1WV4 - JenaLib

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Title :   X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-PHOSPHATE OXIDASE IN TETRAGONAL CRYSTAL FORM

Authors :   M. K. Safo, F. N. Musayev, V. Schirch

Date :   11 Dec 04 (Deposition) - 28 Dec 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Plp, Fmn, Pyridoxal, Pyridoxine 5'-Phosphate, Oxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. K. Safo, F. N. Musayev, V. Schirch
Structure Of Escherichia Coli Pyridoxine 5'-Phosphate Oxidase In A Tetragonal Crystal Form: Insights Into The Mechanistic Pathway Of The Enzyme.
Acta Crystallogr. , Sect. D V. 61 599 2005
PubMed-ID: 15858270 | Reference-DOI: 10.1107/S0907444905005512
(for further references see the PDB file header)

Molecule 1 - PYRIDOXAMINE 5'-PHOSPHATE OXIDASE
	Chains	:	A, B
	EC Number	:	1.4.3.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	PNP/PMP OXIDASE, PNPOX

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:24 , ARG A:215 , HOH A:317	BINDING SITE FOR RESIDUE PO4 A 275
2	AC2	SOFTWARE	ARG B:23 , ARG B:24 , ARG B:25 , ARG B:215	BINDING SITE FOR RESIDUE PO4 B 1275
3	AC3	SOFTWARE	ASP A:49 , ARG A:67 , ILE A:68 , LEU A:70 , LYS A:72 , TYR A:82 , THR A:83 , SER A:87 , ARG A:88 , LYS A:89 , HOH A:291 , HIS B:106 , GLN B:111 , TRP B:191 , ARG B:201	BINDING SITE FOR RESIDUE FMN A 250
4	AC4	SOFTWARE	GLN A:111 , TRP A:191 , ARG A:201 , ASP B:49 , ARG B:67 , ILE B:68 , VAL B:69 , LEU B:70 , TYR B:82 , THR B:83 , SER B:87 , ARG B:88 , LYS B:89 , HOH B:1282	BINDING SITE FOR RESIDUE FMN B 1250

(no "SS Bond" information available for 1WV4)

(no "Cis Peptide Bond" information available for 1WV4)

(no "SAP(SNP)/Variant" information available for 1WV4)

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.	PDXH_SHIFL	188-201	2	A:188-201 B:188-201
1	PYRIDOX_OXIDASE	PS01064	Pyridoxamine 5'-phosphate oxidase signature.	PDXH_ECOLI	188-201	2	A:188-201 B:188-201

(no "Exon" information available for 1WV4)

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
	(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:162
 aligned with PDXH_ECOLI | P0AFI7 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:208
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        
           PDXH_ECOLI    11 AHLRREYTKGGLRRRDLPADPLTLFERWLSQACEAKLADPTAMVVATVDEHGQPYQRIVLLKHYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPWHTLERQVMVIGKAERLSTLEVMKYFHSRPRDSQIGAWVSKQSSRISARGILESKFLELKQKFQQGEVPLPSFWGGFRVSLEQIEFWQGGEHRLHDRFLYQRENDAWKIDRLAP 218
               SCOP domains d1wv4a_ A: Pyridoxine 5'-phoshate oxidase (PNP oxidase)                                                                                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhhh......eeeeeee.....eeeeeee..eee..eeeeeee..hhhhhhhhhh.eeeeeeeehhhheeeeeeeeeee.hhhhhh..----------------------------------------------..eeeeee...eeeeee.......eeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PYRIDOX_OXIDAS----------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wv4 A  11 AHLRREYTKGGLRRRDLPADPLTLFERWLSQACEAKLADPTAMVVATVDEHGQPYQRIVLLKHYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPWHTLERQVMVIGKAERLSTLEVMKY----------------------------------------------SFWGGFRVSLEQIEFWQGGEHRLHDRFLYQRENDAWKIDRLAP 218
                                    20        30        40        50        60        70        80        90       100       110       120        |-         -         -         -         -     | 180       190       200       210        
                                                                                                                                                129                                            176

Chain A from PDB  Type:PROTEIN  Length:162
 aligned with PDXH_SHIFL | P0AFI8 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:208
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        
           PDXH_SHIFL    11 AHLRREYTKGGLRRRDLPADPLTLFERWLSQACEAKLADPTAMVVATVDEHGQPYQRIVLLKHYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPWHTLERQVMVIGKAERLSTLEVMKYFHSRPRDSQIGAWVSKQSSRISARGILESKFLELKQKFQQGEVPLPSFWGGFRVSLEQIEFWQGGEHRLHDRFLYQRENDAWKIDRLAP 218
               SCOP domains d1wv4a_ A: Pyridoxine 5'-phoshate oxidase (PNP oxidase)                                                                                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhhh......eeeeeee.....eeeeeee..eee..eeeeeee..hhhhhhhhhh.eeeeeeeehhhheeeeeeeeeee.hhhhhh..----------------------------------------------..eeeeee...eeeeee.......eeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PYRIDOX_OXIDAS----------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wv4 A  11 AHLRREYTKGGLRRRDLPADPLTLFERWLSQACEAKLADPTAMVVATVDEHGQPYQRIVLLKHYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPWHTLERQVMVIGKAERLSTLEVMKY----------------------------------------------SFWGGFRVSLEQIEFWQGGEHRLHDRFLYQRENDAWKIDRLAP 218
                                    20        30        40        50        60        70        80        90       100       110       120        |-         -         -         -         -     | 180       190       200       210        
                                                                                                                                                129                                            176

Chain B from PDB  Type:PROTEIN  Length:154
 aligned with PDXH_ECOLI | P0AFI7 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:202
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216  
           PDXH_ECOLI    17 YTKGGLRRRDLPADPLTLFERWLSQACEAKLADPTAMVVATVDEHGQPYQRIVLLKHYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPWHTLERQVMVIGKAERLSTLEVMKYFHSRPRDSQIGAWVSKQSSRISARGILESKFLELKQKFQQGEVPLPSFWGGFRVSLEQIEFWQGGEHRLHDRFLYQRENDAWKIDRLAP 218
               SCOP domains d1wv4b_ B: Pyridoxine 5'-phoshate oxidase (PNP oxidase)                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------Pyridox_oxidase-1wv4B01 B:39-125                                                       ----------------------------------------------------PNPOx_C-1wv4B03 B:178-218                 Pfam domains (1)
           Pfam domains (2) ----------------------Pyridox_oxidase-1wv4B02 B:39-125                                                       ----------------------------------------------------PNPOx_C-1wv4B04 B:178-218                 Pfam domains (2)
         Sec.struct. author ......hhhhh..hhhhhhhhhhhhhhhh......eeeeeee.....eeeeeee..eee..eeeeeee..hhhhhhhhhh.eeeeee.hhhh.eeeeeeeeeee.......------------------------------------------------..eeeeee...eeeeee.......eeeeeeee..eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------PYRIDOX_OXIDAS----------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wv4 B  17 YTKGGLRRRDLPADPLTLFERWLSQACEAKLADPTAMVVATVDEHGQPYQRIVLLKHYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPWHTLERQVMVIGKAERLSTLEVM------------------------------------------------SFWGGFRVSLEQIEFWQGGEHRLHDRFLYQRENDAWKIDRLAP 218
                                    26        36        46        56        66        76        86        96       106       116       126|        -         -         -         -       176       186       196       206       216  
                                                                                                                                        127                                              176

Chain B from PDB  Type:PROTEIN  Length:154
 aligned with PDXH_SHIFL | P0AFI8 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:202
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216  
           PDXH_SHIFL    17 YTKGGLRRRDLPADPLTLFERWLSQACEAKLADPTAMVVATVDEHGQPYQRIVLLKHYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPWHTLERQVMVIGKAERLSTLEVMKYFHSRPRDSQIGAWVSKQSSRISARGILESKFLELKQKFQQGEVPLPSFWGGFRVSLEQIEFWQGGEHRLHDRFLYQRENDAWKIDRLAP 218
               SCOP domains d1wv4b_ B: Pyridoxine 5'-phoshate oxidase (PNP oxidase)                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------Pyridox_oxidase-1wv4B01 B:39-125                                                       ----------------------------------------------------PNPOx_C-1wv4B03 B:178-218                 Pfam domains (1)
           Pfam domains (2) ----------------------Pyridox_oxidase-1wv4B02 B:39-125                                                       ----------------------------------------------------PNPOx_C-1wv4B04 B:178-218                 Pfam domains (2)
         Sec.struct. author ......hhhhh..hhhhhhhhhhhhhhhh......eeeeeee.....eeeeeee..eee..eeeeeee..hhhhhhhhhh.eeeeee.hhhh.eeeeeeeeeee.......------------------------------------------------..eeeeee...eeeeee.......eeeeeeee..eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------PYRIDOX_OXIDAS----------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wv4 B  17 YTKGGLRRRDLPADPLTLFERWLSQACEAKLADPTAMVVATVDEHGQPYQRIVLLKHYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPWHTLERQVMVIGKAERLSTLEVM------------------------------------------------SFWGGFRVSLEQIEFWQGGEHRLHDRFLYQRENDAWKIDRLAP 218
                                    26        36        46        56        66        76        86        96       106       116       126|        -         -         -         -       176       186       196       206       216  
                                                                                                                                        127                                              176

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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)

Escherichia coli [TaxId: 562] (7)

1a	d1wv4a_	A:
1b	d1wv4b_	B:

(no "CATH Domain" information available for 1WV4)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: FMN-binding (25)

Family: Pyridox_oxidase (9)

Escherichia coli (strain K12) (2)

1a	Pyridox_oxidase-1wv4B01	B:39-125
1b	Pyridox_oxidase-1wv4B02	B:39-125

Clan: no clan defined [family: PNPOx_C] (4)

Family: PNPOx_C (4)

Escherichia coli (strain K12) (2)

2a	PNPOx_C-1wv4B03	B:178-218
2b	PNPOx_C-1wv4B04	B:178-218

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PDXH_ECOLI | P0AFI7)

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.
	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.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain A,B (PDXH_SHIFL | P0AFI8)

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: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.

Asymmetric/Biological Unit
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UniProtKB/Swiss-Prot
	PDXH_ECOLI \| P0AFI7	:	1dnl 1g76 1g77 1g78 1g79 1jnw
	PDXH_SHIFL \| P0AFI8	:	1dnl 1g76 1g77 1g78 1g79 1jnw

1dnl	STRUCTURE OF BINARY COMPLEX OF E. COLI PNPOX IN TRIGONAL CRYSTAL FORM
1g79	STRUCTURE OF TERNARY COMPLEX OF E. COLI PNPOX IN TRIGONAL CRYSTAL FORM
1jnw	STRUCTURE OF TERNARY COMPLEX OF E. COLI PNPOX IN MONOCLINIC CRYSTAL FORM

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