1l6r

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:30, 14 February 2024) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1l6r.gif|left|200px]]
 
-
<!--
+
==Crystal Structure of Thermoplasma acidophilum 0175 (APC0014)==
-
The line below this paragraph, containing "STRUCTURE_1l6r", creates the "Structure Box" on the page.
+
<StructureSection load='1l6r' size='340' side='right'caption='[[1l6r]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[1l6r]] is a 2 chain structure with sequence from [https://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 [https://proteopedia.org/fgij/fg.htm?mol=1L6R FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4&#8491;</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=FMT:FORMIC+ACID'>FMT</scene></td></tr>
-
{{STRUCTURE_1l6r| PDB=1l6r | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1l6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l6r OCA], [https://pdbe.org/1l6r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l6r RCSB], [https://www.ebi.ac.uk/pdbsum/1l6r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l6r ProSAT], [https://www.topsan.org/Proteins/MCSG/1l6r TOPSAN]</span></td></tr>
-
 
+
</table>
-
'''Crystal Structure of Thermoplasma acidophilum 0175 (APC0014)'''
+
== Function ==
-
 
+
[https://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 ==
-
==Overview==
+
[[Image:Consurf_key_small.gif|200px|right]]
-
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.
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==About this Structure==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l6/1l6r_consurf.spt"</scriptWhenChecked>
-
1L6R is a [[Single protein]] structure of 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].
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==Reference==
+
</jmolCheckbox>
-
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:[http://www.ncbi.nlm.nih.gov/pubmed/14555659 14555659]
+
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1l6r ConSurf].
-
[[Category: Single protein]]
+
<div style="clear:both"></div>
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Thermoplasma acidophilum]]
[[Category: Thermoplasma acidophilum]]
-
[[Category: Cheung, F.]]
+
[[Category: Cheung F]]
-
[[Category: Christendat, D.]]
+
[[Category: Christendat D]]
-
[[Category: Edwards, A M.]]
+
[[Category: Edwards AM]]
-
[[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: Pennycooke M]]
-
[[Category: Pennycooke, M.]]
+
[[Category: Xu X]]
-
[[Category: Xu, X.]]
+
-
[[Category: Hypothetical protein]]
+
-
[[Category: Mcsg]]
+
-
[[Category: Midwest center for structural genomic]]
+
-
[[Category: Protein structure initiative]]
+
-
[[Category: Psi]]
+
-
[[Category: Putative hydrolase]]
+
-
[[Category: Structural genomic]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 23:36:08 2008''
+

Current revision

Crystal Structure of Thermoplasma acidophilum 0175 (APC0014)

PDB ID 1l6r

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1l6r"
Personal tools