1l6r

From Proteopedia

(Difference between revisions)

Revision as of 10:51, 25 December 2014

Crystal Structure of Thermoplasma acidophilum 0175 (APC0014)

Structural highlights

1l6r is a 2 chain structure with sequence from Thermoplasma acidophilum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	1kyt
Gene:	TA0175 (Thermoplasma acidophilum)
Resources:	FirstGlance, OCA, RCSB, PDBsum, TOPSAN

Function

[PGP_THEAC] Catalyzes the dephosphorylation of 2-phosphoglycolate. Also has significant, but less efficient, pyrophosphatase activity, since it is able to catalyze the release of phosphate from inorganic pyrophosphate (PPi).^[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

The protein TA0175 has a large number of sequence homologues, most of which are annotated as unknown and a few as belonging to the haloacid dehalogenase superfamily, but has no known biological function. Using a combination of amino acid sequence analysis, three-dimensional crystal structure information, and kinetic analysis, we have characterized TA0175 as phosphoglycolate phosphatase from Thermoplasma acidophilum. The crystal structure of TA0175 revealed two distinct domains, a larger core domain and a smaller cap domain. The large domain is composed of a centrally located five-stranded parallel beta-sheet with strand order S10, S9, S8, S1, S2 and a small beta-hairpin, strands S3 and S4. This central sheet is flanked by a set of three alpha-helices on one side and two helices on the other. The smaller domain is composed of an open faced beta-sandwich represented by three antiparallel beta-strands, S5, S6, and S7, flanked by two oppositely oriented alpha-helices, H3 and H4. The topology of the large domain is conserved; however, structural variation is observed in the smaller domain among the different functional classes of the haloacid dehalogenase superfamily. Enzymatic assays on TA0175 revealed that this enzyme catalyzed the dephosphorylation of phosphoglycolate in vitro with similar kinetic properties seen for eukaryotic phosphoglycolate phosphatase. Activation by divalent cations, especially Mg2+, and competitive inhibition behavior with Cl- ions are similar between TA0175 and phosphoglycolate phosphatase. The experimental evidence presented for TA0175 is indicative of phosphoglycolate phosphatase.

Structure- and function-based characterization of a new phosphoglycolate phosphatase from Thermoplasma acidophilum.,Kim Y, Yakunin AF, Kuznetsova E, Xu X, Pennycooke M, Gu J, Cheung F, Proudfoot M, Arrowsmith CH, Joachimiak A, Edwards AM, Christendat D J Biol Chem. 2004 Jan 2;279(1):517-26. Epub 2003 Oct 10. PMID:14555659^[2]

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

References

↑ Kim Y, Yakunin AF, Kuznetsova E, Xu X, Pennycooke M, Gu J, Cheung F, Proudfoot M, Arrowsmith CH, Joachimiak A, Edwards AM, Christendat D. Structure- and function-based characterization of a new phosphoglycolate phosphatase from Thermoplasma acidophilum. J Biol Chem. 2004 Jan 2;279(1):517-26. Epub 2003 Oct 10. PMID:14555659 doi:10.1074/jbc.M306054200
↑ Kim Y, Yakunin AF, Kuznetsova E, Xu X, Pennycooke M, Gu J, Cheung F, Proudfoot M, Arrowsmith CH, Joachimiak A, Edwards AM, Christendat D. Structure- and function-based characterization of a new phosphoglycolate phosphatase from Thermoplasma acidophilum. J Biol Chem. 2004 Jan 2;279(1):517-26. Epub 2003 Oct 10. PMID:14555659 doi:10.1074/jbc.M306054200

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/1l6r"

@@ Line 3: / Line 3: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[1l6r]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermoplasma_acidophilum Thermoplasma acidophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L6R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L6R FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene><br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1kyt|1kyt]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1kyt|1kyt]]</td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TA0175 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2303 Thermoplasma acidophilum])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TA0175 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2303 Thermoplasma acidophilum])</td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1l6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l6r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1l6r RCSB], [http://www.ebi.ac.uk/pdbsum/1l6r PDBsum], [http://www.topsan.org/Proteins/MCSG/1l6r 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=1l6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l6r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1l6r RCSB], [http://www.ebi.ac.uk/pdbsum/1l6r PDBsum], [http://www.topsan.org/Proteins/MCSG/1l6r TOPSAN]</span></td></tr>
-<table>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/PGP_THEAC PGP_THEAC]] Catalyzes the dephosphorylation of 2-phosphoglycolate. Also has significant, but less efficient, pyrophosphatase activity, since it is able to catalyze the release of phosphate from inorganic pyrophosphate (PPi).<ref>PMID:14555659</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 31: / Line 33: @@
 </StructureSection>
 [[Category: Thermoplasma acidophilum]]
-[[Category: Cheung, F.]]
+[[Category: Cheung, F]]
-[[Category: Christendat, D.]]
+[[Category: Christendat, D]]
-[[Category: Edwards, A M.]]
+[[Category: Edwards, A M]]
-[[Category: Gu, J.]]
+[[Category: Gu, J]]
-[[Category: Joachimiak, A.]]
+[[Category: Joachimiak, A]]
-[[Category: Kim, Y.]]
+[[Category: Kim, Y]]
-[[Category: MCSG, Midwest Center for Structural Genomics.]]
+[[Category: Structural genomic]]
-[[Category: Pennycooke, M.]]
+[[Category: Pennycooke, M]]
-[[Category: Xu, X.]]
+[[Category: Xu, X]]
 [[Category: Hypothetical protein]]
 [[Category: Mcsg]]
-[[Category: Midwest center for structural genomic]]
+[[Category: PSI, Protein structure initiative]]
-[[Category: Protein structure initiative]]
-[[Category: Psi]]
 [[Category: Putative hydrolase]]
-[[Category: Structural genomic]]
 [[Category: Unknown function]]

1l6r

From Proteopedia

Revision as of 10:51, 25 December 2014

Crystal Structure of Thermoplasma acidophilum 0175 (APC0014)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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