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.

3lio

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

X-ray structure of the iron superoxide dismutase from pseudoalteromonas haloplanktis (crystal form I)

Structural highlights

3lio is a 2 chain structure with sequence from Pseudoalteromonas translucida TAC125. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.5Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SODF_PSET1 Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems.^[1]

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

Superoxide dismutases (SODs) are metalloenzymes catalysing the dismutation of superoxide anion radicals into molecular oxygen and hydrogen peroxide. Here, we present the crystal structure of a cold-adapted Fe-SOD from the Antarctic eubacterium Pseudoalteromonas haloplanktis (PhSOD), and that of its complex with sodium azide. The structures were compared with those of the corresponding homologues having a high sequence identity with PhSOD, such as the mesophilic SOD from Escherichia coli (EcSOD) or Pseudomonas ovalis, and the psychrophilic SOD from Aliivibrio salmonicida (AsSOD). These enzymes shared a large structural similarity, such as a conserved tertiary structure and arrangement of the two monomers, an almost identical total number of inter- and intramolecular hydrogen bonds and salt bridges. However, the two cold-adapted SODs showed an increased flexibility of the active site residues with respect to their mesophilic homologues. Structural information was combined with a characterisation of the chemical and thermal stability performed by CD and fluorescence measurements. Despite of its psychrophilic origin, the denaturation temperature of PhSOD was comparable with that of the mesophilic EcSOD, whereas AsSOD showed a lower denaturation temperature. On the contrary, the values of the denaturant concentration at the transition midpoint were in line with the psychrophilic/mesophilic origin of the proteins. These data provide additional support to the hypothesis that cold-adapted enzymes achieve efficient catalysis at low temperature, by increasing the flexibility of their active site; moreover, our results underline how fine structural modifications can alter enzyme flexibility and/or stability without compromising the overall structure of typical rigid enzymes, such as SODs.

Structure and flexibility in cold-adapted iron superoxide dismutases: The case of the enzyme isolated from Pseudoalteromonas haloplanktis.,Merlino A, Krauss IR, Castellano I, Vendittis ED, Rossi B, Conte M, Vergara A, Sica F J Struct Biol. 2010 Aug 21. PMID:20732427^[2]

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

References

↑ Castellano I, Di Maro A, Ruocco MR, Chambery A, Parente A, Di Martino MT, Parlato G, Masullo M, De Vendittis E. Psychrophilic superoxide dismutase from Pseudoalteromonas haloplanktis: biochemical characterization and identification of a highly reactive cysteine residue. Biochimie. 2006 Oct;88(10):1377-89. Epub 2006 Apr 27. PMID:16713057 doi:http://dx.doi.org/S0300-9084(06)00055-1
↑ Merlino A, Krauss IR, Castellano I, Vendittis ED, Rossi B, Conte M, Vergara A, Sica F. Structure and flexibility in cold-adapted iron superoxide dismutases: The case of the enzyme isolated from Pseudoalteromonas haloplanktis. J Struct Biol. 2010 Aug 21. PMID:20732427 doi:10.1016/j.jsb.2010.08.008

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3lio"

@@ Line 1: / Line 1: @@
 ==X-ray structure of the iron superoxide dismutase from pseudoalteromonas haloplanktis (crystal form I)==
-<StructureSection load='3lio' size='340' side='right' caption='[[3lio]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+<StructureSection load='3lio' size='340' side='right'caption='[[3lio]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3lio]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseht Pseht]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LIO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LIO FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3lio]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudoalteromonas_translucida_TAC125 Pseudoalteromonas translucida TAC125]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LIO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LIO FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=TRE:TREHALOSE'>TRE</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]] 1.5&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3lj9|3lj9]], [[3ljf|3ljf]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PRD_900006:trehalose'>PRD_900006</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PSHAa1215, sodB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=326442 PSEHT])</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=3lio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lio OCA], [https://pdbe.org/3lio PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lio RCSB], [https://www.ebi.ac.uk/pdbsum/3lio PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lio ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </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=3lio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lio OCA], [http://pdbe.org/3lio PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lio RCSB], [http://www.ebi.ac.uk/pdbsum/3lio PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3lio ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SODF_PSEHT SODF_PSEHT]] Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems.<ref>PMID:16713057</ref>
+[https://www.uniprot.org/uniprot/SODF_PSET1 SODF_PSET1] Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems.<ref>PMID:16713057</ref>
 == 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/li/3lio_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/li/3lio_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 33: / Line 31: @@
 ==See Also==
-*[[Superoxide Dismutase|Superoxide Dismutase]]
+*[[Superoxide dismutase 3D structures|Superoxide dismutase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Pseht]]
+[[Category: Large Structures]]
-[[Category: Superoxide dismutase]]
+[[Category: Pseudoalteromonas translucida TAC125]]
-[[Category: Conte, M]]
+[[Category: Conte M]]
-[[Category: Krauss, I Russo]]
+[[Category: Merlino A]]
-[[Category: Merlino, A]]
+[[Category: Rossi B]]
-[[Category: Rossi, B]]
+[[Category: Russo Krauss I]]
-[[Category: Sica, F]]
+[[Category: Sica F]]
-[[Category: Vergara, A]]
+[[Category: Vergara A]]
-[[Category: Cold adaptation]]
-[[Category: Flexibility]]
-[[Category: Metal-binding]]
-[[Category: Oxidoreductase]]
-[[Category: Psychrophilic protein]]
-[[Category: Thermal stability]]

3lio

From Proteopedia

Current revision

X-ray structure of the iron superoxide dismutase from pseudoalteromonas haloplanktis (crystal form I)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox