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.


2fa1

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="2fa1" size="450" color="white" frame="true" align="right" spinBox="true" caption="2fa1, resolution 1.70&Aring;" /> '''Crystal structure of...)
Current revision (09:22, 14 February 2024) (edit) (undo)
 
(17 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2fa1.gif|left|200px]]<br /><applet load="2fa1" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="2fa1, resolution 1.70&Aring;" />
 
-
'''Crystal structure of PhnF C-terminal domain'''<br />
 
-
==Overview==
+
==Crystal structure of PhnF C-terminal domain==
-
The crystal structure of Escherichia coli PhnF C-terminal domain (C-PhnF), was solved at 1.7 A resolution by the single wavelength anomalous, dispersion (SAD) method. The PhnF protein belongs to the HutC subfamily of, the large GntR transcriptional regulator family. Members of this family, share similar N-terminal DNA-binding domains, but are divided into four, subfamilies according to their heterogenic C-terminal domains, which are, involved in effector binding and oligomerization. The C-PhnF structure, provides for the first time the scaffold of this domain for the HutC, subfamily, which covers about 31% of GntR-like regulators. The structure, represents a mixture of alpha-helices and beta-strands, with a, six-stranded antiparallel beta-sheet at the core. C-PhnF monomers form a, dimer by establishing interdomain eight-strand beta-sheets that include, core antiparallel and N-terminal two-strand parallel beta-sheets from each, monomer. C-PhnF shares strong structural similarity with the chorismate, lyase fold, which features a buried active site locked behind two, helix-turn-helix loops. The structural comparison of the C-PhnF and UbiC, proteins allows us to propose that a similar site in the PhnF structure is, adapted for effector binding.
+
<StructureSection load='2fa1' size='340' side='right'caption='[[2fa1]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[2fa1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FA1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FA1 FirstGlance]. <br>
-
2FA1 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with BDF as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2FA1 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]] 1.7&#8491;</td></tr>
-
 
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BDF:BETA-D-FRUCTOPYRANOSE'>BDF</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=2fa1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fa1 OCA], [https://pdbe.org/2fa1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fa1 RCSB], [https://www.ebi.ac.uk/pdbsum/2fa1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fa1 ProSAT], [https://www.topsan.org/Proteins/MCSG/2fa1 TOPSAN]</span></td></tr>
-
Structural characterization of GntR/HutC family signaling domain., Gorelik M, Lunin VV, Skarina T, Savchenko A, Protein Sci. 2006 Jun;15(6):1506-11. Epub 2006 May 2. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16672238 16672238]
+
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/PHNF_ECOLI PHNF_ECOLI] Belongs to an operon involved in alkylphosphonate uptake and C-P lyase. Exact function not known. By similarity could be a transcriptional regulator.
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fa/2fa1_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</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=2fa1 ConSurf].
 +
<div style="clear:both"></div>
 +
__TOC__
 +
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Edwards, A.M.]]
+
[[Category: Edwards AM]]
-
[[Category: Gorelik, M.]]
+
[[Category: Gorelik M]]
-
[[Category: Lunin, V.V.]]
+
[[Category: Joachimiak A]]
-
[[Category: MCSG, Midwest.Center.for.Structural.Genomics.]]
+
[[Category: Lunin VV]]
-
[[Category: Nocek, B.P.]]
+
[[Category: Nocek BP]]
-
[[Category: Savchenko, A.]]
+
[[Category: Savchenko A]]
-
[[Category: Skarina, T.]]
+
[[Category: Skarina T]]
-
[[Category: BDF]]
+
-
[[Category: apc5558]]
+
-
[[Category: effector binding domain]]
+
-
[[Category: mcsg]]
+
-
[[Category: midwest center for structural genomics]]
+
-
[[Category: pnhf]]
+
-
[[Category: protein structure initiative]]
+
-
[[Category: psi]]
+
-
[[Category: regulator]]
+
-
[[Category: transcription]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 10:26:47 2007''
+

Current revision

Crystal structure of PhnF C-terminal domain

PDB ID 2fa1

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/2fa1"
Personal tools