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.


1t6c

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:30, 13 March 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1t6c.jpg|left|200px]]<br /><applet load="1t6c" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1t6c, resolution 1.53&Aring;" />
 
-
'''Structural characterization of the Ppx/GppA protein family: crystal structure of the Aquifex aeolicus family member'''<br />
 
-
==Overview==
+
==Structural characterization of the Ppx/GppA protein family: crystal structure of the Aquifex aeolicus family member==
-
Exopolyphosphatase/guanosine pentaphosphate phosphohydrolase (PPX/GPPA) enzymes play central roles in the bacterial stringent response induced by starvation. The high-resolution crystal structure of the putative Aquifex aeolicus PPX/GPPA phosphatase from the actin-like ATPase domain superfamily has been determined, providing the first insights to features of the common catalytic core of the PPX/GPPA family. The protein has a two-domain structure with an active site located in the interdomain cleft. Two crystal forms were investigated (type I and II) at resolutions of 1.53 and 2.15 A, respectively. This revealed a structural flexibility that has previously been described as a "butterfly-like" cleft opening around the active site in other actin-like superfamily proteins. A calcium ion is observed at the center of this region in type I crystals, substantiating that PPX/GPPA enzymes use metal ions for catalysis. Structural analysis suggests that nucleotides bind at a similar position to that seen in other members of the superfamily.
+
<StructureSection load='1t6c' size='340' side='right'caption='[[1t6c]], [[Resolution|resolution]] 1.53&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[1t6c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus_VF5 Aquifex aeolicus VF5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T6C FirstGlance]. <br>
-
1T6C is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus_vf5 Aquifex aeolicus vf5] with <scene name='pdbligand=IOD:'>IOD</scene>, <scene name='pdbligand=CA:'>CA</scene>, <scene name='pdbligand=CL:'>CL</scene> and <scene name='pdbligand=MPD:'>MPD</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6C OCA].
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.53&#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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
-
==Reference==
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1t6c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6c OCA], [https://pdbe.org/1t6c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t6c RCSB], [https://www.ebi.ac.uk/pdbsum/1t6c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t6c ProSAT]</span></td></tr>
-
Structural characterization of the stringent response related exopolyphosphatase/guanosine pentaphosphate phosphohydrolase protein family., Kristensen O, Laurberg M, Liljas A, Kastrup JS, Gajhede M, Biochemistry. 2004 Jul 20;43(28):8894-900. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15248747 15248747]
+
</table>
-
[[Category: Aquifex aeolicus vf5]]
+
== Function ==
-
[[Category: Single protein]]
+
[https://www.uniprot.org/uniprot/O67040_AQUAE O67040_AQUAE]
-
[[Category: Gajhede, M.]]
+
== Evolutionary Conservation ==
-
[[Category: Kastrup, J S.]]
+
[[Image:Consurf_key_small.gif|200px|right]]
-
[[Category: Kristensen, O.]]
+
Check<jmol>
-
[[Category: Laurberg, M.]]
+
<jmolCheckbox>
-
[[Category: Liljas, A.]]
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/t6/1t6c_consurf.spt"</scriptWhenChecked>
-
[[Category: CA]]
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
[[Category: CL]]
+
<text>to colour the structure by Evolutionary Conservation</text>
-
[[Category: IOD]]
+
</jmolCheckbox>
-
[[Category: MPD]]
+
</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=1t6c ConSurf].
-
[[Category: actin-like fold]]
+
<div style="clear:both"></div>
-
[[Category: alpha/beta protein]]
+
__TOC__
-
 
+
</StructureSection>
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:10:23 2008''
+
[[Category: Aquifex aeolicus VF5]]
 +
[[Category: Large Structures]]
 +
[[Category: Gajhede M]]
 +
[[Category: Kastrup JS]]
 +
[[Category: Kristensen O]]
 +
[[Category: Laurberg M]]
 +
[[Category: Liljas A]]

Current revision

Structural characterization of the Ppx/GppA protein family: crystal structure of the Aquifex aeolicus family member

PDB ID 1t6c

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/1t6c"
Personal tools