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1vbg

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Pyruvate Phosphate Dikinase from Maize

Structural highlights

1vbg is a 1 chain structure with sequence from Zea mays. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.3Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

PPDK1_MAIZE Formation of phosphoenolpyruvate, which is the primary acceptor of CO(2) in C4 and some Crassulacean acid metabolism plants.^[1] ^[2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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.

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^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Sheen J. Molecular mechanisms underlying the differential expression of maize pyruvate, orthophosphate dikinase genes. Plant Cell. 1991 Mar;3(3):225-45. PMID:1668653 doi:http://dx.doi.org/10.1105/tpc.3.3.225
↑ Chastain CJ, Failing CJ, Manandhar L, Zimmerman MA, Lakner MM, Nguyen TH. Functional evolution of C(4) pyruvate, orthophosphate dikinase. J Exp Bot. 2011 May;62(9):3083-91. doi: 10.1093/jxb/err058. Epub 2011 Mar 17. PMID:21414960 doi:http://dx.doi.org/10.1093/jxb/err058
↑ Nakanishi T, Nakatsu T, Matsuoka M, Sakata K, Kato H. Crystal structures of pyruvate phosphate dikinase from maize revealed an alternative conformation in the swiveling-domain motion. Biochemistry. 2005 Feb 1;44(4):1136-44. PMID:15667207 doi:10.1021/bi0484522

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1vbg"

@@ Line 1: / Line 1: @@
 ==Pyruvate Phosphate Dikinase from Maize==
-<StructureSection load='1vbg' size='340' side='right' caption='[[1vbg]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<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 [http://en.wikipedia.org/wiki/Maize Maize]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VBG FirstGlance]. <br>
+<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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1vbh|1vbh]]</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate,_phosphate_dikinase Pyruvate, phosphate dikinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.9.1 2.7.9.1] </span></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>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1vbg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vbg OCA], [http://pdbe.org/1vbg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vbg RCSB], [http://www.ebi.ac.uk/pdbsum/1vbg PDBsum], [http://www.topsan.org/Proteins/RSGI/1vbg TOPSAN]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
+[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>
+    <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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;">
@@ Line 36: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Maize]]
+[[Category: Large Structures]]
-[[Category: Pyruvate, phosphate dikinase]]
+[[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: Structural genomic]]
+[[Category: Sakata K]]
-[[Category: Sakata, K]]
-[[Category: Rsgi]]
-[[Category: Transferase]]

1vbg

From Proteopedia

Current revision

Pyruvate Phosphate Dikinase from Maize

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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