3bos

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "3bos" [edit=sysop:move=sysop])
Current revision (01:38, 21 November 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:3bos.png|left|200px]]
 
-
<!--
+
==Crystal structure of a putative dna replication regulator HDA (SAMA_1916) from Shewanella amazonensis sb2b at 1.75 A resolution==
-
The line below this paragraph, containing "STRUCTURE_3bos", creates the "Structure Box" on the page.
+
<StructureSection load='3bos' size='340' side='right'caption='[[3bos]], [[Resolution|resolution]] 1.75&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'>[[3bos]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_amazonensis_SB2B Shewanella amazonensis SB2B]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BOS 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]] 1.75&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CDP:CYTIDINE-5-DIPHOSPHATE'>CDP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></td></tr>
-
{{STRUCTURE_3bos| PDB=3bos | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bos FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bos OCA], [https://pdbe.org/3bos PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bos RCSB], [https://www.ebi.ac.uk/pdbsum/3bos PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bos ProSAT], [https://www.topsan.org/Proteins/JCSG/3bos TOPSAN]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/A1S6W5_SHEAM A1S6W5_SHEAM]
 +
== 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/bo/3bos_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3bos ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Regulatory inactivation of DnaA is dependent on Hda (homologous to DnaA), a protein homologous to the AAA+ (ATPases associated with diverse cellular activities) ATPase region of the replication initiator DnaA. When bound to the sliding clamp loaded onto duplex DNA, Hda can stimulate the transformation of active DnaA-ATP into inactive DnaA-ADP. The crystal structure of Hda from Shewanella amazonensis SB2B at 1.75 A resolution reveals that Hda resembles typical AAA+ ATPases. The arrangement of the two subdomains in Hda (residues 1-174 and 175-241) differs dramatically from that of DnaA. A CDP molecule anchors the Hda domains in a conformation that promotes dimer formation. The Hda dimer adopts a novel oligomeric assembly for AAA+ proteins in which the arginine finger, crucial for ATP hydrolysis, is fully exposed and available to hydrolyze DnaA-ATP through a typical AAA+ type of mechanism. The sliding clamp binding motifs at the N-terminus of each Hda monomer are partially buried and combine to form an antiparallel beta-sheet at the dimer interface. The inaccessibility of the clamp binding motifs in the CDP-bound structure of Hda suggests that conformational changes are required for Hda to form a functional complex with the clamp. Thus, the CDP-bound Hda dimer likely represents an inactive form of Hda.
-
===Crystal structure of a putative dna replication regulator hda (sama_1916) from Shewanella amazonensis SB2B at 1.75 A resolution===
+
A structural basis for the regulatory inactivation of DnaA.,Xu Q, McMullan D, Abdubek P, Astakhova T, Carlton D, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Elsliger MA, Feuerhelm J, Hale J, Han GW, Jaroszewski L, Jin KK, Johnson HA, Klock HE, Knuth MW, Kozbial P, Sri Krishna S, Kumar A, Marciano D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Oommachen S, Paulsen J, Puckett C, Reyes R, Rife CL, Sefcovic N, Trame C, van den Bedem H, Weekes D, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA J Mol Biol. 2009 Jan 16;385(2):368-80. Epub 2008 Oct 30. PMID:19000695<ref>PMID:19000695</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_19000695}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 3bos" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 19000695 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_19000695}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
[[3bos]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Shewanella_amazonensis Shewanella amazonensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOS OCA].
+
[[Category: Shewanella amazonensis SB2B]]
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:019000695</ref><references group="xtra"/>
+
-
[[Category: Shewanella amazonensis]]
+
-
[[Category: JCSG, Joint Center for Structural Genomics.]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Jcsg]]
+
-
[[Category: Joint center for structural genomic]]
+
-
[[Category: P-loop containing nucleoside triphosphate hydrolase]]
+
-
[[Category: Protein structure initiative]]
+
-
[[Category: Psi-2]]
+
-
[[Category: Structural genomic]]
+

Current revision

Crystal structure of a putative dna replication regulator HDA (SAMA_1916) from Shewanella amazonensis sb2b at 1.75 A resolution

PDB ID 3bos

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/3bos"
Personal tools