5ur0: Difference between revisions
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==Crystallographic structure of glyceraldehyde-3-phosphate dehydrogenase from Naegleria gruberi== | |||
<StructureSection load='5ur0' size='340' side='right'caption='[[5ur0]], [[Resolution|resolution]] 1.94Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5ur0]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Naegleria_gruberi Naegleria gruberi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UR0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UR0 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]] 1.94Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene>, <scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=5ur0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ur0 OCA], [https://pdbe.org/5ur0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ur0 RCSB], [https://www.ebi.ac.uk/pdbsum/5ur0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ur0 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/D2W142_NAEGR D2W142_NAEGR] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Naegleria gruberi is a free life amoeba believed to have more than one billion years of existence; it is not pathogenic and had its genome sequenced, which revealed a high complexity in the metabolic pathways. This paper presents the experimental structure of GAPDH from N. gruberi, the first one belonging to the phylum Percolozoa, comparisons to structures from various species and molecular dynamics studies of some particular features. The final refined structure presents Rcryst=15.54% and Rfree=19.84%. The catalytic domain formed by residues 134 to 313 is highly conserved, as expected, with the exception of Asn145, present only in NgGAPDH, while the other GAPDHs present either Ser or Thr on the corresponding position. Molecular dynamics analysis revealed that Asn145 has correlated motions with residues Ala123, Thr125 and Pro126 that belong to what was called "bonded loop". NgGAPDH residue Met35 presents an extended side chain, closer to the cofactor adenine ring than corresponding (different) residues and conformations found in some parasitic protozoa and the human GAPDHs. The enzyme was previously reported to present positive cooperativity, which is hypothesized to be related to certain atom distances. | |||
Structural studies of glyceraldehyde-3-phosphate dehydrogenase from Naegleria gruberi, the first one from phylum Percolozoa.,Machado ATP, Silva M, Iulek J Biochim Biophys Acta. 2018 Feb 28. pii: S1570-9639(18)30022-0. doi:, 10.1016/j.bbapap.2018.02.006. PMID:29501559<ref>PMID:29501559</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5ur0" style="background-color:#fffaf0;"></div> | ||
[[Category: Machado | |||
[[Category: | ==See Also== | ||
*[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Naegleria gruberi]] | |||
[[Category: Iulek J]] | |||
[[Category: Machado ATP]] | |||
[[Category: Silva M]] | |||
Latest revision as of 16:32, 4 October 2023
Crystallographic structure of glyceraldehyde-3-phosphate dehydrogenase from Naegleria gruberiCrystallographic structure of glyceraldehyde-3-phosphate dehydrogenase from Naegleria gruberi
Structural highlights
FunctionPublication Abstract from PubMedNaegleria gruberi is a free life amoeba believed to have more than one billion years of existence; it is not pathogenic and had its genome sequenced, which revealed a high complexity in the metabolic pathways. This paper presents the experimental structure of GAPDH from N. gruberi, the first one belonging to the phylum Percolozoa, comparisons to structures from various species and molecular dynamics studies of some particular features. The final refined structure presents Rcryst=15.54% and Rfree=19.84%. The catalytic domain formed by residues 134 to 313 is highly conserved, as expected, with the exception of Asn145, present only in NgGAPDH, while the other GAPDHs present either Ser or Thr on the corresponding position. Molecular dynamics analysis revealed that Asn145 has correlated motions with residues Ala123, Thr125 and Pro126 that belong to what was called "bonded loop". NgGAPDH residue Met35 presents an extended side chain, closer to the cofactor adenine ring than corresponding (different) residues and conformations found in some parasitic protozoa and the human GAPDHs. The enzyme was previously reported to present positive cooperativity, which is hypothesized to be related to certain atom distances. Structural studies of glyceraldehyde-3-phosphate dehydrogenase from Naegleria gruberi, the first one from phylum Percolozoa.,Machado ATP, Silva M, Iulek J Biochim Biophys Acta. 2018 Feb 28. pii: S1570-9639(18)30022-0. doi:, 10.1016/j.bbapap.2018.02.006. PMID:29501559[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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