3HY8 - JenaLib

Title :   CRYSTAL STRUCTURE OF HUMAN PYRIDOXINE 5'-PHOSPHATE OXIDASE R229W MUTANT

Authors :   M. K. Safo, F. N. Musayev, M. L. Di Salvo, M. K. Saavedra, V. Schirch

Date :   22 Jun 09 (Deposition) - 28 Jul 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Fmn Binding Protein, Oxidase, Disease Mutation, Epilepsy, Flavoprotein, Fmn, Oxidoreductase, Phosphoprotein, Pyridoxal Phosphate, Pyridoxine Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. N. Musayev, M. L. Di Salvo, M. A. Saavedra, R. Contestabile, M. S. Ghatge, A. Haynes, V. Schirch, M. K. Safo
Molecular Basis Of Reduced Pyridoxine 5'-Phosphate Oxidase Catalytic Activity In Neonatal Epileptic Encephalopathy Disorder
J. Biol. Chem. V. 284 30949 2009
PubMed-ID: 19759001 | Reference-DOI: 10.1074/JBC.M109.038372

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:95 , MET A:96 , LEU A:97 , LEU A:98 , PHE A:110 , THR A:111 , SER A:115 , ARG A:116 , LYS A:117 , TYR A:132 , GLN A:139 , ARG A:141 , GLN A:174 , TRP A:219 , TRP A:229 , HOH A:308 , PLP A:350 , PO4 A:370	BINDING SITE FOR RESIDUE FMN A 390
2	AC2	SOFTWARE	GLU A:77 , LEU A:98 , LYS A:100 , ARG A:161 , PRO A:162 , SER A:165 , TRP A:219 , ARG A:225 , HIS A:227 , FMN A:390	BINDING SITE FOR RESIDUE PLP A 350
3	AC3	SOFTWARE	LYS A:100 , GLY A:101 , ARG A:108 , PHE A:110 , GLU A:153 , TYR A:157	BINDING SITE FOR RESIDUE PO4 A 360
4	AC4	SOFTWARE	ARG A:116 , ARG A:141 , GLU A:143 , GLU A:217 , TRP A:229 , FMN A:390	BINDING SITE FOR RESIDUE PO4 A 370
5	AC5	SOFTWARE	SER A:55 , LYS A:60 , GLU A:251 , HOH A:297 , HOH A:320	BINDING SITE FOR RESIDUE PO4 A 380

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (5, 5)

Asymmetric Unit (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_029358	E	50	K	PNPO_HUMAN	Polymorphism	549477447	A	E	50	K
2	UniProt	VAR_029359	R	116	Q	PNPO_HUMAN	Polymorphism	17679445	A	R	116	Q
3	UniProt	VAR_078229	R	225	H	PNPO_HUMAN	Disease (PNPOD)	550423482	A	R	225	H
4	UniProt	VAR_078643	R	229	Q	PNPO_HUMAN	Disease (PNPOD)	---	A	W	229	Q
5	UniProt	VAR_029360	R	229	W	PNPO_HUMAN	Disease (PNPOD)	104894629	A	W	229	W

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (5, 10)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_029358	E	50	K	PNPO_HUMAN	Polymorphism	549477447	A	E	50	K
2	UniProt	VAR_029359	R	116	Q	PNPO_HUMAN	Polymorphism	17679445	A	R	116	Q
3	UniProt	VAR_078229	R	225	H	PNPO_HUMAN	Disease (PNPOD)	550423482	A	R	225	H
4	UniProt	VAR_078643	R	229	Q	PNPO_HUMAN	Disease (PNPOD)	---	A	W	229	Q
5	UniProt	VAR_029360	R	229	W	PNPO_HUMAN	Disease (PNPOD)	104894629	A	W	229	W

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (1, 1)

Exons (6, 6)

Asymmetric Unit (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000225573	1	ENSE00000812589	chr17:46018889-46019179	291	PNPO_HUMAN	1-46	46	0	-	-
1.2	ENST00000225573	2	ENSE00000735348	chr17:46020672-46020796	125	PNPO_HUMAN	47-88	42	1	A:48-88	41
1.3	ENST00000225573	3	ENSE00000735341	chr17:46021982-46022081	100	PNPO_HUMAN	88-121	34	1	A:88-121	34
1.4	ENST00000225573	4	ENSE00000735332	chr17:46022925-46022978	54	PNPO_HUMAN	122-139	18	1	A:122-139	18
1.5	ENST00000225573	5	ENSE00000812590	chr17:46023227-46023355	129	PNPO_HUMAN	140-182	43	1	A:140-182	43
1.6	ENST00000225573	6	ENSE00000735316	chr17:46023689-46023759	71	PNPO_HUMAN	183-206	24	1	A:183-206	24
1.7	ENST00000225573	7	ENSE00000812591	chr17:46023980-46026673	2694	PNPO_HUMAN	206-261	56	1	A:206-261 (gaps)	56

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:211
 aligned with PNPO_HUMAN | Q9NVS9 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:214
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257    
           PNPO_HUMAN    48 FEETHLTSLDPVKQFAAWFEEAVQCPDIGEANAMCLATCTRDGKPSARMLLLKGFGKDGFRFFTNFESRKGKELDSNPFASLVFYWEPLNRQVRVEGPVKKLPEEEAECYFHSRPKSSQIGAVVSHQSSVIPDREYLRKKNEELEQLYQDQEVPKPKSWGGYVLYPQVMEFWQGQTNRLHDRIVFRRGLPTGDSPLGPMTHRGEEDWLYERLAP 261
               SCOP domains d3hy8a_ A: automated matches                                                                                                                                                                                           SCOP domains
               CATH domains 3hy8A00 A:48-261 Electron Transport, Fmn-binding Protein; Chain A                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhh........eeeeeee.....eeeeeee........eeeeee..hhhhhhhhh..eeeeeeeehhh.eeeeeeeeeee.hhhhhhhhhh..hhhhhhhhhhh.......hhhhhhhhhhhhhhhh..........eeeeee...eeeeee.......eeeeeee....---......ee....eeeee... Sec.struct. author
             SAPs(SNPs) (1) --K-----------------------------------------------------------------Q------------------------------------------------------------------------------------------------------------H---Q-------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------W-------------------------------- SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------PYRIDOX_OXIDAS-------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:48-88 UniProt: 47-88    ---------------------------------Exon 1.4          Exon 1.5  PDB: A:140-182 UniProt: 140-182  Exon 1.6  PDB: A:183-206------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.3  PDB: A:88-121           ------------------------------------------------------------------------------------Exon 1.7  PDB: A:206-261 (gaps) UniProt: 206-261         Transcript 1 (2)
                 3hy8 A  48 FEETHLTSLDPVKQFAAWFEEAVQCPDIGEANAMCLATCTRDGKPSARMLLLKGFGKDGFRFFTNFESRKGKELDSNPFASLVFYWEPLNRQVRVEGPVKKLPEEEAECYFHSRPKSSQIGAVVSHQSSVIPDREYLRKKNEELEQLYQDQEVPKPKSWGGYVLYPQVMEFWQGQTNRLHDWIVFRRGLPT---PLGPMTHRGEEDWLYERLAP 261
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237|   |  247       257    
                                                                                                                                                                                                                        238 242

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

Asymmetric Unit(hide GO term definitions)

Chain A (PNPO_HUMAN | Q9NVS9)

molecular function
	GO:0010181	FMN binding	Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016638	oxidoreductase activity, acting on the CH-NH2 group of donors	Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH2 group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
	GO:0004733	pyridoxamine-phosphate oxidase activity	Catalysis of the reaction: pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + hydrogen peroxide.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0002230	positive regulation of defense response to virus by host	Any host process that results in the promotion of antiviral immune response mechanisms, thereby limiting viral replication.
	GO:0098779	positive regulation of macromitophagy in response to mitochondrial depolarization	The macromitophagy process that is triggered by a detection of the loss of mitochondrial membrane potential.
	GO:0042823	pyridoxal phosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of pyridoxal phosphate, pyridoxal phosphorylated at the hydroxymethyl group of C-5, the active form of vitamin B6.
	GO:0008615	pyridoxine biosynthetic process	The chemical reactions and pathways resulting in the formation of pyridoxine, 2-methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine, one of the vitamin B6 compounds.
	GO:0042816	vitamin B6 metabolic process	The chemical reactions and pathways involving any of the vitamin B6 compounds: pyridoxal, pyridoxamine and pyridoxine and the active form, pyridoxal phosphate.
	GO:0098792	xenophagy	The macroautophagy process in which a region of cytoplasm containing an intracellular pathogen or some part of an intracellular pathogen (e.g. viral capsid) is enclosed in a double membrane bound autophagosome, which then fuses with the lysosome leading to degradation of the contents.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.

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