1ddt
From Proteopedia
(New page: 200px<br /><applet load="1ddt" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ddt, resolution 2.0Å" /> '''THE REFINED STRUCTURE...) |
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| - | [[Image:1ddt.gif|left|200px]]<br /><applet load="1ddt" size=" | + | [[Image:1ddt.gif|left|200px]]<br /><applet load="1ddt" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1ddt, resolution 2.0Å" /> | caption="1ddt, resolution 2.0Å" /> | ||
'''THE REFINED STRUCTURE OF DIMERIC DIPHTHERIA TOXIN AT 2.0 ANGSTROMS RESOLUTION'''<br /> | '''THE REFINED STRUCTURE OF DIMERIC DIPHTHERIA TOXIN AT 2.0 ANGSTROMS RESOLUTION'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The refined structure of dimeric diphtheria toxin (DT) at 2.0 A | + | The refined structure of dimeric diphtheria toxin (DT) at 2.0 A resolution, based on 37,727 unique reflections (F > 1 sigma (F)), yields a final R factor of 19.5% with a model obeying standard geometry. The refined model consists of 523 amino acid residues, 1 molecule of the bound dinucleotide inhibitor adenylyl 3'-5' uridine 3' monophosphate (ApUp), and 405 well-ordered water molecules. The 2.0-A refined model reveals that the binding motif for ApUp includes residues in the catalytic and receptor-binding domains and is different from the Rossmann dinucleotide-binding fold. ApUp is bound in part by a long loop (residues 34-52) that crosses the active site. Several residues in the active site were previously identified as NAD-binding residues. Glu 148, previously identified as playing a catalytic role in ADP-ribosylation of elongation factor 2 by DT, is about 5 A from uracil in ApUp. The trigger for insertion of the transmembrane domain of DT into the endosomal membrane at low pH may involve 3 intradomain and 4 interdomain salt bridges that will be weakened at low pH by protonation of their acidic residues. The refined model also reveals that each molecule in dimeric DT has an "open" structure unlike most globular proteins, which we call an open monomer. Two open monomers interact by "domain swapping" to form a compact, globular dimeric DT structure. The possibility that the open monomer resembles a membrane insertion intermediate is discussed. |
==About this Structure== | ==About this Structure== | ||
| - | 1DDT is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Corynephage_beta Corynephage beta] with APU as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1DDT is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Corynephage_beta Corynephage beta] with <scene name='pdbligand=APU:'>APU</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DDT OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Corynephage beta]] | [[Category: Corynephage beta]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Bennett, M | + | [[Category: Bennett, M J.]] |
[[Category: Eisenberg, D.]] | [[Category: Eisenberg, D.]] | ||
[[Category: APU]] | [[Category: APU]] | ||
[[Category: toxin]] | [[Category: toxin]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:15:36 2008'' |
Revision as of 10:15, 21 February 2008
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THE REFINED STRUCTURE OF DIMERIC DIPHTHERIA TOXIN AT 2.0 ANGSTROMS RESOLUTION
Overview
The refined structure of dimeric diphtheria toxin (DT) at 2.0 A resolution, based on 37,727 unique reflections (F > 1 sigma (F)), yields a final R factor of 19.5% with a model obeying standard geometry. The refined model consists of 523 amino acid residues, 1 molecule of the bound dinucleotide inhibitor adenylyl 3'-5' uridine 3' monophosphate (ApUp), and 405 well-ordered water molecules. The 2.0-A refined model reveals that the binding motif for ApUp includes residues in the catalytic and receptor-binding domains and is different from the Rossmann dinucleotide-binding fold. ApUp is bound in part by a long loop (residues 34-52) that crosses the active site. Several residues in the active site were previously identified as NAD-binding residues. Glu 148, previously identified as playing a catalytic role in ADP-ribosylation of elongation factor 2 by DT, is about 5 A from uracil in ApUp. The trigger for insertion of the transmembrane domain of DT into the endosomal membrane at low pH may involve 3 intradomain and 4 interdomain salt bridges that will be weakened at low pH by protonation of their acidic residues. The refined model also reveals that each molecule in dimeric DT has an "open" structure unlike most globular proteins, which we call an open monomer. Two open monomers interact by "domain swapping" to form a compact, globular dimeric DT structure. The possibility that the open monomer resembles a membrane insertion intermediate is discussed.
About this Structure
1DDT is a Single protein structure of sequence from Corynephage beta with as ligand. Full crystallographic information is available from OCA.
Reference
Refined structure of dimeric diphtheria toxin at 2.0 A resolution., Bennett MJ, Choe S, Eisenberg D, Protein Sci. 1994 Sep;3(9):1444-63. PMID:7833807
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