|
|
| (One intermediate revision not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==Crystal Structure of Human Pyridoxine 5'-Phosphate Oxidase R229W Mutant== | | ==Crystal Structure of Human Pyridoxine 5'-Phosphate Oxidase R229W Mutant== |
| - | <StructureSection load='3hy8' size='340' side='right' caption='[[3hy8]], [[Resolution|resolution]] 2.50Å' scene=''> | + | <StructureSection load='3hy8' size='340' side='right'caption='[[3hy8]], [[Resolution|resolution]] 2.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3hy8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HY8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HY8 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3hy8]] is a 1 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=3HY8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HY8 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.5Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PNPO ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyridoxal_5'-phosphate_synthase Pyridoxal 5'-phosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.5 1.4.3.5] </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=3hy8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hy8 OCA], [https://pdbe.org/3hy8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hy8 RCSB], [https://www.ebi.ac.uk/pdbsum/3hy8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hy8 ProSAT]</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=3hy8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hy8 OCA], [http://pdbe.org/3hy8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hy8 RCSB], [http://www.ebi.ac.uk/pdbsum/3hy8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3hy8 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Disease == | | == Disease == |
| - | [[http://www.uniprot.org/uniprot/PNPO_HUMAN PNPO_HUMAN]] Defects in PNPO are the cause of pyridoxine-5'-phosphate oxidase deficiency (PNPO deficiency) [MIM:[http://omim.org/entry/610090 610090]]; also known as PNPO-related neonatal epileptic encephalopathy. The main feature of neonatal epileptic encephalopathy is the onset within hours of birth of a severe seizure disorder that does not respond to anticonvulsant drugs and can be fatal. Seizures can cease with the administration of PLP, being resistant to treatment with pyridoxine. | + | [https://www.uniprot.org/uniprot/PNPO_HUMAN PNPO_HUMAN] Defects in PNPO are the cause of pyridoxine-5'-phosphate oxidase deficiency (PNPO deficiency) [MIM:[https://omim.org/entry/610090 610090]; also known as PNPO-related neonatal epileptic encephalopathy. The main feature of neonatal epileptic encephalopathy is the onset within hours of birth of a severe seizure disorder that does not respond to anticonvulsant drugs and can be fatal. Seizures can cease with the administration of PLP, being resistant to treatment with pyridoxine. |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PNPO_HUMAN PNPO_HUMAN]] Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP).<ref>PMID:12824491</ref> | + | [https://www.uniprot.org/uniprot/PNPO_HUMAN PNPO_HUMAN] Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP).<ref>PMID:12824491</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 39: |
Line 38: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Human]] | + | [[Category: Homo sapiens]] |
| - | [[Category: Pyridoxal 5'-phosphate synthase]] | + | [[Category: Large Structures]] |
| - | [[Category: Musayev, F N]] | + | [[Category: Di Salvo ML]] |
| - | [[Category: Saavedra, M K]] | + | [[Category: Musayev FN]] |
| - | [[Category: Safo, M K]] | + | [[Category: Saavedra MK]] |
| - | [[Category: Salvo, M L.Di]] | + | [[Category: Safo MK]] |
| - | [[Category: Schirch, V]] | + | [[Category: Schirch V]] |
| - | [[Category: Disease mutation]]
| + | |
| - | [[Category: Epilepsy]]
| + | |
| - | [[Category: Flavoprotein]]
| + | |
| - | [[Category: Fmn]]
| + | |
| - | [[Category: Fmn binding protein]]
| + | |
| - | [[Category: Oxidase]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Phosphoprotein]]
| + | |
| - | [[Category: Pyridoxal phosphate]]
| + | |
| - | [[Category: Pyridoxine biosynthesis]]
| + | |
| Structural highlights
Disease
PNPO_HUMAN Defects in PNPO are the cause of pyridoxine-5'-phosphate oxidase deficiency (PNPO deficiency) [MIM:610090; also known as PNPO-related neonatal epileptic encephalopathy. The main feature of neonatal epileptic encephalopathy is the onset within hours of birth of a severe seizure disorder that does not respond to anticonvulsant drugs and can be fatal. Seizures can cease with the administration of PLP, being resistant to treatment with pyridoxine.
Function
PNPO_HUMAN Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP).[1]
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
Mutations in pyridoxine 5'-phosphate oxidase are known to cause neonatal epileptic encephalopathy. This disorder has no cure or effective treatment and is often fatal. Pyridoxine 5'-phosphate oxidase catalyzes the oxidation of pyridoxine 5'-phosphate to pyridoxal 5'-phosphate, the active cofactor form of vitamin B(6) required by more than 140 different catalytic activities, including enzymes involved in amino acid metabolism and biosynthesis of neurotransmitters. Our aim is to elucidate the mechanism by which a homozygous missense mutation (R229W) in the oxidase, linked to neonatal epileptic encephalopathy, leads to reduced oxidase activity. The R229W variant is approximately 850-fold less efficient than the wild-type enzyme due to an approximately 192-fold decrease in pyridoxine 5'-phosphate affinity and an approximately 4.5-fold decrease in catalytic activity. There is also an approximately 50-fold reduction in the affinity of the R229W variant for the FMN cofactor. A 2.5 A crystal structure of the R229W variant shows that the substitution of Arg-229 at the FMN binding site has led to a loss of hydrogen-bond and/or salt-bridge interactions between FMN and Arg-229 and Ser-175. Additionally, the mutation has led to an alteration of the configuration of a beta-strand-loop-beta-strand structure at the active site, resulting in loss of two critical hydrogen-bond interactions involving residues His-227 and Arg-225, which are important for substrate binding and orientation for catalysis. These results provide a molecular basis for the phenotype associated with the R229W mutation, as well as providing a foundation for understanding the pathophysiological consequences of pyridoxine 5'-phosphate oxidase mutations.
Molecular basis of reduced pyridoxine 5'-phosphate oxidase catalytic activity in neonatal epileptic encephalopathy disorder.,Musayev FN, Di Salvo ML, Saavedra MA, Contestabile R, Ghatge MS, Haynes A, Schirch V, Safo MK J Biol Chem. 2009 Nov 6;284(45):30949-56. Epub 2009 Sep 15. PMID:19759001[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Musayev FN, Di Salvo ML, Ko TP, Schirch V, Safo MK. Structure and properties of recombinant human pyridoxine 5'-phosphate oxidase. Protein Sci. 2003 Jul;12(7):1455-63. PMID:12824491
- ↑ Musayev FN, Di Salvo ML, Saavedra MA, Contestabile R, Ghatge MS, Haynes A, Schirch V, Safo MK. Molecular basis of reduced pyridoxine 5'-phosphate oxidase catalytic activity in neonatal epileptic encephalopathy disorder. J Biol Chem. 2009 Nov 6;284(45):30949-56. Epub 2009 Sep 15. PMID:19759001 doi:10.1074/jbc.M109.038372
|
