5ur0: Difference between revisions

Latest revision as of 13:32, 4 October 2023

Crystallographic structure of glyceraldehyde-3-phosphate dehydrogenase from Naegleria gruberi

Structural highlights

5ur0 is a 4 chain structure with sequence from Naegleria gruberi. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.94Å
Ligands:	CME, CSD, NA, NAD, OCS, PGE
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

D2W142_NAEGR

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^[1]

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

References

↑ Machado ATP, Silva M, Iulek J. Structural studies of glyceraldehyde-3-phosphate dehydrogenase from Naegleria gruberi, the first one from phylum Percolozoa. Biochim Biophys Acta. 2018 Feb 28. pii: S1570-9639(18)30022-0. doi:, 10.1016/j.bbapap.2018.02.006. PMID:29501559 doi:https://dx.doi.org/10.1016/j.bbapap.2018.02.006

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OCA

[1] Machado ATP, Silva M, Iulek J. Structural studies of glyceraldehyde-3-phosphate dehydrogenase from Naegleria gruberi, the first one from phylum Percolozoa. Biochim Biophys Acta. 2018 Feb 28. pii: S1570-9639(18)30022-0. doi:, 10.1016/j.bbapap.2018.02.006. PMID:29501559 doi:https://dx.doi.org/10.1016/j.bbapap.2018.02.006

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='5ur0' size='340' side='right'caption='[[5ur0]], [[Resolution|resolution]] 1.94&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ur0]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Amoeba Amoeba]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UR0 FirstGlance]. <br>
+<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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 1.94&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene>, <scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene>, <scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene></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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NAEGRDRAFT_53883 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5762 Amoeba])</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>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glyceraldehyde-3-phosphate_dehydrogenase_(phosphorylating) Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.12 1.2.1.12] </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=5ur0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ur0 OCA], [http://pdbe.org/5ur0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ur0 RCSB], [http://www.ebi.ac.uk/pdbsum/5ur0 PDBsum], [http://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 ==
@@ Line 26: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Amoeba]]
 [[Category: Large Structures]]
-[[Category: Iulek, J]]
-[[Category: Machado, A T.P]]
-[[Category: Silva, M]]
-[[Category: Glyceraldehyde-3-phosphate dehydrogenase]]
 [[Category: Naegleria gruberi]]
-[[Category: Oxidoreductase]]
+[[Category: Iulek J]]
+[[Category: Machado ATP]]
+[[Category: Silva M]]

5ur0: Difference between revisions

Latest revision as of 13:32, 4 October 2023

Crystallographic structure of glyceraldehyde-3-phosphate dehydrogenase from Naegleria gruberi

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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