3fhx: Difference between revisions

Latest revision as of 13:13, 26 July 2023

Crystal structure of D235A mutant of human pyridoxal kinase

Structural highlights

3fhx is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.5Å
Ligands:	ATP, MG, MPD, NA, PLP, PXL, SO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PDXK_HUMAN Required for synthesis of pyridoxal-5-phosphate from vitamin B6.

Publication Abstract from PubMed

Pyridoxal kinase catalyzes the phosphorylation of pyridoxal (PL) to pyridoxal 5'-phosphate (PLP). A D235A variant shows 7-fold and 15-fold decreases in substrate affinity and activity, respectively. A D235N variant shows approximately 2-fold decrease in both PL affinity and activity. The crystal structure of D235A (2.5 A) shows bound ATP, PL and PLP, while D235N (2.3 A) shows bound ATP and sulfate. These results document the role of Asp235 in PL kinase activity. The observation that the active site of PL kinase can accommodate both ATP and PLP suggests that formation of a ternary Enz.PLP.ATP complex could occur in the wild-type enzyme, consistent with severe MgATP substrate inhibition of PL kinase in the presence of PLP.

Kinetic and structural studies of the role of the active site residue Asp235 of human pyridoxal kinase.,Gandhi AK, Ghatge MS, Musayev FN, Sease A, Aboagye SO, di Salvo ML, Schirch V, Safo MK Biochem Biophys Res Commun. 2009 Mar 27;381(1):12-5. Epub 2009 Feb 4. PMID:19351586^[1]

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

References

↑ Gandhi AK, Ghatge MS, Musayev FN, Sease A, Aboagye SO, di Salvo ML, Schirch V, Safo MK. Kinetic and structural studies of the role of the active site residue Asp235 of human pyridoxal kinase. Biochem Biophys Res Commun. 2009 Mar 27;381(1):12-5. Epub 2009 Feb 4. PMID:19351586 doi:10.1016/j.bbrc.2009.01.170

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Gandhi AK, Ghatge MS, Musayev FN, Sease A, Aboagye SO, di Salvo ML, Schirch V, Safo MK. Kinetic and structural studies of the role of the active site residue Asp235 of human pyridoxal kinase. Biochem Biophys Res Commun. 2009 Mar 27;381(1):12-5. Epub 2009 Feb 4. PMID:19351586 doi:10.1016/j.bbrc.2009.01.170

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='3fhx' size='340' side='right'caption='[[3fhx]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3fhx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FHX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FHX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3fhx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FHX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FHX FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=PXL:3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE'>PXL</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]] 2.5&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3fhy|3fhy]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=PXL:3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE'>PXL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">C21orf124, C21orf97, PDXK, PKH, PNK ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pyridoxal_kinase Pyridoxal kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.35 2.7.1.35] </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=3fhx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fhx OCA], [https://pdbe.org/3fhx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fhx RCSB], [https://www.ebi.ac.uk/pdbsum/3fhx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fhx ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/PDXK_HUMAN PDXK_HUMAN]] Required for synthesis of pyridoxal-5-phosphate from vitamin B6.
+[https://www.uniprot.org/uniprot/PDXK_HUMAN PDXK_HUMAN] Required for synthesis of pyridoxal-5-phosphate from vitamin B6.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 28: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Pyridoxal kinase]]
+[[Category: Di Salvo ML]]
-[[Category: Gandhi, A K]]
+[[Category: Gandhi AK]]
-[[Category: Ghatge, M]]
+[[Category: Ghatge M]]
-[[Category: Musayev, F N]]
+[[Category: Musayev FN]]
-[[Category: Safo, M K]]
+[[Category: Safo MK]]
-[[Category: Salvo, M L.Di]]
+[[Category: Schirch V]]
-[[Category: Schirch, V]]
-[[Category: Atp complex]]
-[[Category: Atp-binding]]
-[[Category: Beta sheet with alpha helix]]
-[[Category: Kinase]]
-[[Category: Metal ion]]
-[[Category: Metal-binding]]
-[[Category: Nucleotide-binding]]
-[[Category: Transferase]]

3fhx: Difference between revisions

Latest revision as of 13:13, 26 July 2023

Crystal structure of D235A mutant of human pyridoxal kinase

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools