Hydroxylases 3D structures: Difference between revisions

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Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
{{#tree:id=OrganizedByTopic|openlevels=0|
{{#tree:id=OrganizedByTopic|openlevels=0|
*Phenylalanine hydroxylase
 
*Phenylalanine hydroxylase (cofactor tetrahydrobiopterin)


**[[6n1k]] – hPAH (mutant) – human<br />
**[[6n1k]] – hPAH (mutant) – human<br />
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**[[1tg2]], [[1lrm]] - hPAH catalytic domain (mutant) + cofactor<br />
**[[1tg2]], [[1lrm]] - hPAH catalytic domain (mutant) + cofactor<br />
**[[1mmk]], [[1mmt]], [[1kw0]] - hPAH catalytic domain + cofactor + substrate<br />
**[[1mmk]], [[1mmt]], [[1kw0]] - hPAH catalytic domain + cofactor + substrate<br />
**[[4anp]] - hPAH catalytic domain + pyrimidine derivative<br />
**[[4anp]] - hPAH catalytic domain + pyrimidine derivative
**[[5fii]], [[5fgi]] - hPAH residues 19-118 + phenylalanine<br />
**[[5fii]], [[5fgi]] - hPAH residues 19-118 + phenylalanine<br />
**[[1phz]], [[2phm]], [[5den]], [[5fgj]], [[5den]] – rPAH - rat<br />
**[[1phz]], [[2phm]], [[5den]], [[5fgj]], [[5den]] – rPAH - rat<br />
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**[[2v27]], [[2v28]] – PAH – ''Colwellia psychrerythraea''<br />
**[[2v27]], [[2v28]] – PAH – ''Colwellia psychrerythraea''<br />
**[[1ltu]], [[1ltv]] – CvPAH – ''Chromobacterium violaceum''<br />
**[[1ltu]], [[1ltv]] – CvPAH – ''Chromobacterium violaceum''<br />
**[[1phz]], [[2phm]], [[5fgj]], [[5den]] – rPAH - rat<br />
**[[5egq]] - rPAH (mutant) <br />
**[[4bpt]] – PAH –'' Legionella pneumophila''<br />
**[[4bpt]] – PAH –'' Legionella pneumophila''<br />
**[[1ltz]] - CvPAH + cofactor<br />
**[[1ltz]] - CvPAH + cofactor<br />
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**[[4jpx]] - CvPAH (mutant) + Co + phenylalanine<br />
**[[4jpx]] - CvPAH (mutant) + Co + phenylalanine<br />
**[[4jpy]] - CvPAH + Fe + phenylalanine<br />
**[[4jpy]] - CvPAH + Fe + phenylalanine<br />
**[[7vgm]] - PAH + Fe – Bacillus cereus<br />


*Tyrosine hydroxylase
*Tyrosine hydroxylase (cofactor tetrahydrobiopterin)


**[[2xsn]] – hTH catalytic domain <br />
**[[7a2g]] – hTH – Cryo EM<br />
**[[2toh]], [[1toh]] – TH catalytic and tetramerization domains - rat<br />
**[[6zn2]], [[6zvp]], [[7pim]] – hTH + dopamine – Cryo EM<br />
**[[7kqr]], [[7kqs]], [[7kqt]], [[7kqu]] – TH + heme + Tyr derivative – ''Streptomyces sclerotialus'' <br />
**[[2xsn]], [[6zzu]] – hTH catalytic domain 193-528<br />
**[2toh]], [[1toh]] – rTH catalytic and tetramerization domains 160-498 – rat
**[[2mda]] – rTH regulatory domain 65-159 – NMR<br />
**[[7kqr]], [[7kqs]], [[7kqt]], [[7kqu]] – TH + heme + Tyr derivative – Streptomyces sclerotialus <br />


*Tryptophan hydroxylase
*Tryptophan hydroxylase


**[[3hf8]], [[3hfb]], [[3hf6]], [[5tpg]], [[5l01]], [[5j6d]] – hTPH 1 catalytic domain+ inhibitor + Fe <br />
**[[7wiy]] – hTPH 2 + Fe – Cryo EM<br />
**[[3hf8]], [[3hfb]], [[3hf6]], [[5tpg]], [[5l01]], [[5j6d]], [[7zig]], [[7zih]], [[7zif]], [[7zii]], [[7zij]], [[7zik]] – hTPH 1 catalytic domain 105-401 + inhibitor + Fe <br />
**[[1mlw]] – hTPH catalytic domain+ biopterin + Fe<br />
**[[1mlw]] – hTPH catalytic domain+ biopterin + Fe<br />
**[[4v06]] - hTPH 2 catalytic domain + Fe<br />
**[[4v06]] - hTPH 2 catalytic domain + Fe<br />
**[[7qri]] - hTPH 2 regulatory domain 48-145 + Phe - NMR<br />
**[[3e2t]] – TPH 1 catalytic domain + Trp + Fe – chicken
**[[3e2t]] – TPH 1 catalytic domain + Trp + Fe – chicken


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**[[1phh]] – PfPHBH + FAD + DHB – ''Pseudomonas fluorescens''<br />
**[[1phh]] – PfPHBH + FAD + DHB – ''Pseudomonas fluorescens''<br />
**[[1dob]], [[1doc]], [[1pxa]], [[1pxb]], [[1pxc]] – PaPHBH + FAD + PHB – ''Pseudomonas aeruginosa''<br />
**[[2phh]] – PfPHBH + adenosine diphosphoribose + PHB <br />
**[[2phh]] – PfPHBH + adenosine diphosphoribose + PHB <br />
**[[1pbb]] – PfPHBH + FAD + 2,4-DHB <br />
**[[1pbb]] – PfPHBH + FAD + 2,4-DHB <br />
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**[[1cj2]], [[1cj3]], [[1cj4]] – PfPHBH (mutant) + FAD derivative + PHB <br />
**[[1cj2]], [[1cj3]], [[1cj4]] – PfPHBH (mutant) + FAD derivative + PHB <br />
**[[1dob]], [[1doc]], [[1pxa]], [[1pxb]], [[1pxc]] – PaPHBH + FAD + PHB – ''Pseudomonas aeruginosa''<br />
**[[1dob]], [[1doc]], [[1pxa]], [[1pxb]], [[1pxc]] – PaPHBH + FAD + PHB – ''Pseudomonas aeruginosa''<br />
**[[1dod]], [[1doe]], [[1iuv]], [[1iuw]], [[1iux]] – PaPHBH + FAD + DHB derivative <br />
**[[1dod]], [[1doe]], [[1iuv]], [[1iuw]], [[1iux]] – PaPHBH + FAD + DHB derivative<br />
**[[1ius]], [[1iut]], [[1iuu]] – PaPHBH + FAD + 4-aminobenzoate <br />
**[[1ius]], [[1iut]], [[1iuu]] – PaPHBH + FAD + 4-aminobenzoate <br />
**[[6ju1]] – PaPHBH (mutant) + FAD  + DHB derivative <br />
**[[6ju1]] – PaPHBH (mutant) + FAD  + DHB derivative <br />
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**[[1k0j]] – PaPHBH (mutant) + FAD + NADPH <br />
**[[1k0j]] – PaPHBH (mutant) + FAD + NADPH <br />
**[[1k0l]] – PaPHBH (mutant) + FAD  <br />
**[[1k0l]] – PaPHBH (mutant) + FAD  <br />
**[[6dll]] – PfPHBH + FAD – ''Pseudomonas putida''<br />
**[[5tti]], [[6dll]] – PfPHBH + FAD – ''Pseudomonas putida''<br />
**[[2dki]] – CtPHBH + FAD – ''Comamonas testosteroni''<br />
**[[2dki]] – CtPHBH + FAD – Comamonas testosteroni<br />
**[[2dkh]] – CtPHBH + FAD + hydroxy-benzoate <br />
**[[2dkh]] – CtPHBH + FAD + hydroxy-benzoate <br />


*Apartyl/asparaginyl β-hydroxylase; Domain – oxygenase and TPR 301-758
*Apartyl/asparaginyl b-hydroxylase; Domain – oxygenase and TPR 301-758


**[[6qa5]] – hAAH oxygenase and TPR domain<br />
**[[6qa5]] – hAAH oxygenase and TPR domain<br />
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**[[6yyu]], [[6yyv]] – hAAH oxygenase and TPR domain + oxoglutarate + Mn <br />
**[[6yyu]], [[6yyv]] – hAAH oxygenase and TPR domain + oxoglutarate + Mn <br />
**[[6yyw]], [[6yyx]], [[6yyy]], [[6z6q]] – hAAH oxygenase and TPR domain + oxoglutarate + Mn + coagulation factor X peptide<br />
**[[6yyw]], [[6yyx]], [[6yyy]], [[6z6q]] – hAAH oxygenase and TPR domain + oxoglutarate + Mn + coagulation factor X peptide<br />
**[[5jz8]], [[5jzu]], [[6rk9]], [[5jqy]], [[6rk9]], [[6z6r]] – hAAH oxygenase and TPR domain + oxalyl derivative + Mn + coagulation factor X peptide<br />
**[[5jz8]], [[5jzu]], [[5jzz]], [[5jqy]], [[6rk9]], [[6z6r]] – hAAH oxygenase and TPR domain + oxalyl derivative + Mn + coagulation factor X peptide<br />
**[[7e6j]] – hAAH oxygenase and TPR domain (mutant) + coagulation factor X peptide<br />
**[[7e6j]] – hAAH oxygenase and TPR domain (mutant) + coagulation factor X peptide<br />
**[[6q9f]], [[6q9i]] – hAAH oxygenase and TPR domain (mutant) + oxalylglycine + Mn + coagulation factor X peptide<br />
**[[6q9f]], [[6q9i]] – hAAH oxygenase and TPR domain (mutant) + oxalylglycine + Mn + coagulation factor X peptide<br />
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*Alpha-ketoglutarate-dependent L-arginine hydroxylase
*Alpha-ketoglutarate-dependent L-arginine hydroxylase


**[[6dax]], [[6alm]], [[6aln]], [[6mp8]] – SvAAH + arginine + oxoglutarate + Fe – ''Streptomyces vinaceus''<br />
**[[6dax]], [[6alm]], [[6aln]], [[6mp8]] – SvAAH + arginine + oxoglutarate + Fe – Streptomyces vinaceus<br />
**[[6daz]], [[6alo]], [[6alp]], [[6alq]], [[6y12]] – SvAAH + arginine + succinate + Fe <br />
**[[6daz]], [[6alo]], [[6alp]], [[6alq]], [[6y12]] – SvAAH + arginine + succinate + Fe <br />
**[[6y0n]] – SvAAH + arginine + AKG + Fe <br />
**[[6y0n]] – SvAAH + arginine + AKG + Fe <br />
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*PLP-dependent L-arginine hydroxylase
*PLP-dependent L-arginine hydroxylase


**[[6c9b]] – SwAAH + PLP – ''Streptomyces wadayamensis''<br />
**[[6c9b]] – SwAAH + PLP – Streptomyces wadayamensis<br />
**[[5dj1]] – SwAAH + PLP + Mg<br />
**[[5dj1]] – SwAAH + PLP + Mg<br />
**[[5dj3]] – SwAAH + PLP-arginine + Mg<br />
**[[5dj3]] – SwAAH + PLP-arginine + Mg<br />
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*Leucine hydroxylase
*Leucine hydroxylase


**[[5nch]] – StAAH – ''Streptomyces'' <br />
**[[5nch]] – StAAH – Streptomyces <br />
**[[5nci]] – StAAH + leucine derivative + oxoglutarate + Co <br />
**[[5nci]] – StAAH + leucine derivative + oxoglutarate + Co <br />
**[[5ncj]] – StAAH + leucine derivative + succinate + Mn <br />
**[[5ncj]] – StAAH + leucine derivative + succinate + Mn <br />
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*L-arginine b-hydroxylase or non-heme iron oxygenase
*L-arginine b-hydroxylase or non-heme iron oxygenase


**[[4m23]] – SlORFP – ''Streptomyces lavendulae''<br />
**[[4m23]] – SlORFP – Streptomyces lavendulae<br />
**[[4m2i]] – SlORFP + Fe <br />
**[[4m2i]] – SlORFP + Fe <br />
**[[4m25]] – SlORFP + Fe + ketoglutarate <br />
**[[4m25]] – SlORFP + Fe + ketoglutarate <br />
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**[[4m2f]] – SlORFP + Fe + canavanine<br />
**[[4m2f]] – SlORFP + Fe + canavanine<br />
**[[4m2g]], [[4m26]] – SlORFP + Fe + succinate + Arg derivative<br />
**[[4m2g]], [[4m26]] – SlORFP + Fe + succinate + Arg derivative<br />
**[[2wbo]] – SvVIOC + Fe + Arg – ''Streptomyces vinaceus''<br />
**[[2wbo]] – SvVIOC + Fe + Arg – Streptomyces vinaceus<br />
**[[2wbq]] – SvVIOC + Arg derivative<br />
**[[2wbq]] – SvVIOC + Arg derivative<br />
**[[2wbp]] – SvVIOC + Fe + succinate + Arg derivative<br />
**[[2wbp]] – SvVIOC + Fe + succinate + Arg derivative<br />
**[[6daw]] – NAPI + Fe + Arg – ''Streptomyces lusitanus''<br />
**[[6daw]] – NAPI + Fe + Arg – Streptomyces lusitanus<br />


*Prolyl 4-hydroxylase
*Prolyl 4-hydroxylase


**[[4bt8]], [[2yq8]] - hPH a1 subunit collagen-binding domain<br />
**[[4bt8]], [[2yq8]] - hPH a1 subunit collagen-binding domain<br />
**[[1tjc]] - hPH a1 subunit collagen-binding domain (mutant)<br />
**[[1tjc]] - hPH a1 subunit collagen-binding domain (mutant)<br />
**[[4btb]], [[4bta]], [[4bt9]] - hPH a1 subunit + peptide<br />
**[[2v5f]], [[4btb]], [[4bta]], [[4bt9]] - hPH a1 subunit + peptide<br />
**[[6evl]] - hPH a2 subunit <br />
**[[6evl]] - hPH a2 subunit <br />
**[[6evm]], [[6evn]], [[6evo]], [[6evp]] - hPH a2 subunit + peptide<br />
**[[6evm]], [[6evn]], [[6evo]], [[6evp]] - hPH a2 subunit + peptide<br />
**[[5hv0]] - PH + Cd – ''Bacillus anthracis'' <br />
**[[3itq]], [[5hv0]] - BaPH – Bacillus anthracis <br />
**[[5hv4]] - BaPH + ketoglutarate<br />
**[[5c5u]] - PcvPH + Mn – Paramecium chlorella virus <br />
**[[5c5u]] - PcvPH + Mn – Paramecium chlorella virus <br />
**[[5c5t]] - PcvPH + Mn + Zn <br />
**[[5c5t]] - PcvPH + Mn + Zn <br />
**[[4p7x]] - RlPH + Co + pipecolic acid – ''Rhizobium loti'' <br />
**[[4p7x]] - RlPH + Co + pipecolic acid – Rhizobium loti <br />
**[[4p7w]] - RlPH + Co + proline<br />
**[[4p7w]] - RlPH + Co + proline<br />
**[[6iuq]] - PH + Fe – ''Phytophthora capsici''<br />
**[[6iuq]] - PH + Fe – Phytophthora capsici<br />
**[[2v4a]], [[2jij]] - CrPH – ''Chlamydomonas reinhardtii'' <br />
**[[2v4a]], [[2jij]] - CrPH – Chlamydomonas reinhardtii <br />
**[[2jig]] - CrPH + Zn + pyridine derivative<br />
**[[2jig]] - CrPH + Zn + pyridine derivative<br />
**[[3gze]] - CrPH + Zn + peptide<br />
*HIF prolyl  hydroxylase  or egl nine homolog


*HIF prolyl hydroxylase or egl nine homolog See [[Prolyl hydroxylase domain]]
See [[Prolyl hydroxylase domain]]


*Lysine 4-hydroxylase
*Lysine 4-hydroxylase


**[[6f9p]] – FlL4H + Fe – ''Flavobacterium'' <br />
**[[6f9p]] – FlL4H + Fe – Flavobacterium <br />
**[[6exf]] – FlL4H + Fe + lysine <br />
**[[6exf]] – FlL4H + Fe + lysine <br />
**[[6euo]] – FlL4H + Fe + succinate derivative<br />
**[[6euo]] – FlL4H + Fe + succinate derivative<br />
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**[[6exh]] – FlL4H + Fe + lysine + succinate<br />
**[[6exh]] – FlL4H + Fe + lysine + succinate<br />


*Lysine 3-hydroxylase
*Lysine 3-hydroxylase


**[[6f2e]] – CaL3H – ''Catenulispora acidiphila'' <br />
**[[6f2e]] – CaL3H – Catenulispora acidiphila <br />
**[[6f2b]] – CaL3H + Fe + oxoglutarate  <br />
**[[6f2b]] – CaL3H + Fe + oxoglutarate  <br />
**[[6f2a]] – CaL3H + Fe + lysine  <br />
**[[6f2a]] – CaL3H + Fe + lysine  <br />
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*Salicylate hydroxylase
*Salicylate hydroxylase


**[[6bz5]] - PpSH <br />
**[[5evy]] - PpSH + FAD + salicilate <br />
**[[5evy]] - PpSH + FAD + salicilate <br />
**[[7c8z]] - SH + Fe2S2 + Fe - Ralstonia <br />


*Dopamine β-hydroxylase
*Dopamine b-hydroxylase (cofactor ascorbic acid)


**[[4zel]] - hDH + Cu <br />
**[[4zel]] - hDH + Cu <br />
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*Ectoine hydroxylase
*Ectoine hydroxylase


**[[4mhr]] - SaEH – ''Sphingopyxis alaskensis'' <br />
**[[4mhr]] - SaEH – Sphingopyxis alaskensis <br />
**[[4mhu]] - SaEH + Fe  <br />
**[[4mhu]] - SaEH + Fe  <br />
**[[4q5o]] - SaEH + Fe + 5-hydroxyectoine<br />
**[[4q5o]] - SaEH + Fe + 5-hydroxyectoine <br />
**[[4nmi]] - VsEH – ''Virgibacillus salexigens''<br />
**[[4nmi]] - VsEH – Virgibacillus salexigens<br />
**[[3emr]] - VsEH + Fe  <br />
**[[3emr]] - VsEH + Fe  <br />


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**[[6tto]] - dHH + Ni + oxoglutaratee <br />
**[[6tto]] - dHH + Ni + oxoglutaratee <br />


*Cytochrome P450  hydroxylase See [[Cytochrome P450 hydroxylase]]
*Cytochrome P450  hydroxylase  
 
See [[Cytochrome P450 hydroxylase]]
 
*Toluene/o-xylene monooxygenase  hydroxylase
 
See [[Monooxygenase]]
 
*Ornithine  hydroxylase
 
See [[Monooxygenase]]
 
*Methane  monooxygenase hydroxylase
 
See [[Methane monooxygenase]]
 
*Kynurenine  3-hydroxylase or KMO
 
See [[Monooxygenase]]
 
*Trans-3/4-proline hydroxylase H11
 
See [[Dioxygenase]]


}}
}}


[[Category:Topic Page]]
[[Category:Topic Page]]

Revision as of 10:14, 24 May 2023

3D structures of hydroxylases

Updated on 24-May-2023

See Prolyl hydroxylase domain

  • Lysine 4-hydroxylase
    • 6f9p – FlL4H + Fe – Flavobacterium
    • 6exf – FlL4H + Fe + lysine
    • 6euo – FlL4H + Fe + succinate derivative
    • 6eur – FlL4H + Fe + oxoglutarate
    • 6exh – FlL4H + Fe + lysine + succinate
  • Lysine 3-hydroxylase
    • 6f2e – CaL3H – Catenulispora acidiphila
    • 6f2b – CaL3H + Fe + oxoglutarate
    • 6f2a – CaL3H + Fe + lysine
    • 6f6j – CaL3H + Fe + succinate + hydroxyl lysine
  • Salicylate hydroxylase
    • 6bz5 - PpSH
    • 5evy - PpSH + FAD + salicilate
    • 7c8z - SH + Fe2S2 + Fe - Ralstonia
  • Dopamine b-hydroxylase (cofactor ascorbic acid)
  • Ectoine hydroxylase
    • 4mhr - SaEH – Sphingopyxis alaskensis
    • 4mhu - SaEH + Fe
    • 4q5o - SaEH + Fe + 5-hydroxyectoine
    • 4nmi - VsEH – Virgibacillus salexigens
    • 3emr - VsEH + Fe
  • Hyoscyamine 6 b-hydroxylase
    • 6ttm, 6ttn - dHH + Ni + oxalylglycine + hyoscyamine – datura
    • 6tto - dHH + Ni + oxoglutaratee
  • Cytochrome P450 hydroxylase

See Cytochrome P450 hydroxylase

  • Toluene/o-xylene monooxygenase hydroxylase

See Monooxygenase

  • Ornithine hydroxylase

See Monooxygenase

  • Methane monooxygenase hydroxylase

See Methane monooxygenase

  • Kynurenine 3-hydroxylase or KMO

See Monooxygenase

  • Trans-3/4-proline hydroxylase H11

See Dioxygenase

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Jaime Prilusky, Joel L. Sussman

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