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1wr8

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Revision as of 21:07, 10 September 2015

Crystal structure of hypothetical protein PH1421 from Pyrococcus horikoshii.

Structural highlights

1wr8 is a 2 chain structure with sequence from Pyrho. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	PH1421 (PYRHO)
Activity:	Phosphoglycolate phosphatase, with EC number 3.1.3.18
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, TOPSAN

Function

[PGP_PYRHO] Catalyzes the dephosphorylation of 2-phosphoglycolate (By similarity). Has phosphatase activity towards p-nitrophenylphosphate (in vitro).[HAMAP-Rule:MF_01419]

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

PH1421 from the hyperthermophilic archaeon Pyrococcus horikoshii OT3 is a hypothetical protein belonging to the haloacid dehalogenase (HAD) superfamily. To gain insight into its biological function and thermostabilization mechanism, the crystal structure of PH1421 has been determined at 1.6 A resolution. The crystallographic asymmetric unit contains a homodimer. The monomeric protomer is composed of two distinct domains, a small cap domain and a large core domain, which agrees well with the typical domain organization of HAD subfamily II. Based on structure-based amino-acid sequence alignment and enzymatic analysis, PH1421 is suggested to be a magnesium-dependent phosphatase that is similar to the dimeric HAD phosphatase TA0175 from the mesothermophilic archaeon Thermoplasma acidophilum. Further comparison between the crystal structures of PH1421 and TA0175 revealed a marked structural similarity in the interprotomer dimer association. The common dimer interface with interprotomer twofold symmetry is characterized by a well conserved hydrophobic core consisting of the beta1-alpha1 loop and helices alpha1 and alpha2 of the core domain and additional contacts including the beta7-beta8 loop of the cap domain, which constitutes part of the putative active site of the enzyme. Several factors that potentially contribute to the higher thermal stability of PH1421 were identified: (i) an increase in intraprotomer hydrophobic interactions, (ii) a decrease in denaturation entropy from amino-acid composition and (iii) an increased number of intraprotomer ion pairs. These results suggest that the PH1421 protomer itself has an intrinsically higher thermal stability when compared with the mesothermophilic orthologue TA0175.

Structure of a haloacid dehalogenase superfamily phosphatase PH1421 from Pyrococcus horikoshii OT3: oligomeric state and thermoadaptation mechanism.,Yamamoto H, Takio K, Sugahara M, Kunishima N Acta Crystallogr D Biol Crystallogr. 2008 Oct;64(Pt 10):1068-77. Epub 2008, Sep 19. PMID:18931414^[1]

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

References

↑ Yamamoto H, Takio K, Sugahara M, Kunishima N. Structure of a haloacid dehalogenase superfamily phosphatase PH1421 from Pyrococcus horikoshii OT3: oligomeric state and thermoadaptation mechanism. Acta Crystallogr D Biol Crystallogr. 2008 Oct;64(Pt 10):1068-77. Epub 2008, Sep 19. PMID:18931414 doi:10.1107/S0907444908025948

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/1wr8"

@@ Line 2: / Line 2: @@
 <StructureSection load='1wr8' size='340' side='right' caption='[[1wr8]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1wr8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WR8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WR8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1wr8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrho Pyrho]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WR8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WR8 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PH1421 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 Pyrococcus horikoshii])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PH1421 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 PYRHO])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoglycolate_phosphatase Phosphoglycolate phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.18 3.1.3.18] </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=1wr8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wr8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wr8 RCSB], [http://www.ebi.ac.uk/pdbsum/1wr8 PDBsum], [http://www.topsan.org/Proteins/RSGI/1wr8 TOPSAN]</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=1wr8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wr8 OCA], [http://pdbe.org/1wr8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wr8 RCSB], [http://www.ebi.ac.uk/pdbsum/1wr8 PDBsum], [http://www.topsan.org/Proteins/RSGI/1wr8 TOPSAN]</span></td></tr>
 </table>
 == Function ==
@@ Line 28: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1wr8" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 33: / Line 34: @@
 </StructureSection>
 [[Category: Phosphoglycolate phosphatase]]
-[[Category: Pyrococcus horikoshii]]
+[[Category: Pyrho]]
 [[Category: Kunishima, N]]
 [[Category: Structural genomic]]

1wr8

From Proteopedia

Revision as of 21:07, 10 September 2015

Crystal structure of hypothetical protein PH1421 from Pyrococcus horikoshii.

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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