1p4a

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:05, 14 February 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1p4a.gif|left|200px]]
 
-
<!--
+
==Crystal Structure of the PurR complexed with cPRPP==
-
The line below this paragraph, containing "STRUCTURE_1p4a", creates the "Structure Box" on the page.
+
<StructureSection load='1p4a' size='340' side='right'caption='[[1p4a]], [[Resolution|resolution]] 2.22&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'>[[1p4a]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P4A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P4A 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]] 2.22&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PCP:1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-ALPHA-DIHYDROXY-4-BETA-CYCLOPENTANE-METHANOL-5-PHOSPHATE'>PCP</scene></td></tr>
-
{{STRUCTURE_1p4a| PDB=1p4a | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1p4a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p4a OCA], [https://pdbe.org/1p4a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p4a RCSB], [https://www.ebi.ac.uk/pdbsum/1p4a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p4a ProSAT]</span></td></tr>
-
 
+
</table>
-
'''Crystal Structure of the PurR complexed with cPRPP'''
+
== Function ==
-
 
+
[https://www.uniprot.org/uniprot/PURR_BACSU PURR_BACSU] Controls the transcription of the pur operon for purine biosynthetic genes, binds to the control region of the operon. DNA binding is inhibited by 5-phosphoribosyl 1-pyrophosphate.
-
 
+
== Evolutionary Conservation ==
-
==Overview==
+
[[Image:Consurf_key_small.gif|200px|right]]
-
Bacillus subtilis PurR represses transcription of several genes involved in purine synthesis, metabolism, and transport and cofactor synthesis. PurR binds specifically to DNAs containing an inverted repeat of a 14-nucleotide "PurBox" located in the upstream control regions of genes in the PurR regulon. Further biochemical investigation of the interaction of PurR with a series of shortened upstream DNA fragments of the pur operon determined the minimum length and specificity elements of the operator. The relative affinities of the two PurBoxes differ significantly, such that upstream PurBox1 (-81 to -68 relative to the transcription start site) is designated "strong" and downstream PurBox2 (-49 to -36) is designated "weak." Two PurBoxes are required for high-affinity PurR binding, and one of these must be strong. The shortest DNA construct with high affinity for PurR is a 74-bp perfect palindrome in which weak PurBox2 and its flanking sequences are replaced by strong PurBox1 and flanking sequences. Two PurR dimers bind to this symmetric construct. Phosphoribosylpyrophosphate (PRPP), the effector molecule that reduces affinity of PurR for DNA, requires one weak PurBox in the DNA construct to inhibit PurR binding. PRPP binds, as expected, to a PRPP-motif in PurR. A tracks outside the central conserved CGAA sequence of the PurBox may facilitate DNA bending, leading to a proposal for strong and weak designations of PurBoxes in the control regions of other genes regulated by PurR.
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==About this Structure==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p4/1p4a_consurf.spt"</scriptWhenChecked>
-
1P4A is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P4A OCA].
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==Reference==
+
</jmolCheckbox>
-
Functional dissection of the Bacillus subtilis pur operator site., Bera AK, Zhu J, Zalkin H, Smith JL, J Bacteriol. 2003 Jul;185(14):4099-109. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12837784 12837784]
+
</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=1p4a ConSurf].
 +
<div style="clear:both"></div>
 +
__TOC__
 +
</StructureSection>
[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Bera, A K.]]
+
[[Category: Bera AK]]
-
[[Category: Smith, J L.]]
+
[[Category: Smith JL]]
-
[[Category: Zalkin, H.]]
+
[[Category: Zalkin H]]
-
[[Category: Zhu, J.]]
+
[[Category: Zhu J]]
-
[[Category: Transcription]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 04:40:00 2008''
+

Current revision

Crystal Structure of the PurR complexed with cPRPP

PDB ID 1p4a

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/1p4a"
Personal tools