[5ibx]] – TIM – ''Streptococcus pneumoniae''<br />
	**[[5csr]] – TaTIM – ''Thermoplasma acidophilum''<br />		**[[5csr]] – TaTIM – ''Thermoplasma acidophilum''<br />
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	**[[4y8f]] – TIM – ''Clostridium perfringens''<br />		**[[4y8f]] – TIM – ''Clostridium perfringens''<br />
	**[[4x22]] - LiTIM – ''Leptospira interrogans''<br />		**[[4x22]] - LiTIM – ''Leptospira interrogans''<br />
		+	**[[4mkn]] - TIM – ''Chlamydomonas reinhardtii''<br />

	*TIM binary complexes with phosphoglycolate		*TIM binary complexes with phosphoglycolate

		+	**[[6oog]] - TIM + 2-phosphoglycolate – pork tapeworm<br />
	**[[2ypi]] - yTIM + 2-phosphoglycolate<br />		**[[2ypi]] - yTIM + 2-phosphoglycolate<br />
	**[[1aw1]] – MmTIM + 2-phosphoglycolate – ''Moritella marina''<br />		**[[1aw1]] – MmTIM + 2-phosphoglycolate – ''Moritella marina''<br />
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	**[[1lyx]], [[1lzo]] - PfTIM + 2-phosphoglycolate<br />		**[[1lyx]], [[1lzo]] - PfTIM + 2-phosphoglycolate<br />
	**[[4bi7]], [[4bi6]] - GiTIM (mutant) + 2-phosphoglycolate<br />		**[[4bi7]], [[4bi6]] - GiTIM (mutant) + 2-phosphoglycolate<br />
		+	**[[6ooi]] - TIM + 2-phosphoglycolate – ''Schistosoma mansoni''<br />
		+	**[[6bve]] - TIM + 2-phosphoglycolate – ''Synechocystis''<br />

	*TIM binary complexes with phosphoglycerate		*TIM binary complexes with phosphoglycerate
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	*TIM binary complexes with phosphoglycohydroxamate		*TIM binary complexes with phosphoglycohydroxamate

-	**[[2vxn]] - LmTIM (mutant) + phosphoglycohydroxamate<br />
	**[[1tph]] – cTIM + phosphoglycohydroxamate<br />		**[[1tph]] – cTIM + phosphoglycohydroxamate<br />
-	**[[3tao]] - MtTIM + phosphoglycohydroxamate<br />
	**[[7tim]] - yTIM + phosphoglycohydroxamate<br />		**[[7tim]] - yTIM + phosphoglycohydroxamate<br />
		+	**[[2vxn]] - LmTIM (mutant) + phosphoglycohydroxamate<br />
		+	**[[3tao]] - MtTIM + phosphoglycohydroxamate<br />

	*Other TIM binary complexes		*Other TIM binary complexes

-	**[[~~1ag1~~]] – ~~TbTIM~~ + ~~phosphate~~<br />	+	**[[4owg]] – rTIM + phosphoenolpyruvate<br />
		+	**[[1ney]]– yTIM + dihydroxyacetonephosphate<br />
		+	**[[1nf0]] – yTIM (mutant) + dihydroxyacetonephosphate<br />
	**[[1aw2]] – MmTIM + sulfate<br />		**[[1aw2]] – MmTIM + sulfate<br />
	**[[1hg3]] – TIM + carboxyethylphosphonate – ''Pyrococcus woesei''<br />		**[[1hg3]] – TIM + carboxyethylphosphonate – ''Pyrococcus woesei''<br />
Line 181:		Line 192:
	**[[2y61]], [[2y62]] - LmTIM (mutant) + glycidol phosphate<br />		**[[2y61]], [[2y62]] - LmTIM (mutant) + glycidol phosphate<br />
	**[[2y63]] - LmTIM (mutant) + hydroxyacetonephosphate<br />		**[[2y63]] - LmTIM (mutant) + hydroxyacetonephosphate<br />
		+	**[[1ag1]] – TbTIM + phosphate<br />
	**[[1iig]] - TbTIM + 3-phosphonopropionate<br />		**[[1iig]] - TbTIM + 3-phosphonopropionate<br />
	**[[1tsi]] – TbTIM + phosphonobutanamide<br />		**[[1tsi]] – TbTIM + phosphonobutanamide<br />
-	**[[1ney]]– yTIM + dihydroxyacetonephosphate<br />
-	**[[1nf0]] – yTIM (mutant) + dihydroxyacetonephosphate<br />
	**[[4ymz]] - LiTIM + dihydroxyacetonephosphate <br />		**[[4ymz]] - LiTIM + dihydroxyacetonephosphate <br />
	**[[5ujw]] – TIM + dihydroxyacetonephosphate – ''Francisella tularensis''<br />		**[[5ujw]] – TIM + dihydroxyacetonephosphate – ''Francisella tularensis''<br />
Line 191:		Line 201:
	**[[2oma]] – TcTIM + dithiobenzylamine<br />		**[[2oma]] – TcTIM + dithiobenzylamine<br />
	**[[4mva]] – EcTIM + acetyl phosphate<br />		**[[4mva]] – EcTIM + acetyl phosphate<br />
-	**[[4owg]] – rTIM + phosphoenolpyruvate<br />

	*MonoTIM – stable monomeric variant of TIM		*MonoTIM – stable monomeric variant of TIM

Michal Harel at 17:09, 27 September 2018

2018-09-27T17:09:47Z

←Older revision		Revision as of 17:09, 27 September 2018
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	**[[1amk]] – LmTIM – ''Leishmania mexicana''<br />		**[[1amk]] – LmTIM – ''Leishmania mexicana''<br />
	**[[1qds]] - LmTIM (mutant) <br />		**[[1qds]] - LmTIM (mutant) <br />
-	**[[~~2vom~~]], [[~~4pod~~]], [[~~4unk~~]], [[~~4unl~~]], [[~~4zvj~~]] – hTIM ~~(mutant) –~~ human<br />	+	**[[1wyi]], [[1hti]], [[2jk2]], [[4br1]], [[4poc]], [[6d43]] – hTIM - human<br />
-	**[[~~1wyi~~]], [[~~1hti~~]], [[~~2jk2~~]], [[~~4br1~~]], [[~~4poc~~]] – hTIM<br />	+	**[[2vom]], [[4pod]], [[4unk]], [[4unl]], [[4zvj]], [[6c2g]] – hTIM (mutant)<br />
	**[[2j27]], [[1kv5]], [[2j24]], [[2v0t]], [[2v2c]], [[2v2d]], [[2v2h]], [[2y6z]], [[2y70]], [[5i3f]], [[5i3g]], [[5i3h]], [[5i3j]], [[5i3i]], [[5i3k]] - TbTIM (mutant) – ''Trypanosoma brucei''<br />		**[[2j27]], [[1kv5]], [[2j24]], [[2v0t]], [[2v2c]], [[2v2d]], [[2v2h]], [[2y6z]], [[2y70]], [[5i3f]], [[5i3g]], [[5i3h]], [[5i3j]], [[5i3i]], [[5i3k]] - TbTIM (mutant) – ''Trypanosoma brucei''<br />
	**[[1dkw]], [[1ml1]], [[1mss]], [[1tpd]], [[1tpe]], [[1tpf]], [[1trd]], [[2v5l]], [[3tim]] - TbTIM		**[[1dkw]], [[1ml1]], [[1mss]], [[1tpd]], [[1tpe]], [[1tpf]], [[1trd]], [[2v5l]], [[3tim]] - TbTIM
Line 127:		Line 127:
	**[[1m6j]] – TIM – ''Entamoeba histolytica''<br />		**[[1m6j]] – TIM – ''Entamoeba histolytica''<br />
	**[[1r2r]], [[1r2s]], [[1r2t]] – rTIM – rabbit<br />		**[[1r2r]], [[1r2s]], [[1r2t]] – rTIM – rabbit<br />
-	**[[1vga]], [[2vfd]], [[2vff]], [[3psv]], [[3psw]], [[3pwa]], [[3py2]], [[5gzp]], [[5gv4]], [[5brb]], [[5bnk]], [[5bmw]], [[5bmx]], [[4zz9]], [[4z0j]], [[4z0s]], [[4yxg]], [[4ywi]] – PfTIM (mutant) ~~– ''Plasmodium falciparum''<br />~~	+	**[[1ydv]] – PfTIM – ''Plasmodium falciparum''<br />
-	**[[1ydv]] - PfTIM<br />	+	**[[1vga]], [[2vfd]], [[2vff]], [[3psv]], [[3psw]], [[3pwa]], [[3py2]], [[5gzp]], [[5gv4]], [[5brb]], [[5bnk]], [[5bmw]], [[5bmx]], [[4zz9]], [[4z0j]], [[4z0s]], [[4yxg]], [[4ywi]] – PfTIM (mutant) <br />
	**[[1w0m]] – TIM – ''Thermoproteus tenax''<br />		**[[1w0m]] – TIM – ''Thermoproteus tenax''<br />
	**[[2btm]] – GsTIM – ''Geobacillus stearothermophilus''<br />		**[[2btm]] – GsTIM – ''Geobacillus stearothermophilus''<br />

Michal Harel at 09:14, 12 November 2017

2017-11-12T09:14:54Z

←Older revision		Revision as of 09:14, 12 November 2017
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	**[[1amk]] – LmTIM – ''Leishmania mexicana''<br />		**[[1amk]] – LmTIM – ''Leishmania mexicana''<br />
	**[[1qds]] - LmTIM (mutant) <br />		**[[1qds]] - LmTIM (mutant) <br />
-	**[[2vom]], [[4pod]], [[4unk]], [[4unl]] – hTIM (mutant) – human<br />	+	**[[2vom]], [[4pod]], [[4unk]], [[4unl]], [[4zvj]] – hTIM (mutant) – human<br />
	**[[1wyi]], [[1hti]], [[2jk2]], [[4br1]], [[4poc]] – hTIM<br />		**[[1wyi]], [[1hti]], [[2jk2]], [[4br1]], [[4poc]] – hTIM<br />
-	**[[2j27]], [[1kv5]], [[2j24]], [[2v0t]], [[2v2c]], [[2v2d]], [[2v2h]], [[2y6z]], [[2y70]] - TbTIM (mutant) – ''Trypanosoma brucei''<br />	+	**[[2j27]], [[1kv5]], [[2j24]], [[2v0t]], [[2v2c]], [[2v2d]], [[2v2h]], [[2y6z]], [[2y70]], [[5i3f]], [[5i3g]], [[5i3h]], [[5i3j]], [[5i3i]], [[5i3k]] - TbTIM (mutant) – ''Trypanosoma brucei''<br />
	**[[1dkw]], [[1ml1]], [[1mss]], [[1tpd]], [[1tpe]], [[1tpf]], [[1trd]], [[2v5l]], [[3tim]] - TbTIM		**[[1dkw]], [[1ml1]], [[1mss]], [[1tpd]], [[1tpe]], [[1tpf]], [[1trd]], [[2v5l]], [[3tim]] - TbTIM
	**[[1ci1]], [[1tcd]] - TcTIM – ''Trypanosoma cruzi''<br />		**[[1ci1]], [[1tcd]] - TcTIM – ''Trypanosoma cruzi''<br />
Line 127:		Line 127:
	**[[1m6j]] – TIM – ''Entamoeba histolytica''<br />		**[[1m6j]] – TIM – ''Entamoeba histolytica''<br />
	**[[1r2r]], [[1r2s]], [[1r2t]] – rTIM – rabbit<br />		**[[1r2r]], [[1r2s]], [[1r2t]] – rTIM – rabbit<br />
-	**[[1vga]], [[2vfd]], [[2vff]], [[3psv]], [[3psw]], [[3pwa]], [[3py2]] – PfTIM (mutant) – ''Plasmodium falciparum''<br />	+	**[[1vga]], [[2vfd]], [[2vff]], [[3psv]], [[3psw]], [[3pwa]], [[3py2]], [[5gzp]], [[5gv4]], [[5brb]], [[5bnk]], [[5bmw]], [[5bmx]], [[4zz9]], [[4z0j]], [[4z0s]], [[4yxg]], [[4ywi]] – PfTIM (mutant) – ''Plasmodium falciparum''<br />
	**[[1ydv]] - PfTIM<br />		**[[1ydv]] - PfTIM<br />
	**[[1w0m]] – TIM – ''Thermoproteus tenax''<br />		**[[1w0m]] – TIM – ''Thermoproteus tenax''<br />
Line 139:		Line 139:
	**[[4g1k]] – TIM – ''Burkholderia thailandensis''<br />		**[[4g1k]] – TIM – ''Burkholderia thailandensis''<br />
	**[[4nvt]] – TIM – ''Brucella melitensis''<br />		**[[4nvt]] – TIM – ''Brucella melitensis''<br />
-	**[[4ohq]] – TIM – ''Arabidopsis thaliana''<br />	+	**[[4ohq]], [[4obt]] – TIM – ''Arabidopsis thaliana''<br />
		+	**[[5ibx]] – TIM – ''Streptococcus pneumoniae''<br />
		+	**[[5csr]] – TaTIM – ''Thermoplasma acidophilum''<br />
		+	**[[4y9a]] – TIM – ''Streptomyces coelicolor''<br />
		+	**[[4y96]] – TIM – ''Gemmata obscuriglobus''<br />
		+	**[[4y90]] – TIM – ''Deinococcus radiodurans''<br />
		+	**[[4y8f]] – TIM – ''Clostridium perfringens''<br />
		+	**[[4x22]] - LiTIM – ''Leptospira interrogans''<br />

	*TIM binary complexes with phosphoglycolate		*TIM binary complexes with phosphoglycolate
Line 156:		Line 163:
	**[[1o5x]], [[1woa]], [[2vfe]], [[2vfg]], [[2vfh]], [[2vfi]] - PfTIM (mutant) + 3-phosphoglycerate<br />		**[[1o5x]], [[1woa]], [[2vfe]], [[2vfg]], [[2vfh]], [[2vfi]] - PfTIM (mutant) + 3-phosphoglycerate<br />
	**[[1m7o]], [[1m7p]] - PfTIM + 3-phosphoglycerate<br />		**[[1m7o]], [[1m7p]] - PfTIM + 3-phosphoglycerate<br />
-	**[[3uwu]], [[3uwv]], [[3uww]], [[3uwz]] - SaTIM + 3-phosphoglycerate	+	**[[3uwu]], [[3uwv]], [[3uww]], [[3uwz]] - SaTIM + 3-phosphoglycerate<br />
		+	**[[5css]] - TaTIM + 3-phosphoglycerate<br />

	*TIM binary complexes with phosphoglycohydroxamate		*TIM binary complexes with phosphoglycohydroxamate
Line 177:		Line 185:
	**[[1ney]]– yTIM + dihydroxyacetonephosphate<br />		**[[1ney]]– yTIM + dihydroxyacetonephosphate<br />
	**[[1nf0]] – yTIM (mutant) + dihydroxyacetonephosphate<br />		**[[1nf0]] – yTIM (mutant) + dihydroxyacetonephosphate<br />
		+	**[[4ymz]] - LiTIM + dihydroxyacetonephosphate <br />
		+	**[[5ujw]] – TIM + dihydroxyacetonephosphate – ''Francisella tularensis''<br />
	**[[1wob]] - PfTIM (mutant) + sulfate<br />		**[[1wob]] - PfTIM (mutant) + sulfate<br />
	**[[1sux]] – TcTIM + sulfonic acid derivative<br />		**[[1sux]] – TcTIM + sulfonic acid derivative<br />

Michal Harel at 09:26, 27 November 2016

2016-11-27T09:26:03Z

←Older revision		Revision as of 09:26, 27 November 2016
Line 131:		Line 131:
	**[[1w0m]] – TIM – ''Thermoproteus tenax''<br />		**[[1w0m]] – TIM – ''Thermoproteus tenax''<br />
	**[[2btm]] – GsTIM – ''Geobacillus stearothermophilus''<br />		**[[2btm]] – GsTIM – ''Geobacillus stearothermophilus''<br />
-	**[[2dp3~~]], [[2yc8~~]], [[3pf3]], [[4bi5]] - GiTIM (mutant) – ''Giardia intestinalis''<br />	+	**[[2dp3]], [[3pf3]], [[4bi5]] - GiTIM (mutant) – ''Giardia intestinalis''<br />
	**[[2h6r]]– TIM – ''Methanocaldococcus jannaschii''<br />		**[[2h6r]]– TIM – ''Methanocaldococcus jannaschii''<br />
	**[[2jgq]] – TIM – ''Helicobacter pylori''<br />		**[[2jgq]] – TIM – ''Helicobacter pylori''<br />
Line 149:		Line 149:
	**[[3pvf]] - PfTIM (mutant) + 2-phosphoglycolate<br />		**[[3pvf]] - PfTIM (mutant) + 2-phosphoglycolate<br />
	**[[1lyx]], [[1lzo]] - PfTIM + 2-phosphoglycolate<br />		**[[1lyx]], [[1lzo]] - PfTIM + 2-phosphoglycolate<br />
-	**~~[[2yc6]], [[2yc7]],~~ [[4bi7]], [[4bi6]] - GiTIM (mutant) + 2-phosphoglycolate<br />	+	**[[4bi7]], [[4bi6]] - GiTIM (mutant) + 2-phosphoglycolate<br />

	*TIM binary complexes with phosphoglycerate		*TIM binary complexes with phosphoglycerate

Michal Harel at 09:35, 22 September 2016

2016-09-22T09:35:10Z

←Older revision		Revision as of 09:35, 22 September 2016
Line 8:		Line 8:
	scene='' >		scene='' >
	[[Image:TriosePhosphateIsomerase_Ribbon_pastel_photo_small.jpg\|thumb\|left\|260px\| Ribbon drawing of the "TIM barrel" fold]]		[[Image:TriosePhosphateIsomerase_Ribbon_pastel_photo_small.jpg\|thumb\|left\|260px\| Ribbon drawing of the "TIM barrel" fold]]
		+	==Introduction==
	[[Triose Phosphate Isomerase]] (TPI or TIM) is a ubiquitous dimeric enzyme with a molecular weight of ~54 kD (27 kD per subunit) which catalyzes the reversible interconversion of the triose phosphate isomers <scene name='Triose_Phosphate_Isomerase/Morph/1'>dihydroxyacetone phosphate (DHAP)</scene> and <scene name='Triose_Phosphate_Isomerase/Morph/2'>D-glyceraldehyde-3-phosphate (GAP)</scene>, an essential process in the glycolytic pathway. More simply, the enzyme catalyzes the <scene name='Triose_Phosphate_Isomerase/Morph/3'>isomerization of a ketose (DHAP) to an aldose (GAP)</scene>, also referred to as '''PGAL'''. In regards to the two isomers, at equilibrium, roughly 96% of the triose phosphate is in the DHAP isomer form; however, the isomerization reaction proceeds due to the rapid removal of GAP from the subsequent reactions of glycolysis. The TPI tertiary structure is the classic example of the "TIM barrel" fold (see image at left). The TPI structure is shown on the right (PDB entry [[2ypi]]) in complex with the inhibitor 2-phosphoglycolic acid (PGA), which is bound to each of its two active sites. TPI is an example of a catalytically perfect enzyme, indicating that for almost every enzyme-substrate encounter, a product is formed and that this interaction is limited only by the substrate diffusion rate. See [[Glycolysis Enzymes]] and [[Isomerases]].		[[Triose Phosphate Isomerase]] (TPI or TIM) is a ubiquitous dimeric enzyme with a molecular weight of ~54 kD (27 kD per subunit) which catalyzes the reversible interconversion of the triose phosphate isomers <scene name='Triose_Phosphate_Isomerase/Morph/1'>dihydroxyacetone phosphate (DHAP)</scene> and <scene name='Triose_Phosphate_Isomerase/Morph/2'>D-glyceraldehyde-3-phosphate (GAP)</scene>, an essential process in the glycolytic pathway. More simply, the enzyme catalyzes the <scene name='Triose_Phosphate_Isomerase/Morph/3'>isomerization of a ketose (DHAP) to an aldose (GAP)</scene>, also referred to as '''PGAL'''. In regards to the two isomers, at equilibrium, roughly 96% of the triose phosphate is in the DHAP isomer form; however, the isomerization reaction proceeds due to the rapid removal of GAP from the subsequent reactions of glycolysis. The TPI tertiary structure is the classic example of the "TIM barrel" fold (see image at left). The TPI structure is shown on the right (PDB entry [[2ypi]]) in complex with the inhibitor 2-phosphoglycolic acid (PGA), which is bound to each of its two active sites. TPI is an example of a catalytically perfect enzyme, indicating that for almost every enzyme-substrate encounter, a product is formed and that this interaction is limited only by the substrate diffusion rate. See [[Glycolysis Enzymes]] and [[Isomerases]].

Angel Herraez: adding BAMBED ref

2016-09-08T08:31:24Z

adding BAMBED ref

←Older revision		Revision as of 08:31, 8 September 2016
Line 1:		Line 1:
		+	{{BAMBED
		+	\|DATE=June 30, 2011
		+	\|OLDID=1265234
		+	\|BAMBEDDOI=10.1002/bmb.20550
		+	}}
	<StructureSection load='2ypi' size='350'		<StructureSection load='2ypi' size='350'
	caption='TPI (yeast) at 2.5 Å [[resolution]] ([[2ypi]]) dimer. The two identical chains are in grey and green. Ligand is the inhibitor 2-phosphoglycolic acid (PGA). '		caption='TPI (yeast) at 2.5 Å [[resolution]] ([[2ypi]]) dimer. The two identical chains are in grey and green. Ligand is the inhibitor 2-phosphoglycolic acid (PGA). '
Line 195:		Line 200:

	[[Category: Topic Page]]		[[Category: Topic Page]]
		+	[[Category:Featured in BAMBED]]

	<references/>		<references/>

Michal Harel at 11:50, 10 February 2016

2016-02-10T11:50:27Z

←Older revision		Revision as of 11:50, 10 February 2016
Line 3:		Line 3:
	scene='' >		scene='' >
	[[Image:TriosePhosphateIsomerase_Ribbon_pastel_photo_small.jpg\|thumb\|left\|260px\| Ribbon drawing of the "TIM barrel" fold]]		[[Image:TriosePhosphateIsomerase_Ribbon_pastel_photo_small.jpg\|thumb\|left\|260px\| Ribbon drawing of the "TIM barrel" fold]]
-	[[Triose Phosphate Isomerase]] (TPI or TIM) is a ubiquitous dimeric enzyme with a molecular weight of ~54 kD (27 kD per subunit) which catalyzes the reversible interconversion of the triose phosphate isomers <scene name='Triose_Phosphate_Isomerase/Morph/1'>dihydroxyacetone phosphate (DHAP)</scene> and <scene name='Triose_Phosphate_Isomerase/Morph/2'>D-glyceraldehyde-3-phosphate (GAP)</scene>, an essential process in the glycolytic pathway. More simply, the enzyme catalyzes the <scene name='Triose_Phosphate_Isomerase/Morph/3'>isomerization of a ketose (DHAP) to an aldose (GAP)</scene>, also referred to as '''PGAL'''. In regards to the two isomers, at equilibrium, roughly 96% of the triose phosphate is in the DHAP isomer form; however, the isomerization reaction proceeds due to the rapid removal of GAP from the subsequent reactions of glycolysis. The TPI tertiary structure is the classic example of the "TIM barrel" fold (see image at left). The TPI structure is shown on the right (PDB entry [[2ypi]]) in complex with the inhibitor 2-phosphoglycolic acid (PGA), which is bound to each of its two active sites. TPI is an example of a catalytically perfect enzyme, indicating that for almost every enzyme-substrate encounter, a product is formed and that this interaction is limited only by the substrate diffusion rate. See [[Glycolysis Enzymes]].	+	[[Triose Phosphate Isomerase]] (TPI or TIM) is a ubiquitous dimeric enzyme with a molecular weight of ~54 kD (27 kD per subunit) which catalyzes the reversible interconversion of the triose phosphate isomers <scene name='Triose_Phosphate_Isomerase/Morph/1'>dihydroxyacetone phosphate (DHAP)</scene> and <scene name='Triose_Phosphate_Isomerase/Morph/2'>D-glyceraldehyde-3-phosphate (GAP)</scene>, an essential process in the glycolytic pathway. More simply, the enzyme catalyzes the <scene name='Triose_Phosphate_Isomerase/Morph/3'>isomerization of a ketose (DHAP) to an aldose (GAP)</scene>, also referred to as '''PGAL'''. In regards to the two isomers, at equilibrium, roughly 96% of the triose phosphate is in the DHAP isomer form; however, the isomerization reaction proceeds due to the rapid removal of GAP from the subsequent reactions of glycolysis. The TPI tertiary structure is the classic example of the "TIM barrel" fold (see image at left). The TPI structure is shown on the right (PDB entry [[2ypi]]) in complex with the inhibitor 2-phosphoglycolic acid (PGA), which is bound to each of its two active sites. TPI is an example of a catalytically perfect enzyme, indicating that for almost every enzyme-substrate encounter, a product is formed and that this interaction is limited only by the substrate diffusion rate. See [[Glycolysis Enzymes]] and [[Isomerases]].

	In addition to its role in glycolysis, TPI is also involved in several additional metabolic biological processes including gluconeogenesis, the pentose phosphate shunt, and fatty acid biosynthesis. A point mutation to a glutamate residue (Glu104) of TPI results in triose phosphate isomerase deficiency, an autosomal recessive inherited disorder characterized by an increased accumulation of DHAP in erythrocytes. Structurally, this point mutation abolishes TPI’s ability to dimerize, subsequently inhibiting its catalytic activity. More details in<br />		In addition to its role in glycolysis, TPI is also involved in several additional metabolic biological processes including gluconeogenesis, the pentose phosphate shunt, and fatty acid biosynthesis. A point mutation to a glutamate residue (Glu104) of TPI results in triose phosphate isomerase deficiency, an autosomal recessive inherited disorder characterized by an increased accumulation of DHAP in erythrocytes. Structurally, this point mutation abolishes TPI’s ability to dimerize, subsequently inhibiting its catalytic activity. More details in<br />

Michal Harel at 09:05, 3 February 2016

2016-02-03T09:05:52Z

←Older revision		Revision as of 09:05, 3 February 2016
Line 3:		Line 3:
	scene='' >		scene='' >
	[[Image:TriosePhosphateIsomerase_Ribbon_pastel_photo_small.jpg\|thumb\|left\|260px\| Ribbon drawing of the "TIM barrel" fold]]		[[Image:TriosePhosphateIsomerase_Ribbon_pastel_photo_small.jpg\|thumb\|left\|260px\| Ribbon drawing of the "TIM barrel" fold]]
-	[[Triose Phosphate Isomerase]] (TPI or TIM) is a ubiquitous dimeric enzyme with a molecular weight of ~54 kD (27 kD per subunit) which catalyzes the reversible interconversion of the triose phosphate isomers <scene name='Triose_Phosphate_Isomerase/Morph/1'>dihydroxyacetone phosphate (DHAP)</scene> and <scene name='Triose_Phosphate_Isomerase/Morph/2'>D-glyceraldehyde-3-phosphate (GAP)</scene>, an essential process in the glycolytic pathway. More simply, the enzyme catalyzes the <scene name='Triose_Phosphate_Isomerase/Morph/3'>isomerization of a ketose (DHAP) to an aldose (GAP)</scene>, also referred to as '''PGAL'''. In regards to the two isomers, at equilibrium, roughly 96% of the triose phosphate is in the DHAP isomer form; however, the isomerization reaction proceeds due to the rapid removal of GAP from the subsequent reactions of glycolysis. The TPI tertiary structure is the classic example of the "TIM barrel" fold (see image at left). The TPI structure is shown on the right (PDB entry [[2ypi]]) in complex with the inhibitor 2-phosphoglycolic acid (PGA), which is bound to each of its two active sites. TPI is an example of a catalytically perfect enzyme, indicating that for almost every enzyme-substrate encounter, a product is formed and that this interaction is limited only by the substrate diffusion rate.	+	[[Triose Phosphate Isomerase]] (TPI or TIM) is a ubiquitous dimeric enzyme with a molecular weight of ~54 kD (27 kD per subunit) which catalyzes the reversible interconversion of the triose phosphate isomers <scene name='Triose_Phosphate_Isomerase/Morph/1'>dihydroxyacetone phosphate (DHAP)</scene> and <scene name='Triose_Phosphate_Isomerase/Morph/2'>D-glyceraldehyde-3-phosphate (GAP)</scene>, an essential process in the glycolytic pathway. More simply, the enzyme catalyzes the <scene name='Triose_Phosphate_Isomerase/Morph/3'>isomerization of a ketose (DHAP) to an aldose (GAP)</scene>, also referred to as '''PGAL'''. In regards to the two isomers, at equilibrium, roughly 96% of the triose phosphate is in the DHAP isomer form; however, the isomerization reaction proceeds due to the rapid removal of GAP from the subsequent reactions of glycolysis. The TPI tertiary structure is the classic example of the "TIM barrel" fold (see image at left). The TPI structure is shown on the right (PDB entry [[2ypi]]) in complex with the inhibitor 2-phosphoglycolic acid (PGA), which is bound to each of its two active sites. TPI is an example of a catalytically perfect enzyme, indicating that for almost every enzyme-substrate encounter, a product is formed and that this interaction is limited only by the substrate diffusion rate. See [[Glycolysis Enzymes]].

	In addition to its role in glycolysis, TPI is also involved in several additional metabolic biological processes including gluconeogenesis, the pentose phosphate shunt, and fatty acid biosynthesis. A point mutation to a glutamate residue (Glu104) of TPI results in triose phosphate isomerase deficiency, an autosomal recessive inherited disorder characterized by an increased accumulation of DHAP in erythrocytes. Structurally, this point mutation abolishes TPI’s ability to dimerize, subsequently inhibiting its catalytic activity. More details in<br />		In addition to its role in glycolysis, TPI is also involved in several additional metabolic biological processes including gluconeogenesis, the pentose phosphate shunt, and fatty acid biosynthesis. A point mutation to a glutamate residue (Glu104) of TPI results in triose phosphate isomerase deficiency, an autosomal recessive inherited disorder characterized by an increased accumulation of DHAP in erythrocytes. Structurally, this point mutation abolishes TPI’s ability to dimerize, subsequently inhibiting its catalytic activity. More details in<br />

Michal Harel at 11:44, 1 February 2016

2016-02-01T11:44:02Z

←Older revision		Revision as of 11:44, 1 February 2016
Line 1:		Line 1:
-	<StructureSection load='2ypi' size='~~400~~'	+	<StructureSection load='2ypi' size='350'
	caption='TPI (yeast) at 2.5 Å [[resolution]] ([[2ypi]]) dimer. The two identical chains are in grey and green. Ligand is the inhibitor 2-phosphoglycolic acid (PGA). '		caption='TPI (yeast) at 2.5 Å [[resolution]] ([[2ypi]]) dimer. The two identical chains are in grey and green. Ligand is the inhibitor 2-phosphoglycolic acid (PGA). '
	scene='' >		scene='' >