We apologize for Proteopedia being slow to respond. For the past two years, a new implementation of Proteopedia has been being built. Soon, it will replace this 18-year old system. All existing content will be moved to the new system at a date that will be announced here.

Dioxygenase 3D structures

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 50: Line 50:
**[[2xsu]] – ArCTD + Fe+3 + phosphoinositol derivative – ''Acinetobacter radioresistens''<br />
**[[2xsu]] – ArCTD + Fe+3 + phosphoinositol derivative – ''Acinetobacter radioresistens''<br />
**[[2xsv]], [[2xsr]] – ArCTD + Fe+3 + phosphoinositol derivative <br />
**[[2xsv]], [[2xsr]] – ArCTD + Fe+3 + phosphoinositol derivative <br />
 +
 +
*Catechol 2,3-dioxygenase (CT23D)
 +
 +
**[[5zsz]] – DiCT23D + Fe+3 - ''Diaphorobacter''<br />
 +
**[[5znh]], [[5zsx]] – DiCTD + Fe+3 + catechol derivative<br />
*Chlorocatechol 1,2-dioxygenase (CCTD)
*Chlorocatechol 1,2-dioxygenase (CCTD)
Line 90: Line 95:
**[[4zhn]] – EcAlkb (mutant) + Co+2 + oxoglutarate + trinucleotide<br />
**[[4zhn]] – EcAlkb (mutant) + Co+2 + oxoglutarate + trinucleotide<br />
**[[2fd8]] – EcAlkb (mutant) + Fe+2 + oxoglutarate <br />
**[[2fd8]] – EcAlkb (mutant) + Fe+2 + oxoglutarate <br />
 +
**[[6f9p]] – FlAlkb + Re+2 - ''Flavobacterium''<br />
 +
**[[6exf]] – FlAlkb + Fe+3 + lysine <br />
 +
**[[6eur]] – FlAlkb + Fe+3 + oxoglutarate <br />
 +
**[[6euo]] – FlAlkb + Fe+3 + succinate <br />
 +
**[[6exh]] – FlAlkb + Fe+3 + succinate + hydroxylysine <br />
 +
**[[6f6e]], [[6p77]] – CaAlkb – ''Catenulispora acidiphila''<br />
 +
**[[6f2b]] – CaAlkb + Fe+2 + oxoglutarate <br />
 +
**[[6f2a]] – CaAlkb + Fe+2 + lysine <br />
 +
**[[6f6j]] – CaAlkb + Fe+3 + succinate + hydroxylysine <br />
*''Alkb complex with DNA''
*''Alkb complex with DNA''
Line 110: Line 124:
*α-ketoglutarate-dependent dioxygenase homolog (Alkbh)
*α-ketoglutarate-dependent dioxygenase homolog (Alkbh)
 +
**[[6ima]] – hAlkbh1 catalytic domain 37-369<br />
 +
**[[6ie3]] – hAlkbh1 + Mn <br />
 +
**[[6ie2]] – hAlkbh1 + Mn + oxoglutarate <br />
 +
**[[6ksf]] – mAlkbh1 catalytic domain + succinate + DNA<br />
**[[4nj4]], [[4o7x]] – hAlkbh5 residues 66-292 + Mn<br />
**[[4nj4]], [[4o7x]] – hAlkbh5 residues 66-292 + Mn<br />
**[[4o61]] – hAlkbh5 residues 74-294 + citrate<br />
**[[4o61]] – hAlkbh5 residues 74-294 + citrate<br />
Line 130: Line 148:
**[[4qkn]] – hFto + Mn+2 + meclofenamic acid<br />
**[[4qkn]] – hFto + Mn+2 + meclofenamic acid<br />
**[[4cxw]], [[4cxx]], [[4cxy]] – hFto + Ni+2 + inhibitor<br />
**[[4cxw]], [[4cxx]], [[4cxy]] – hFto + Ni+2 + inhibitor<br />
 +
**[[6aej]] – hFto + Zn+2 + inhibitor<br />
 +
**[[6ak4]] – hFto (mutant) + Zn+2 + inhibitor<br />
**[[6akw]] – hFto + oxoglutarate + inhibitor<br />
**[[6akw]] – hFto + oxoglutarate + inhibitor<br />
**[[5f8p]], [[5dab]] – hFto + Fe+2 + oxoglutarate + inhibitor<br />
**[[5f8p]], [[5dab]] – hFto + Fe+2 + oxoglutarate + inhibitor<br />
Line 143: Line 163:
**[[5zm2]] – EvANDA – ''Emericella variicolor''<br />
**[[5zm2]] – EvANDA – ''Emericella variicolor''<br />
**[[5zm4]], [[5zm3]] – EvANDA + Fe+3 + oxoglutarate + preandiloid<br />
**[[5zm4]], [[5zm3]] – EvANDA + Fe+3 + oxoglutarate + preandiloid<br />
 +
 +
* α-ketoglutarate-dependent dioxygenase (DAO)
 +
 +
**[[6kun]] – DAO + oxoglutarate – rice<br />
*Leucoanthocyanidin dioxygenase (LACD)
*Leucoanthocyanidin dioxygenase (LACD)
Line 151: Line 175:
*Methylcytosine dioxygenase (TET)
*Methylcytosine dioxygenase (TET)
 +
**[[6asd]] – hTET1 + DNA <br />
**[[5d9y]], [[5deu]], [[4nm6]] – hTET2 + DNA <br />
**[[5d9y]], [[5deu]], [[4nm6]] – hTET2 + DNA <br />
**[[4z3c]] – hTET3 + DNA <br />
**[[4z3c]] – hTET3 + DNA <br />
Line 189: Line 214:
**[[5zsz]] – DiMPC + Fe+3 - ''Diaphorobacter''<br />
**[[5zsz]] – DiMPC + Fe+3 - ''Diaphorobacter''<br />
**[[5znh]] – DiMPC + Fe+3 + catechol derivative<br />
**[[5znh]] – DiMPC + Fe+3 + catechol derivative<br />
 +
**[[6l3w]] – MPC + Fe+3 - metagenome<br />
*Naphthalene 1,2-dioxygenase (NDO)
*Naphthalene 1,2-dioxygenase (NDO)
Line 265: Line 291:
**[[4pw8]] - hTDO + Co+2 <br />
**[[4pw8]] - hTDO + Co+2 <br />
**[[5tia]], [[5ti9]] – hTDO + heme + tryptophan <br />
**[[5tia]], [[5ti9]] – hTDO + heme + tryptophan <br />
 +
**[[6pyy]], [[6pyz]], [[6vbn]] – hTDO + heme + inhibitor<br />
**[[6a4i]] – hTDO + heme + tryptophan + inhibitor<br />
**[[6a4i]] – hTDO + heme + tryptophan + inhibitor<br />
**[[1yw0]] – XcTDO + Mg – ''Xanthomonas campestris''<br />
**[[1yw0]] – XcTDO + Mg – ''Xanthomonas campestris''<br />
Line 285: Line 312:
**[[5fdb]] – rCysDO (mutant) <br />
**[[5fdb]] – rCysDO (mutant) <br />
**[[4yni]] – rCysDO <br />
**[[4yni]] – rCysDO <br />
-
**[[5i0r]], [[4xet]], [[4xfb]], [[4xfc]], [[4pix]] – rCysDO (mutant) + Fe+3 <br />
+
**[[6u4s]], [[6u4v]] – rCysDO + Fe+3 <br />
 +
**[[5i0r]], [[4xet]], [[4xfb]], [[4xfc]], [[4pix]], [[6u1m]], [[6u4l]] – rCysDO (mutant) + Fe+3 <br />
**[[3eln]] – rCysDO + Fe+2 + cysteine derivative<br />
**[[3eln]] – rCysDO + Fe+2 + cysteine derivative<br />
**[[4z82]] – rCysDO (mutant) + Fe+2 + cysteine derivative<br />
**[[4z82]] – rCysDO (mutant) + Fe+2 + cysteine derivative<br />
Line 303: Line 331:
**[[1sqd]], [[1sp9]] – AtHPPD + Fe+3 <br />
**[[1sqd]], [[1sp9]] – AtHPPD + Fe+3 <br />
**[[1tfz]], [[1tg5]], [[6j63]], [[5ywh]], [[5ywg]] - AtHPPD + Fe+3 + inhibitor <br />
**[[1tfz]], [[1tg5]], [[6j63]], [[5ywh]], [[5ywg]] - AtHPPD + Fe+3 + inhibitor <br />
 +
**[[6jx9]] – AtHPPD + Co+2 + inhibitor <br />
**[[5xgk]] – AtHPPD + Fe+3 + hydroxyphenylpyruvate <br />
**[[5xgk]] – AtHPPD + Fe+3 + hydroxyphenylpyruvate <br />
**[[6isd]] – AtHPPD + Fe+3 + sulcotrione <br />
**[[6isd]] – AtHPPD + Fe+3 + sulcotrione <br />
Line 310: Line 339:
**[[5hmq]] – PpHPPD + Mg+2 <br />
**[[5hmq]] – PpHPPD + Mg+2 <br />
-
*Quercetin 2,3-dioxygenase (QDO)
+
*Quercetin 2,3-dioxygenase (QDO) or pirin
**[[1juh]] – AjQDO + Cu+2 – ''Aspergillus japonicus''<br />
**[[1juh]] – AjQDO + Cu+2 – ''Aspergillus japonicus''<br />
Line 317: Line 346:
**[[1h1i]] – AjQDO + Cu+2 + quercetin<br />
**[[1h1i]] – AjQDO + Cu+2 + quercetin<br />
**[[1h1m]] – AjQDO + Cu+2 + kaempferol<br />
**[[1h1m]] – AjQDO + Cu+2 + kaempferol<br />
 +
**[[6d0g]], [[6d0p]] – QDO + Mn+2 – ''Acinetobacter baumannii''<br />
 +
**[[6uts]] – EcQDO + Ni+2 <br />
*Taurine/α-ketoglutarate dioxygenase (TauD)
*Taurine/α-ketoglutarate dioxygenase (TauD)
**[[1gqw]], [[1gy9]], [[1os7]] – EcTauD + Fe+2 + taurine + oxoglutarate <br />
**[[1gqw]], [[1gy9]], [[1os7]] – EcTauD + Fe+2 + taurine + oxoglutarate <br />
 +
**[[6edh]] – EcTauD + VO+2 + taurine + succinate <br />
**[[1otj]] – EcTauD + taurine <br />
**[[1otj]] – EcTauD + taurine <br />
**[[3pvj]], [[3v15]] – PpTauD <br />
**[[3pvj]], [[3v15]] – PpTauD <br />
Line 327: Line 359:
**[[4j5i]] – HAD + Fe+3 – ''Mycobacterium smegmatis''<br />
**[[4j5i]] – HAD + Fe+3 – ''Mycobacterium smegmatis''<br />
**[[3swt]] – HAD + Fe+3 – ''Mycobacterium marinum''<br />
**[[3swt]] – HAD + Fe+3 – ''Mycobacterium marinum''<br />
 +
**[[6l86]] – HAD + Fe+3 + malate – S''treptomyces thioluteus''<br />
**[[5keu]] – BxHAD + Mg+2<br />
**[[5keu]] – BxHAD + Mg+2<br />
**[[5vn6]] – BaHAD + Mg+2<br />
**[[5vn6]] – BaHAD + Mg+2<br />
Line 343: Line 376:
**[[1yfw]] – CmHAD + Fe+3 + O2 + hydroxyanthranilate<br />
**[[1yfw]] – CmHAD + Fe+3 + O2 + hydroxyanthranilate<br />
**[[1yfx]] – CmHAD + Fe+3 + NO + hydroxyanthranilate<br />
**[[1yfx]] – CmHAD + Fe+3 + NO + hydroxyanthranilate<br />
 +
**[[6vi7]] – CmHAD + Fe+2 + hydroxyanthranilate<br />
**[[1yfy]] – CmHAD + Fe+3 + hydroxyanthranilate<br />
**[[1yfy]] – CmHAD + Fe+3 + hydroxyanthranilate<br />
**[[6d62]], [[6d61]], [[6cd3]], [[6bvs]], [[6bvq]] – CmHAD (mutant) + Fe+2 + hydroxyanthranilate derivative<br />
**[[6d62]], [[6d61]], [[6cd3]], [[6bvs]], [[6bvq]] – CmHAD (mutant) + Fe+2 + hydroxyanthranilate derivative<br />
Line 405: Line 439:
**[[5c6x]] – TcGBD + Co+2 <br />
**[[5c6x]] – TcGBD + Co+2 <br />
**[[5v0f]] – TcGBD + Fe+3 + roxasone <br />
**[[5v0f]] – TcGBD + Fe+3 + roxasone <br />
-
**[[4z04]] – GBD + Zn+2 + glutathione – ''Brucella abortu''s <br />
+
**[[4z04]] – GBD + Zn+2 + glutathione – ''Brucella abortus'' <br />
 +
**[[6a4x]] – GBD + Fe+2 – ''Streptomyces curacoi''<br />
* Procollagen-proline dioxygenase (PPD)
* Procollagen-proline dioxygenase (PPD)
Line 411: Line 446:
**[[5iat]] – BaPDD – ''Bacillus anthracis''<br />
**[[5iat]] – BaPDD – ''Bacillus anthracis''<br />
**[[5iax]] – BaPDD + Co+2 + oxoglutarate <br />
**[[5iax]] – BaPDD + Co+2 + oxoglutarate <br />
 +
**[[5v7y]] – BaPDD + Co+2 + oxoglutarate + imidazole<br />
**[[5iav]] – BaPDD + Co+2 + malonate<br />
**[[5iav]] – BaPDD + Co+2 + malonate<br />
Line 426: Line 462:
**[[6azu]] – hIAD + heme <br />
**[[6azu]] – hIAD + heme <br />
-
**[[6e45]], [[6e44]] – hIAD 1 (mutant) + heme <br />
+
**[[6e45]], [[6e44]], [[6tue]] – hIAD 1 (mutant) + heme <br />
**[[5ek2]], [[5ek3]], [[5ek4]], [[4pk5]], [[5xe1]], [[5wn8]] – hIAD + heme + imidazole derivative<br />
**[[5ek2]], [[5ek3]], [[5ek4]], [[4pk5]], [[5xe1]], [[5wn8]] – hIAD + heme + imidazole derivative<br />
**[[4u72]], [[4u74]], [[6e42]], [[6e41]], [[6e40]] – hIAD (mutant) + heme + imidazole derivative<br />
**[[4u72]], [[4u74]], [[6e42]], [[6e41]], [[6e40]] – hIAD (mutant) + heme + imidazole derivative<br />
**[[6f0a]] – hIAD + heme + imidazole derivative + Ala<br />
**[[6f0a]] – hIAD + heme + imidazole derivative + Ala<br />
-
**[[6azw]], [[6azv]] – hIAD + inhibitor<br />
+
**[[6azw]], [[6azv]], [[6v52]] – hIAD + inhibitor<br />
-
**[[5etw]], [[6mq6]], [[6dpr]], [[6dpq]] – hIAD + heme + inhibitor<br />
+
**[[5etw]], [[6mq6]], [[6dpr]], [[6dpq]], [[6kof]], [[6kps]], [[6kw7]], [[6o3i]], [[6pu7]], [[6pz1]], [[6r63]] – hIAD + heme + inhibitor<br />
**[[5wmu]], [[6e35]] – hIAD + heme + CN + Trp<br />
**[[5wmu]], [[6e35]] – hIAD + heme + CN + Trp<br />
**[[5wmw]], [[6cxv]], [[6cxu]] – hIAD (mutant) + heme + CN + Trp<br />
**[[5wmw]], [[6cxv]], [[6cxu]] – hIAD (mutant) + heme + CN + Trp<br />
Line 462: Line 498:
**[[6d3m]] – ShFTTD + Co+2 + oxoglutarate + quinoxalin<br />
**[[6d3m]] – ShFTTD + Co+2 + oxoglutarate + quinoxalin<br />
**[[6d3i]], [[6d3h]] – ShFTTD + Co+2 + oxoglutarate + phenoxy derivative<br />
**[[6d3i]], [[6d3h]] – ShFTTD + Co+2 + oxoglutarate + phenoxy derivative<br />
 +
 +
*Ring-cleavage dioxygenase (RCD)
 +
 +
**[[5vg2]] – RCD + Fe+3 – spider mite<br />
 +
 +
*L-dopa dioxygenase (LDD)
 +
 +
**[[6on1]] – SsLDD + Fe+3 – ''Streptomyces sclerotialus''<br />
 +
**[[6on3]] – SsLDD + Fe+3 + Phe derivative<br />
 +
 +
*Kanamycin B dioxygenase (KBD)
 +
 +
**[[6s0r]], [[6s0t]] – SkKBD + Ni+2 – ''Streptomyces kanamyceticus''<br />
 +
**[[6s0v]] – SkKBD + Ni+2 + neamine<br />
 +
**[[6s0w]] – SkKBD + Ni+2 + kanamycin<br />
 +
**[[6s0u]] – SkKBD + Ni+2 + oxoglutarate<br />
 +
**[[6s0s]] – SkKBD + Ni+2 + ribostamycin + oxoglutarate<br />
}}
}}
[[Category:Topic Page]]
[[Category:Topic Page]]

Revision as of 10:00, 15 July 2020

3D structures of dioxygenase

Updated on 15-July-2020

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Joel L. Sussman

Retrieved from "http://52.214.119.220/wiki/index.php/Dioxygenase_3D_structures"
Personal tools