1vbh

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[[Image:1vbh.gif|left|200px]]
 
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==Pyruvate Phosphate Dikinase with bound Mg-PEP from Maize==
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The line below this paragraph, containing "STRUCTURE_1vbh", creates the "Structure Box" on the page.
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<StructureSection load='1vbh' size='340' side='right'caption='[[1vbh]], [[Resolution|resolution]] 2.30&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'>[[1vbh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Zea_mays Zea mays]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VBH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VBH 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]] 2.3&#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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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{{STRUCTURE_1vbh| PDB=1vbh | 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=1vbh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vbh OCA], [https://pdbe.org/1vbh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vbh RCSB], [https://www.ebi.ac.uk/pdbsum/1vbh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vbh ProSAT], [https://www.topsan.org/Proteins/RSGI/1vbh TOPSAN]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PPDK1_MAIZE PPDK1_MAIZE] Formation of phosphoenolpyruvate, which is the primary acceptor of CO(2) in C4 and some Crassulacean acid metabolism plants.<ref>PMID:1668653</ref> <ref>PMID:21414960</ref>
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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/vb/1vbh_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=1vbh 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) reversibly catalyzes the conversion of ATP, phosphate, and pyruvate into AMP, pyrophosphate, and phosphoenolpyruvate (PEP), respectively. Since the nucleotide binding site (in the N-terminal domain) and the pyruvate/PEP binding site (in the C-terminal domain) are separated by approximately 45 A, it has been proposed that an intermediary domain, called the central domain, swivels between these remote domains to transfer the phosphate. However, no direct structural evidence for the swiveling central domain has been found. In this study, the crystal structures of maize PPDK with and without PEP have been determined at 2.3 A resolution. These structures revealed that the central domain is located near the pyruvate/PEP binding C-terminal domain, in contrast to the PPDK from Clostridium symbiosum, wherein the central domain is located near the nucleotide-binding N-terminal domain. Structural comparisons between the maize and C. symbiosum PPDKs demonstrated that the swiveling motion of the central domain consists of a rotation of at least 92 degrees and a translation of 0.5 A. By comparing the maize PPDK structures with and without PEP, we have elucidated the mode of binding of PEP to the C-terminal domain and the induced conformational changes in the central domain.
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'''Pyruvate Phosphate Dikinase with bound Mg-PEP from Maize'''
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Crystal structures of pyruvate phosphate dikinase from maize revealed an alternative conformation in the swiveling-domain motion.,Nakanishi T, Nakatsu T, Matsuoka M, Sakata K, Kato H Biochemistry. 2005 Feb 1;44(4):1136-44. PMID:15667207<ref>PMID:15667207</ref>
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==Overview==
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Pyruvate phosphate dikinase (PPDK) reversibly catalyzes the conversion of ATP, phosphate, and pyruvate into AMP, pyrophosphate, and phosphoenolpyruvate (PEP), respectively. Since the nucleotide binding site (in the N-terminal domain) and the pyruvate/PEP binding site (in the C-terminal domain) are separated by approximately 45 A, it has been proposed that an intermediary domain, called the central domain, swivels between these remote domains to transfer the phosphate. However, no direct structural evidence for the swiveling central domain has been found. In this study, the crystal structures of maize PPDK with and without PEP have been determined at 2.3 A resolution. These structures revealed that the central domain is located near the pyruvate/PEP binding C-terminal domain, in contrast to the PPDK from Clostridium symbiosum, wherein the central domain is located near the nucleotide-binding N-terminal domain. Structural comparisons between the maize and C. symbiosum PPDKs demonstrated that the swiveling motion of the central domain consists of a rotation of at least 92 degrees and a translation of 0.5 A. By comparing the maize PPDK structures with and without PEP, we have elucidated the mode of binding of PEP to the C-terminal domain and the induced conformational changes in the central domain.
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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1VBH is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Zea_mays Zea mays]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VBH OCA].
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</div>
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<div class="pdbe-citations 1vbh" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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Crystal structures of pyruvate phosphate dikinase from maize revealed an alternative conformation in the swiveling-domain motion., Nakanishi T, Nakatsu T, Matsuoka M, Sakata K, Kato H, Biochemistry. 2005 Feb 1;44(4):1136-44. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15667207 15667207]
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*[[Pyruvate phosphate dikinase|Pyruvate phosphate dikinase]]
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[[Category: Pyruvate, phosphate dikinase]]
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== References ==
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[[Category: Single protein]]
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Zea mays]]
[[Category: Zea mays]]
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[[Category: Kato, H.]]
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[[Category: Kato H]]
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[[Category: Matsuoka, M.]]
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[[Category: Matsuoka M]]
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[[Category: Nakanishi, T.]]
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[[Category: Nakanishi T]]
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[[Category: Nakatsu, T.]]
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[[Category: Nakatsu T]]
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[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
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[[Category: Sakata K]]
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[[Category: Sakata, K.]]
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[[Category: Maize]]
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[[Category: Riken structural genomics/proteomics initiative]]
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[[Category: Rsgi]]
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[[Category: Structural genomic]]
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[[Category: Transferase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 12:20:00 2008''
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Current revision

Pyruvate Phosphate Dikinase with bound Mg-PEP from Maize

PDB ID 1vbh

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