3hdl

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of Highly Glycosylated Peroxidase from Royal Palm Tree

Structural highlights

3hdl is a 1 chain structure with sequence from Roystonea regia. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.85Å
Ligands:	, , , , , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

D1MPT2_ROYRE

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

Royal palm tree peroxidase (RPTP) is a very stable enzyme in regards to acidity, temperature, H(2)O(2), and organic solvents. Thus, RPTP is a promising candidate for developing H(2)O(2)-sensitive biosensors for diverse applications in industry and analytical chemistry. RPTP belongs to the family of class III secretory plant peroxidases, which include horseradish peroxidase isozyme C, soybean and peanut peroxidases. Here we report the X-ray structure of native RPTP isolated from royal palm tree (Roystonea regia) refined to a resolution of 1.85A. RPTP has the same overall folding pattern of the plant peroxidase superfamily, and it contains one heme group and two calcium-binding sites in similar locations. The three-dimensional structure of RPTP was solved for a hydroperoxide complex state, and it revealed a bound 2-(N-morpholino) ethanesulfonic acid molecule (MES) positioned at a putative substrate-binding secondary site. Nine N-glycosylation sites are clearly defined in the RPTP electron-density maps, revealing for the first time conformations of the glycan chains of this highly glycosylated enzyme. Furthermore, statistical coupling analysis (SCA) of the plant peroxidase superfamily was performed. This sequence-based method identified a set of evolutionarily conserved sites that mapped to regions surrounding the heme prosthetic group. The SCA matrix also predicted a set of energetically coupled residues that are involved in the maintenance of the structural folding of plant peroxidases. The combination of crystallographic data and SCA analysis provides information about the key structural elements that could contribute to explaining the unique stability of RPTP.

Crystal structure and statistical coupling analysis of highly glycosylated peroxidase from royal palm tree (Roystonea regia).,Watanabe L, de Moura PR, Bleicher L, Nascimento AS, Zamorano LS, Calvete JJ, Sanz L, Perez A, Bursakov S, Roig MG, Shnyrov VL, Polikarpov I J Struct Biol. 2010 Feb;169(2):226-42. Epub 2009 Oct 23. PMID:19854274^[1]

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

References

↑ Watanabe L, de Moura PR, Bleicher L, Nascimento AS, Zamorano LS, Calvete JJ, Sanz L, Perez A, Bursakov S, Roig MG, Shnyrov VL, Polikarpov I. Crystal structure and statistical coupling analysis of highly glycosylated peroxidase from royal palm tree (Roystonea regia). J Struct Biol. 2010 Feb;169(2):226-42. Epub 2009 Oct 23. PMID:19854274 doi:10.1016/j.jsb.2009.10.009

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/3hdl"

@@ Line 3: / Line 3: @@
 <StructureSection load='3hdl' size='340' side='right'caption='[[3hdl]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3hdl]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Roystonea_regia Roystonea regia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HDL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3HDL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3hdl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Roystonea_regia Roystonea regia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HDL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HDL FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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]] 1.85&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=XYZ:BETA-D-XYLOFURANOSE'>XYZ</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=XYZ:BETA-D-XYLOFURANOSE'>XYZ</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3hdl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hdl OCA], [http://pdbe.org/3hdl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hdl RCSB], [http://www.ebi.ac.uk/pdbsum/3hdl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3hdl ProSAT]</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=3hdl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hdl OCA], [https://pdbe.org/3hdl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hdl RCSB], [https://www.ebi.ac.uk/pdbsum/3hdl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hdl ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/D1MPT2_ROYRE D1MPT2_ROYRE]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 13: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hd/3hdl_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 33: / Line 35: @@
 [[Category: Large Structures]]
 [[Category: Roystonea regia]]
-[[Category: Bleicher, L]]
+[[Category: Bleicher L]]
-[[Category: Bursakov, S]]
+[[Category: Bursakov S]]
-[[Category: Calvete, J J]]
+[[Category: Calvete JJ]]
-[[Category: Moura, P R]]
+[[Category: Moura PR]]
-[[Category: Nascimento, A S]]
+[[Category: Nascimento AS]]
-[[Category: Polikarpov, I]]
+[[Category: Polikarpov I]]
-[[Category: Roig, M G]]
+[[Category: Roig MG]]
-[[Category: Shnyrov, V L]]
+[[Category: Shnyrov VL]]
-[[Category: Watanabe, L]]
+[[Category: Watanabe L]]
-[[Category: Zamorano, L S]]
+[[Category: Zamorano LS]]
-[[Category: Glycosylated]]
-[[Category: Oxidoreductase]]
-[[Category: Palm tree]]
-[[Category: Peroxidase]]

3hdl

From Proteopedia

Current revision

Crystal Structure of Highly Glycosylated Peroxidase from Royal Palm Tree

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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