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Difference between revisions of "Talk:Glycoside Hydrolase Family 3"

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== Comment from [[User:Brian Mark|Brian Mark]], April 2013 ==
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The GH3 page has received a comprehensive update.  The following comments have been addressed.  Thank-you for the input!
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== Comment from [[User:Shinya Fushinobu|Shinya Fushinobu]], Sept. 2011 ==
 
Litzinger et al. (2010) suggested that the acid/base catalyst of 2 domain NagZs (and also 1 domain NagZs) is an Asp-His dyad in the (&beta;/&alpha;)<sub>8</sub> domain. pmid: 20826810.
 
Litzinger et al. (2010) suggested that the acid/base catalyst of 2 domain NagZs (and also 1 domain NagZs) is an Asp-His dyad in the (&beta;/&alpha;)<sub>8</sub> domain. pmid: 20826810.
  
 
== Update to Catalytic Residues section needed? ==
 
== Update to Catalytic Residues section needed? ==
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Given the growing amount of information about the identity of the GH3 catalytic residues - and in particular the acid/base - in different enzymes/subfamilies, I wonder if a update of this section isn't needed?
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Given the growing amount of information about the identity of the GH3 catalytic residues, and in particular the acid/base, in different enzymes/subfamilies, I wonder if a update of this section isn't needed?
 
  
 
Here are some key acid/base ID references <cite>Thongpoo2012 Bacik2012 Litzinger2010 Pozzo2010 Yoshida2010 Li2006 Paal2004 Chir2002 Li2002</cite>, one of which also confirms the catalytic nucleophile <cite>Paal2004</cite>.  These references are nucleophile-specific studies <cite>Vocadlo2000 Dan2000</cite>:
 
Here are some key acid/base ID references <cite>Thongpoo2012 Bacik2012 Litzinger2010 Pozzo2010 Yoshida2010 Li2006 Paal2004 Chir2002 Li2002</cite>, one of which also confirms the catalytic nucleophile <cite>Paal2004</cite>.  These references are nucleophile-specific studies <cite>Vocadlo2000 Dan2000</cite>:
  
 
=== References ===
 
=== References ===
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<biblio>
 
<biblio>
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#Thongpoo2012 pmid=23201198 // Subfamily 4, via kinetic analysis & azide rescue
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#Thongpoo2012 pmid=23201198 // Subfamily 4, 3-D homology model, mutagenesis, kinetic analysis, pH profile, azide rescue
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#Bacik2012 pmid=23177201 // NagZ subfamily, ligand complex
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#Bacik2012 pmid=23177201 // 1-domain Nag, experimental structure, ligand complex, mobile loop bearing acid/base
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#Litzinger2010 pmid=20826810 // NagZ sunfamily, kinetic analysis
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#Litzinger2010 pmid=20826810 // 2-domain Nag, strucuture, mutagenesis, kinetic analysis, pH profile, azide rescue unsuccessful
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#Pozzo2010 pmid=20138890 // Subfamily 5
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#Pozzo2010 pmid=20138890 // Subfamily 5, experimental structure, complexes, reduced Km for mutant with PNP-Glc
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#Yoshida2010 pmid=20662765 // Subfamily 5
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#Yoshida2010 pmid=20662765 // Subfamily 5, experimental structure, product complex
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#Li2006 pmid=16717412 //double-check
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#Li2006 pmid=16717412 //Nag - relevant? Appears to be mis-identification.
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#Paal2004 pmid=14561218 //Subfamily 5
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#Paal2004 pmid=14561218 //Subfamily 5, kinetic analysis, pH profile, azide rescue
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#Chir2002 pmid=11978178 // Subfamily 5
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#Chir2002 pmid=11978178 // Subfamily 5, Glu-473 labelled by N-bromoacetyl-beta-d-glucosylamine
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#Li2002 pmid=11851422 // Nag - relevant? Mis-identification.
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#Li2002 pmid=11851422 //Subfamily 5, kinetic analysis, pH profile, azide rescue
 
#Vocadlo2000 pmid=10625486
 
#Vocadlo2000 pmid=10625486
 
#Dan2000 pmid=10671536
 
#Dan2000 pmid=10671536

Latest revision as of 13:10, 18 December 2021

Comment from Brian Mark, April 2013

The GH3 page has received a comprehensive update. The following comments have been addressed. Thank-you for the input!

Comment from Shinya Fushinobu, Sept. 2011

Litzinger et al. (2010) suggested that the acid/base catalyst of 2 domain NagZs (and also 1 domain NagZs) is an Asp-His dyad in the (β/α)8 domain. pmid: 20826810.

Update to Catalytic Residues section needed?

Given the growing amount of information about the identity of the GH3 catalytic residues - and in particular the acid/base - in different enzymes/subfamilies, I wonder if a update of this section isn't needed?

Here are some key acid/base ID references [1, 2, 3, 4, 5, 6, 7, 8, 9], one of which also confirms the catalytic nucleophile [7]. These references are nucleophile-specific studies [10, 11]:

References

Error fetching PMID 23201198:
Error fetching PMID 23177201:
Error fetching PMID 20826810:
Error fetching PMID 20138890:
Error fetching PMID 20662765:
Error fetching PMID 16717412:
Error fetching PMID 14561218:
Error fetching PMID 11978178:
Error fetching PMID 11851422:
Error fetching PMID 10625486:
Error fetching PMID 10671536:
  1. Error fetching PMID 23201198: [Thongpoo2012]

    Subfamily 4, 3-D homology model, mutagenesis, kinetic analysis, pH profile, azide rescue

  2. Error fetching PMID 23177201: [Bacik2012]

    1-domain Nag, experimental structure, ligand complex, mobile loop bearing acid/base

  3. Error fetching PMID 20826810: [Litzinger2010]

    2-domain Nag, strucuture, mutagenesis, kinetic analysis, pH profile, azide rescue unsuccessful

  4. Error fetching PMID 20138890: [Pozzo2010]

    Subfamily 5, experimental structure, complexes, reduced Km for mutant with PNP-Glc

  5. Error fetching PMID 20662765: [Yoshida2010]

    Subfamily 5, experimental structure, product complex

  6. Error fetching PMID 16717412: [Li2006]

    Nag - relevant? Appears to be mis-identification.

  7. Error fetching PMID 14561218: [Paal2004]

    Subfamily 5, kinetic analysis, pH profile, azide rescue

  8. Error fetching PMID 11978178: [Chir2002]

    Subfamily 5, Glu-473 labelled by N-bromoacetyl-beta-d-glucosylamine

  9. Error fetching PMID 11851422: [Li2002]

    Subfamily 5, kinetic analysis, pH profile, azide rescue

  10. Error fetching PMID 10625486: [Vocadlo2000]
  11. Error fetching PMID 10671536: [Dan2000]

All Medline abstracts: PubMed


Harry Brumer (talk) 17:55, 14 December 2012 (PST)

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