User:Tilman Schirmer/Sandbox 204

From Proteopedia

back

WspR

Overview

Jmol._Canvas2D (Jmol) "jmolApplet1"[x] script 1 started pdbGetHeader = true FileManager opening url http://52.214.119.220/wiki/extensions/Proteopedia/spt/functions.spt?1733933141 loadScript /wiki/extensions/jsmol/j2s/core/coretext.z.js JSmol exec jmolApplet2 start applet null Jmol JavaScript applet jmolApplet2__2577421549354386__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(jmolApplet2__2577421549354386__) vwrOptions: { "name":"jmolApplet2","applet":true,"documentBase":"http://52.214.119.220/wiki/index.php/User:Tilman_Schirmer/Sandbox_204","platform":"J.awtjs2d.Platform","fullName":"jmolApplet2__2577421549354386__","codePath":"http:/wiki/extensions/jsmol/j2s/","display":"jmolApplet2_canvas2d","loadStructCallback":"manageLoadStructCallback","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"2577421549354386","messageCallback":"msgCb","bgcolor":"white" } setting document base to "http://52.214.119.220/wiki/index.php/User:Tilman_Schirmer/Sandbox_204" (C) 2015 Jmol Development Jmol Version: 14.31.8 2020-09-26 10:04 java.vendor: Java2Script (HTML5) java.version: 2019-06-08 00:17:46 (JSmol/j2s) os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com) Access: ALL memory: 0.0/0.0 processors available: 1 useCommandThread: false appletId:jmolApplet2 (signed) Jmol getValue emulate null defaults = "Jmol" Jmol getValue boxbgcolor null Jmol getValue bgcolor white backgroundColor = "white" Jmol getValue ANIMFRAMECallback null Jmol getValue APPLETREADYCallback Jmol._readyCallback APPLETREADYCallback = "Jmol._readyCallback" StatusManager callback set for APPLETREADYCallback f=Jmol._readyCallback cb=APPLETREADY Jmol getValue ATOMMOVEDCallback null Jmol getValue AUDIOCallback null Jmol getValue CLICKCallback null Jmol getValue DRAGDROPCallback null Jmol getValue ECHOCallback null Jmol getValue ERRORCallback null Jmol getValue EVALCallback null Jmol getValue HOVERCallback null Jmol getValue IMAGECallback null Jmol getValue LOADSTRUCTCallback manageLoadStructCallback LOADSTRUCTCallback = "manageLoadStructCallback" StatusManager callback set for LOADSTRUCTCallback f=manageLoadStructCallback cb=LOADSTRUCT Jmol getValue MEASURECallback null Jmol getValue MESSAGECallback msgCb MESSAGECallback = "msgCb" StatusManager callback set for MESSAGECallback f=msgCb cb=MESSAGE Jmol getValue MINIMIZATIONCallback null Jmol getValue SERVICECallback null Jmol getValue PICKCallback null Jmol getValue RESIZECallback null Jmol getValue SCRIPTCallback null Jmol getValue SYNCCallback null Jmol getValue STRUCTUREMODIFIEDCallback null Jmol getValue doTranslate null language=en_US Jmol getValue doTranslate null Note -- Presence of message callback disables disable translation; to enable message translation use jmolSetTranslation(true) prior to jmolApplet() Note -- language translation disabled Jmol getValue popupMenu null Jmol getValue script null Jmol getValue loadInline null Jmol getValue load null Jmol applet jmolApplet2__2577421549354386__ ready spinqualitylabelsall models WspR 3bre Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

WspR from Pseudomonas aeruginosa is a response regulator with an catalytic, diguanylate cyclase, output domain. It is composed of a canonical CheY-like response regulator receiver domain (Rec) and a C-terminal catalytic GGDEF domain domain that confers the catalytic activity with all canonical active site residues present.

Although not modified (i.e. phosphorylated) at the active Asp (Asp70), the Rec domains mediate formation of dimeric WspR. Two dimers, in turn, are associated by head-to-head contact to a tetramer of approximate 222 (D2) symmetry.

Allosteric product binding site

Jmol._Canvas2D (Jmol) "jmolApplet2"[x] loadScript /wiki/extensions/jsmol/j2s/core/package.js loadScript /wiki/extensions/jsmol/j2s/core/corejmol.z.js loadScript /wiki/extensions/jsmol/j2s/J/translation/PO.js loadScript /wiki/extensions/jsmol/j2s/core/corescript.z.js JSmol exec jmolApplet1 start applet null Jmol JavaScript applet jmolApplet1__2577421549354386__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(jmolApplet1__2577421549354386__) vwrOptions: { "name":"jmolApplet1","applet":true,"documentBase":"http://52.214.119.220/wiki/index.php/User:Tilman_Schirmer/Sandbox_204","platform":"J.awtjs2d.Platform","fullName":"jmolApplet1__2577421549354386__","codePath":"http:/wiki/extensions/jsmol/j2s/","display":"jmolApplet1_canvas2d","loadStructCallback":"manageLoadStructCallback","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"2577421549354386","messageCallback":"msgCb","bgcolor":"white" } setting document base to "http://52.214.119.220/wiki/index.php/User:Tilman_Schirmer/Sandbox_204" (C) 2015 Jmol Development Jmol Version: 14.31.8 2020-09-26 10:04 java.vendor: Java2Script (HTML5) java.version: 2019-06-08 00:17:46 (JSmol/j2s) os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com) Access: ALL memory: 0.0/0.0 processors available: 1 useCommandThread: false appletId:jmolApplet1 (signed) Jmol getValue emulate null defaults = "Jmol" Jmol getValue boxbgcolor null Jmol getValue bgcolor white backgroundColor = "white" Jmol getValue ANIMFRAMECallback null Jmol getValue APPLETREADYCallback Jmol._readyCallback APPLETREADYCallback = "Jmol._readyCallback" StatusManager callback set for APPLETREADYCallback f=Jmol._readyCallback cb=APPLETREADY Jmol getValue ATOMMOVEDCallback null Jmol getValue AUDIOCallback null Jmol getValue CLICKCallback null Jmol getValue DRAGDROPCallback null Jmol getValue ECHOCallback null Jmol getValue ERRORCallback null Jmol getValue EVALCallback null Jmol getValue HOVERCallback null Jmol getValue IMAGECallback null Jmol getValue LOADSTRUCTCallback manageLoadStructCallback LOADSTRUCTCallback = "manageLoadStructCallback" StatusManager callback set for LOADSTRUCTCallback f=manageLoadStructCallback cb=LOADSTRUCT Jmol getValue MEASURECallback null Jmol getValue MESSAGECallback msgCb MESSAGECallback = "msgCb" StatusManager callback set for MESSAGECallback f=msgCb cb=MESSAGE Jmol getValue MINIMIZATIONCallback null Jmol getValue SERVICECallback null Jmol getValue PICKCallback null Jmol getValue RESIZECallback null Jmol getValue SCRIPTCallback null Jmol getValue SYNCCallback null Jmol getValue STRUCTUREMODIFIEDCallback null Jmol getValue doTranslate null language=en_US Jmol getValue doTranslate null Note -- Presence of message callback disables disable translation; to enable message translation use jmolSetTranslation(true) prior to jmolApplet() Note -- language translation disabled Jmol getValue popupMenu null Jmol getValue script null Jmol getValue loadInline null Jmol getValue load null Jmol applet jmolApplet1__2577421549354386__ ready script 1 started pdbGetHeader = true FileManager opening url http://52.214.119.220/wiki/extensions/Proteopedia/spt/functions.spt?1733933141 Loading, please wait ... Loading, please wait ... platformSpeed = 8 FileManager opening url http://52.214.119.220/wiki/scripts/User:Tilman_Schirmer/Sandbox_204/Ip/3.spt loadScript /wiki/extensions/jsmol/j2s/J/thread/MoveToThread.js platformSpeed = 8 FileManager opening url http://52.214.119.220/wiki/scripts/User:Tilman_Schirmer/Sandbox_204/Protomer/3.spt spinqualitylabelsall models WspR 3bre Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

There are two allosteric sites (primary inhibition site, Ip, and secondary inhibition site, Is) that become cross-linked by (c-di-GMP)₂ dimers in the tetrameric molecule. For a close-up click here (Ip-site, Is-site, (c-di-GMP dimer)2). Note that there are four (c-di-GMP)₂ dimers per WspR tetramer.

References

WspR structure 3bre:

• De N, Pirruccello M, Krasteva PV, Bae N, Raghavan RV, Sondermann H. Phosphorylation-independent regulation of the diguanylate cyclase WspR. PLoS Biol. 2008 Mar 25;6(3):e67. PMID:18366254 doi:10.1371/journal.pbio.0060067