1yf1

From Proteopedia

(Difference between revisions)

Current revision

Structural and biochemical analysis of the link between enzymatic activity and oligomerization in AhpC, a bacterial peroxiredoxin.

Structural highlights

1yf1 is a 10 chain structure with sequence from Salmonella enterica subsp. enterica serovar Typhimurium. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.6Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AHPC_SALTY Directly reduces alkyl hydroperoxides with the use of electrons donated by the 57 kDa flavoprotein alkyl hydroperoxide reductase.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Peroxiredoxins (Prxs) make up a ubiquitous class (proposed EC 1.11.1.15) of cysteine-dependent peroxidases with roles in oxidant protection and signal transduction. An intriguing biophysical property of typical 2-Cys Prxs is the redox-dependent modulation of their oligomeric state between decamers and dimers at physiological concentrations. The functional consequences of this linkage are unknown, but on the basis of structural considerations, we hypothesized that decamer-building (dimer-dimer) interactions serve to stabilize a loop that forms the peroxidatic active site. Here, we address this important issue by studying mutations of Thr77 at the decamer-building interface of AhpC from Salmonella typhimurium. Ultracentrifugation studies revealed that two of the substitutions (T77I and T77D) successfully disrupted the decamer, while the third (T77V) actually enhanced decamer stability. Crystal structures of the decameric forms of all three mutant proteins provide a rationale for their properties. A new assay allowed the first ever measurement of the true k(cat) and K(m) values of wild-type AhpC with H(2)O(2), placing the catalytic efficiency at 4 x 10(7) M(-)(1) s(-)(1). T77V had slightly higher activity than wild-type enzyme, and both T77I and T77D exhibited ca. 100-fold lower catalytic efficiency, indicating that the decameric structure is quite important for, but not essential to, activity. The interplay between decamer formation and active site loop dynamics is emphasized by a decreased susceptibility of T77I and T77D to peroxide-mediated inactivation, and by an increase in the crystallographic B-factors in the active site loop, rather than at the site of the mutation, in the T77D variant.

Analysis of the link between enzymatic activity and oligomeric state in AhpC, a bacterial peroxiredoxin.,Parsonage D, Youngblood DS, Sarma GN, Wood ZA, Karplus PA, Poole LB Biochemistry. 2005 Aug 9;44(31):10583-92. PMID:16060667^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Parsonage D, Youngblood DS, Sarma GN, Wood ZA, Karplus PA, Poole LB. Analysis of the link between enzymatic activity and oligomeric state in AhpC, a bacterial peroxiredoxin. Biochemistry. 2005 Aug 9;44(31):10583-92. PMID:16060667 doi:10.1021/bi050448i

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1yf1"

@@ Line 1: / Line 1: @@
 ==Structural and biochemical analysis of the link between enzymatic activity and oligomerization in AhpC, a bacterial peroxiredoxin.==
-<StructureSection load='1yf1' size='340' side='right' caption='[[1yf1]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+<StructureSection load='1yf1' size='340' side='right'caption='[[1yf1]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1yf1]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YF1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YF1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1yf1]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YF1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YF1 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1kyg|1kyg]], [[1yf0|1yf0]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxiredoxin Peroxiredoxin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.15 1.11.1.15] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yf1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yf1 OCA], [https://pdbe.org/1yf1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yf1 RCSB], [https://www.ebi.ac.uk/pdbsum/1yf1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yf1 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yf1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yf1 OCA], [http://pdbe.org/1yf1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yf1 RCSB], [http://www.ebi.ac.uk/pdbsum/1yf1 PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/AHPC_SALTY AHPC_SALTY]] Directly reduces alkyl hydroperoxides with the use of electrons donated by the 57 kDa flavoprotein alkyl hydroperoxide reductase.
+[https://www.uniprot.org/uniprot/AHPC_SALTY AHPC_SALTY] Directly reduces alkyl hydroperoxides with the use of electrons donated by the 57 kDa flavoprotein alkyl hydroperoxide reductase.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yf/1yf1_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yf/1yf1_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Peroxiredoxin]]
+[[Category: Large Structures]]
-[[Category: Karplus, P A]]
+[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
-[[Category: Parsonage, D]]
+[[Category: Karplus PA]]
-[[Category: Poole, L B]]
+[[Category: Parsonage D]]
-[[Category: Sarma, G N]]
+[[Category: Poole LB]]
-[[Category: Wood, Z A]]
+[[Category: Sarma GN]]
-[[Category: Youngblood, D S]]
+[[Category: Wood ZA]]
-[[Category: Ahpc]]
+[[Category: Youngblood DS]]
-[[Category: Alkyl hydroperoxide reductase subunit c]]
-[[Category: Oxidoreductase]]

1yf1

From Proteopedia

Current revision

Structural and biochemical analysis of the link between enzymatic activity and oligomerization in AhpC, a bacterial peroxiredoxin.

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox