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Title :   PNP OXIDASE FROM SACCHAROMYCES CEREVISIAE

Authors :   W. Shi, D. A. Ostrov, S. E. Gerchman, V. Graziano, H. Kycia, B. Studier, S. C. Almo, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)

Date :   06 Apr 99 (Deposition) - 25 Aug 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym./Biol. Unit : A,B

Keywords :   Oxidase, B6 Metabolism, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Shi, D. A. Ostrov, S. E. Gerchman, V. Graziano, H. Kycia, B. Studier, S. C. Almo
The Structure Of Pnp Oxidase From S. Cerevisiae
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PROTEIN (PNP OXIDASE)
	Chains	:	A, B
	EC Number	:	1.4.3.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:111 , GLN A:118 , ARG A:120 , TRP A:199 , ARG A:209 , ARG B:73 , ILE B:74 , LEU B:75 , TYR B:88 , SER B:89 , SER B:94 , ARG B:95 , LYS B:96 , GLN B:153 , SER B:154	BINDING SITE FOR RESIDUE FMN B 300
2	AC2	SOFTWARE	ARG A:73 , ILE A:74 , LEU A:75 , TYR A:88 , SER A:89 , SER A:94 , ARG A:95 , LYS A:96 , GLN A:153 , SER A:154 , PHE B:111 , GLN B:118 , ARG B:120 , TRP B:199 , ARG B:209	BINDING SITE FOR RESIDUE FMN A 301

(no "SS Bond" information available for 1CI0)

(no "Cis Peptide Bond" information available for 1CI0)

(no "SAP(SNP)/Variant" information available for 1CI0)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PYRIDOX_OXIDASE	PS01064	Pyridoxamine 5'-phosphate oxidase signature.	PDX3_YEAST	196-209	2	A:196-209 B:196-209

Asymmetric/Biological Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YBR035C	1	YBR035C.1	II:306955-306269	687	PDX3_YEAST	1-228	228	2	A:24-228 B:25-228	205 204

Asymmetric/Biological 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
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Chain A from PDB  Type:PROTEIN  Length:205
 aligned with PDX3_YEAST | P38075 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:205
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223     
           PDX3_YEAST    24 FTLNEKQLTDDPIDLFTKWFNEAKEDPRETLPEAITFSSAELPSGRVSSRILLFKELDHRGFTIYSNWGTSRKAHDIATNPNAAIVFFWKDLQRQVRVEGITEHVNRETSERYFKTRPRGSKIGAWASRQSDVIKNREELDELTQKNTERFKDAEDIPCPDYWGGLRIVPLEIEFWQGRPSRLHDRFVYRRKTENDPWKVVRLAP 228
               SCOP domains d1ci0a_ A: Pyridoxine 5'-phoshate oxidase (PNP oxidase)                                                                                                                                                       SCOP domains
               CATH domains 1ci0A00 A:24-228 Electron Transport, Fmn-binding Protein; Chain A                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh..hhhhhhhhhhhhhhhh.......eeeeeeee....eeeeeeee..ee....eeeeee...hhhhhhhhhh.eeeeeeee....eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh....ee.hhhhhhhhhhhhhhhh...........eeeeeeeeeeeeeee.......eeeeee........eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------PYRIDOX_OXIDAS------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:24-228 UniProt: 1-228 [INCOMPLETE]                                                                                                                                                           Transcript 1
                 1ci0 A  24 FTLNEKQLTDDPIDLFTKWFNEAKEDPRETLPEAITFSSAELPSGRVSSRILLFKELDHRGFTIYSNWGTSRKAHDIATNPNAAIVFFWKDLQRQVRVEGITEHVNRETSERYFKTRPRGSKIGAWASRQSDVIKNREELDELTQKNTERFKDAEDIPCPDYWGGLRIVPLEIEFWQGRPSRLHDRFVYRRKTENDPWKVVRLAP 228
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223

Chain B from PDB  Type:PROTEIN  Length:204
 aligned with PDX3_YEAST | P38075 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:204
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224    
           PDX3_YEAST    25 TLNEKQLTDDPIDLFTKWFNEAKEDPRETLPEAITFSSAELPSGRVSSRILLFKELDHRGFTIYSNWGTSRKAHDIATNPNAAIVFFWKDLQRQVRVEGITEHVNRETSERYFKTRPRGSKIGAWASRQSDVIKNREELDELTQKNTERFKDAEDIPCPDYWGGLRIVPLEIEFWQGRPSRLHDRFVYRRKTENDPWKVVRLAP 228
               SCOP domains d1ci0b_ B: Pyridoxine 5'-phoshate oxidase (PNP oxidase)                                                                                                                                                      SCOP domains
               CATH domains 1ci0B00 B:25-228 Electron Transport, Fmn-binding Protein; Chain A                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh..hhhhhhhhhhhhhhhh.......eeeeeeee....eeeeeeee..ee....eeeeee...hhhhhhhhhh.eeeeeeee....eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh....ee.hhhhhhhhhhhhhhhh...........eeeeeeeeeeeeeee.......eeeeee........eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------PYRIDOX_OXIDAS------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:25-228 UniProt: 1-228 [INCOMPLETE]                                                                                                                                                          Transcript 1
                 1ci0 B  25 TLNEKQLTDDPIDLFTKWFNEAKEDPRETLPEAITFSSAELPSGRVSSRILLFKELDHRGFTIYSNWGTSRKAHDIATNPNAAIVFFWKDLQRQVRVEGITEHVNRETSERYFKTRPRGSKIGAWASRQSDVIKNREELDELTQKNTERFKDAEDIPCPDYWGGLRIVPLEIEFWQGRPSRLHDRFVYRRKTENDPWKVVRLAP 228
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224

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 '\|'

Asymmetric/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

)

Organisms( (-)

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Class: All beta proteins (24004)

Fold: Split barrel-like (99)

Superfamily: FMN-binding split barrel (90)

Family: PNP-oxidase like (53)

Protein domain: Pyridoxine 5'-phoshate oxidase (PNP oxidase) (16)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (1)

1a	d1ci0a_	A:
1b	d1ci0b_	B:

Asymmetric/Biological Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: Pnp Oxidase; Chain A (68)

Homologous Superfamily: Electron Transport, Fmn-binding Protein; Chain A (67)

Baker's yeast (Saccharomyces cerevisiae) (1)

1a	1ci0B00	B:25-228
1b	1ci0A00	A:24-228

(no "Pfam Domain" information available for 1CI0)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PDX3_YEAST | P38075)

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:0009443	pyridoxal 5'-phosphate salvage	Any process that generates pyridoxal 5'-phosphate, the active form of vitamin B6, from derivatives of it without de novo synthesis.
	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.
cellular component
	GO:0005758	mitochondrial intermembrane space	The region between the inner and outer lipid bilayers of the mitochondrial envelope.

Asymmetric/Biological Unit
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