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[[Image:1vbg.gif|left|200px]]
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{{STRUCTURE_1vbg|  PDB=1vbg  |  SCENE=  }}
'''Pyruvate Phosphate Dikinase from Maize'''


==Pyruvate Phosphate Dikinase from Maize==
<StructureSection load='1vbg' size='340' side='right'caption='[[1vbg]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1vbg]] 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=1VBG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VBG FirstGlance]. <br>
</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>
<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=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1vbg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vbg OCA], [https://pdbe.org/1vbg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vbg RCSB], [https://www.ebi.ac.uk/pdbsum/1vbg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vbg ProSAT], [https://www.topsan.org/Proteins/RSGI/1vbg TOPSAN]</span></td></tr>
</table>
== Function ==
[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>
== 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/vb/1vbg_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1vbg ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


==Overview==
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>
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.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
1VBG 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=1VBG OCA].
</div>
<div class="pdbe-citations 1vbg" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
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]
*[[Pyruvate phosphate dikinase|Pyruvate phosphate dikinase]]
[[Category: Pyruvate, phosphate dikinase]]
== References ==
[[Category: Single protein]]
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Zea mays]]
[[Category: Zea mays]]
[[Category: Kato, H.]]
[[Category: Kato H]]
[[Category: Matsuoka, M.]]
[[Category: Matsuoka M]]
[[Category: Nakanishi, T.]]
[[Category: Nakanishi T]]
[[Category: Nakatsu, T.]]
[[Category: Nakatsu T]]
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
[[Category: Sakata K]]
[[Category: Sakata, K.]]
[[Category: Maize]]
[[Category: Riken structural genomics/proteomics initiative]]
[[Category: Rsgi]]
[[Category: Structural genomic]]
[[Category: Transferase]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 12:20:00 2008''

Latest revision as of 07:51, 25 October 2023

Pyruvate Phosphate Dikinase from Maize

1vbg, resolution 2.30Å

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