2r82

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{{Seed}}
 
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[[Image:2r82.png|left|200px]]
 
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==Pyruvate phosphate dikinase (PPDK) triple mutant R219E/E271R/S262D adapts a second conformational state==
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The line below this paragraph, containing "STRUCTURE_2r82", creates the "Structure Box" on the page.
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<StructureSection load='2r82' size='340' side='right'caption='[[2r82]], [[Resolution|resolution]] 3.60&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2r82]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_symbiosum Clostridium symbiosum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R82 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R82 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.6&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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{{STRUCTURE_2r82| PDB=2r82 | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2r82 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r82 OCA], [https://pdbe.org/2r82 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r82 RCSB], [https://www.ebi.ac.uk/pdbsum/2r82 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r82 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PPDK_CLOSY PPDK_CLOSY] Catalyzes the reversible phosphorylation of pyruvate and phosphate. In E.histolytica and C.symbiosus, PPDK functions in the direction of ATP synthesis.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r8/2r82_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2r82 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Pyruvate phosphate dikinase (PPDK) catalyzes the reversible conversion of phosphoenolpyruvate (PEP), AMP, and Pi to pyruvate and ATP. The enzyme contains two remotely located reaction centers: the nucleotide partial reaction takes place at the N-terminal domain, and the PEP/pyruvate partial reaction takes place at the C-terminal domain. A central domain, tethered to the N- and C-terminal domains by two closely associated linkers, contains a phosphorylatable histidine residue (His455). The molecular architecture suggests a swiveling domain mechanism that shuttles a phosphoryl group between the two reaction centers. In an early structure of PPDK from Clostridium symbiosum, the His445-containing domain (His domain) was positioned close to the nucleotide binding domain and did not contact the PEP/pyruvate-binding domain. Here, we present the crystal structure of a second conformational state of C. symbiosum PPDK with the His domain adjacent to the PEP-binding domain. The structure was obtained by producing a three-residue mutant protein (R219E/E271R/S262D) that introduces repulsion between the His and nucleotide-binding domains but preserves viable interactions with the PEP/pyruvate-binding domain. Accordingly, the mutant enzyme is competent in catalyzing the PEP/pyruvate half-reaction but the overall activity is abolished. The new structure confirms the swivel motion of the His domain. In addition, upon detachment from the His domain, the two nucleotide-binding subdomains undergo a hinge motion that opens the active-site cleft. A similar hinge motion is expected to accompany nucleotide binding (cleft closure) and release (cleft opening). A model of the coupled swivel and cleft opening motions was generated by interpolation between two end conformations, each with His455 positioned for phosphoryl group transfer from/to one of the substrates. The trajectory of the His domain avoids major clashes with the partner domains while preserving the association of the two linker segments.
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===Pyruvate phosphate dikinase (PPDK) triple mutant R219E/E271R/S262D adapts a second conformational state===
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Swiveling domain mechanism in pyruvate phosphate dikinase.,Lim K, Read RJ, Chen CC, Tempczyk A, Wei M, Ye D, Wu C, Dunaway-Mariano D, Herzberg O Biochemistry. 2007 Dec 25;46(51):14845-53. Epub 2007 Dec 4. PMID:18052212<ref>PMID:18052212</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2r82" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_11790099}}, adds the Publication Abstract to the page
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*[[Pyruvate phosphate dikinase|Pyruvate phosphate dikinase]]
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(as it appears on PubMed at http://www.pubmed.gov), where 11790099 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_11790099}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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2R82 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Clostridium_symbiosum Clostridium symbiosum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R82 OCA].
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[[Category: Chen CC]]
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[[Category: Herzberg O]]
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==Reference==
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[[Category: Lim K]]
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Pyruvate site of pyruvate phosphate dikinase: crystal structure of the enzyme-phosphonopyruvate complex, and mutant analysis., Herzberg O, Chen CC, Liu S, Tempczyk A, Howard A, Wei M, Ye D, Dunaway-Mariano D, Biochemistry. 2002 Jan 22;41(3):780-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11790099 11790099]
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[[Category: Read RJ]]
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[[Category: Clostridium symbiosum]]
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[[Category: Pyruvate, phosphate dikinase]]
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[[Category: Single protein]]
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[[Category: Chen, C.]]
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[[Category: Herzberg, O.]]
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[[Category: Lim, K.]]
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[[Category: Read, R J.]]
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[[Category: Atp-binding]]
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[[Category: Conformational transition]]
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[[Category: Kinase]]
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[[Category: Magnesium]]
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[[Category: Metal-binding]]
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[[Category: Nucleotide-binding]]
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[[Category: Phosphorylation]]
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[[Category: Phosphotransferase]]
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[[Category: Remote active site]]
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[[Category: Swiveling domain]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 14 14:21:00 2008''
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Current revision

Pyruvate phosphate dikinase (PPDK) triple mutant R219E/E271R/S262D adapts a second conformational state

PDB ID 2r82

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