This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2hag

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 07:35, 17 March 2021

Crystal structure of a putative dyp-type peroxidase protein (so_0740) from shewanella oneidensis at 2.75 A resolution

Structural highlights

2hag is a 1 chain structure with sequence from Atcc 700550. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
NonStd Res:
Gene:	np_716371.1 (ATCC 700550)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

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

BtDyP from Bacteroides thetaiotaomicron (strain VPI-5482) and TyrA from Shewanella oneidensis are dye-decolorizing peroxidases (DyPs), members of a new family of heme-dependent peroxidases recently identified in fungi and bacteria. Here, we report the crystal structures of BtDyP and TyrA at 1.6 and 2.7 A, respectively. BtDyP assembles into a hexamer, while TyrA assembles into a dimer; the dimerization interface is conserved between the two proteins. Each monomer exhibits a two-domain, alpha+beta ferredoxin-like fold. A site for heme binding was identified computationally, and modeling of a heme into the proposed active site allowed for identification of residues likely to be functionally important. Structural and sequence comparisons with other DyPs demonstrate a conservation of putative heme-binding residues, including an absolutely conserved histidine. Isothermal titration calorimetry experiments confirm heme binding, but with a stoichiometry of 0.3:1 (heme:protein).

Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif.,Zubieta C, Krishna SS, Kapoor M, Kozbial P, McMullan D, Axelrod HL, Miller MD, Abdubek P, Ambing E, Astakhova T, Carlton D, Chiu HJ, Clayton T, Deller MC, Duan L, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Hampton E, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kumar A, Marciano D, Morse AT, Nigoghossian E, Okach L, Oommachen S, Reyes R, Rife CL, Schimmel P, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA Proteins. 2007 Nov 1;69(2):223-33. PMID:17654545^[1]

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

References

↑ Zubieta C, Krishna SS, Kapoor M, Kozbial P, McMullan D, Axelrod HL, Miller MD, Abdubek P, Ambing E, Astakhova T, Carlton D, Chiu HJ, Clayton T, Deller MC, Duan L, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Hampton E, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kumar A, Marciano D, Morse AT, Nigoghossian E, Okach L, Oommachen S, Reyes R, Rife CL, Schimmel P, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif. Proteins. 2007 Nov 1;69(2):223-33. PMID:17654545 doi:10.1002/prot.21550

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2hag"

@@ Line 1: / Line 1: @@
 ==Crystal structure of a putative dyp-type peroxidase protein (so_0740) from shewanella oneidensis at 2.75 A resolution==
-<StructureSection load='2hag' size='340' side='right' caption='[[2hag]], [[Resolution|resolution]] 2.75&Aring;' scene=''>
+<StructureSection load='2hag' size='340' side='right'caption='[[2hag]], [[Resolution|resolution]] 2.75&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2hag]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_700550 Atcc 700550]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HAG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HAG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2hag]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_700550 Atcc 700550]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HAG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HAG FirstGlance]. <br>
 </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">np_716371.1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70863 ATCC 700550])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">np_716371.1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70863 ATCC 700550])</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=2hag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hag OCA], [http://pdbe.org/2hag PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hag RCSB], [http://www.ebi.ac.uk/pdbsum/2hag PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2hag ProSAT], [http://www.topsan.org/Proteins/JCSG/2hag TOPSAN]</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=2hag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hag OCA], [https://pdbe.org/2hag PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hag RCSB], [https://www.ebi.ac.uk/pdbsum/2hag PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hag ProSAT], [https://www.topsan.org/Proteins/JCSG/2hag TOPSAN]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 12: / Line 12: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ha/2hag_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ha/2hag_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 32: / Line 32: @@
 </StructureSection>
 [[Category: Atcc 700550]]
+[[Category: Large Structures]]
 [[Category: Structural genomic]]
 [[Category: Ferredoxin-like fold]]

2hag

From Proteopedia

Revision as of 07:35, 17 March 2021

Crystal structure of a putative dyp-type peroxidase protein (so_0740) from shewanella oneidensis at 2.75 A resolution

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox