Pyridoxine/pyridoxamine 5'-phosphate oxidase - Escherichia coli (strain K12)

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Reviewed, UniProtKB/Swiss-Prot P0AFI7 (PDXH_ECOLI)

Last modified June 16, 2009. Version 40. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    Pyridoxine/pyridoxamine 5'-phosphate oxidase
    EC=1.4.3.5
Alternative name(s):
    PNP/PMP oxidase
      Short name=PNPOx
    Pyridoxal 5'-phosphate synthase

Gene names

Name:	pdxH
Ordered Locus Names:	b1638, JW1630

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

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Protein attributes

Sequence length	218 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP). HAMAP MF_01629
Catalytic activity	Pyridoxamine 5'-phosphate + H₂O + O₂ = pyridoxal 5'-phosphate + NH₃ + H₂O₂. HAMAP MF_01629 Pyridoxine 5'-phosphate + O₂ = pyridoxal 5'-phosphate + H₂O₂. HAMAP MF_01629
Cofactor	Binds 1 FMN per subunit. HAMAP MF_01629
Pathway	Cofactor biosynthesis; B6 vitamer interconversion; pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate: step 1/1. HAMAP MF_01629 Cofactor biosynthesis; B6 vitamer interconversion; pyridoxal 5'-phosphate from pyridoxine 5'-phosphate: step 1/1.
Subunit structure	Homodimer. Ref.7 Ref.8 Ref.9 Ref.10
Miscellaneous	Can bind a second molecule of pyridoxamine 5'-phosphate at a non-catalytic site in a cleft at the protein surface. HAMAP MF_01629
Sequence similarities	Belongs to the pyridoxamine 5'-phosphate oxidase family.
Biophysicochemical properties	Kinetic parameters: K_M=0.3 µM for pyridoxamine 5'-phosphate HAMAP MF_01629

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Ontologies

Keywords
Biological process	Pyridoxine biosynthesis
Ligand	FMN Flavoprotein
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW pyridoxine biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	FMN binding Inferred from electronic annotation. Source: HAMAP pyridoxamine-phosphate oxidase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.5

Chain

2 – 218

217

Pyridoxine/pyridoxamine 5'-phosphate oxidase HAMAP MF_01629

PRO_0000167706

Regions

Nucleotide binding

82 – 83

FMN HAMAP MF_01629

Nucleotide binding

146 – 147

FMN HAMAP MF_01629

Region

14 – 17

Substrate binding HAMAP MF_01629

Region

197 – 199

Substrate binding HAMAP MF_01629

Sites

Binding site

FMN HAMAP MF_01629

Binding site

FMN; via amide nitrogen HAMAP MF_01629

Binding site

Substrate HAMAP MF_01629

Binding site

FMN HAMAP MF_01629

Binding site

129

Substrate HAMAP MF_01629

Binding site

133

Substrate HAMAP MF_01629

Binding site

137

Substrate HAMAP MF_01629

Experimental info

Mutagenesis

R → E: Reduces affinity for substrate about 7-fold, but has no effect on catalytic activity. Ref.9

Mutagenesis

R → M: Reduces affinity for substrate about 9-fold, but has no effect on catalytic activity. Ref.9

Mutagenesis

Y → F: Reduces affinity for substrate 3-fold, but has about 5-fold increase in catalytic activity. Ref.9

Mutagenesis

D → A: Reduces affinity for substrate 3-fold and catalytic activity 2-fold. Ref.9

Mutagenesis

197

R → E: Reduces affinity for substrate 8000-fold and catalytic activity 16-fold. Ref.9

Mutagenesis

197

R → M: Reduces affinity for substrate 300-fold and catalytic activity about 4-fold. Ref.9

Mutagenesis

199

H → A: Reduces affinity for substrate 230-fold, but has no effect on catalytic activity. Ref.9

Mutagenesis

199

H → N: Reduces catalytic activity about 4-fold, but has no effect on affinity for substrate. Ref.9

Secondary structure

218

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P0AFI7-1 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: 8B47CEEEA6CEF5F9
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FASTA

218

25,545

        10         20         30         40         50         60 
MSDNDELQQI AHLRREYTKG GLRRRDLPAD PLTLFERWLS QACEAKLADP TAMVVATVDE 

        70         80         90        100        110        120 
HGQPYQRIVL LKHYDEKGMV FYTNLGSRKA HQIENNPRVS LLFPWHTLER QVMVIGKAER 

       130        140        150        160        170        180 
LSTLEVMKYF HSRPRDSQIG AWVSKQSSRI SARGILESKF LELKQKFQQG EVPLPSFWGG 

       190        200        210 
FRVSLEQIEF WQGGEHRLHD RFLYQRENDA WKIDRLAP

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Characterization of the complex pdxH-tyrS operon of Escherichia coli K-12 and pleiotropic phenotypes caused by pdxH insertion mutations." Lam H.-M., Winkler M.E. J. Bacteriol. 174:6033-6045(1992) [PubMed: 1356963] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map." Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T., Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K. Horiuchi T. DNA Res. 3:363-377(1996) [PubMed: 9097039] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Kinetic limitation and cellular amount of pyridoxine (pyridoxamine) 5'-phosphate oxidase of Escherichia coli K-12." Zhao G., Winkler M.E. J. Bacteriol. 177:883-891(1995) [PubMed: 7860596] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-11, CHARACTERIZATION. Strain: K12.
[6]	"Expression, purification, and characterization of recombinant Escherichia coli pyridoxine 5'-phosphate oxidase." di Salvo M., Yang E., Zhao G., Winkler M.E., Schirch V. Protein Expr. Purif. 13:349-356(1998) [PubMed: 9693059] [Abstract] Cited for: CHARACTERIZATION.
[7]	"X-ray structure of Escherichia coli pyridoxine 5'-phosphate oxidase complexed with FMN at 1.8-A resolution." Safo M.K., Mathews I., Musayev F.N., di Salvo M.L., Thiel D.J., Abraham D.J., Schirch V. Structure 8:751-762(2000) [PubMed: 10903950] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 20-218 IN COMPLEX WITH FMN, SUBUNIT.
[8]	"X-ray structure of Escherichia coli pyridoxine 5'-phosphate oxidase complexed with pyridoxal 5'-phosphate at 2.0 A resolution." Safo M.K., Musayev F.N., di Salvo M.L., Schirch V. J. Mol. Biol. 310:817-826(2001) [PubMed: 11453690] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEXES WITH PYRIDOXAL 5'-PHOSPHATE AND FMN, SUBUNIT.
[9]	"Active site structure and stereospecificity of Escherichia coli pyridoxine-5'-phosphate oxidase." di Salvo M.L., Ko T.-P., Musayev F.N., Raboni S., Schirch V., Safo M.K. J. Mol. Biol. 315:385-397(2002) [PubMed: 11786019] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.07 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL 5'-PHOSPHATE AND FMN, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF ARG-14; TYR-17; ASP-49; ARG-197 AND HIS-199.
[10]	"Structure of Escherichia coli pyridoxine 5'-phosphate oxidase in a tetragonal crystal form: insights into the mechanistic pathway of the enzyme." Safo M.K., Musayev F.N., Schirch V. Acta Crystallogr. D 61:599-604(2005) [PubMed: 15858270] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL 5'-PHOSPHATE AND FMN, SUBUNIT.

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Cross-references

Sequence databases

M92351 Genomic DNA. Translation: AAA24709.1.
U00096 Genomic DNA. Translation: AAC74710.1.
AP009048 Genomic DNA. Translation: BAA15399.1.

PIR

B43261.

RefSeq

AP_002260.1.
NP_416155.1.

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1DNL	X-ray	1.80	A	20-218	[»]
1G76	X-ray	2.20	A	1-218	[»]
1G77	X-ray	2.10	A	1-218	[»]
1G78	X-ray	2.20	A	1-218	[»]
1G79	X-ray	2.00	A	1-218	[»]
1JNW	X-ray	2.07	A	1-218	[»]
1WV4	X-ray	2.60	A/B	1-218	[»]

ModBase

Search...

Genome annotation databases

GeneID

946806.

GenomeReviews

Gene locus JW1630 in contig AP009048_GR.
Gene locus b1638 in contig U00096_GR.

KEGG

ecj:JW1630.
eco:b1638.

Organism-specific databases

EchoBASE

EB1450.

EcoGene

EG11487. pdxH.

CMR

Search...

Phylogenomic databases

HOGENOM

P0AFI7.

OMA

P0AFI7. FTFFTNY.

Enzyme and pathway databases

BioCyc

EcoCyc:PDXH-MON.
MetaCyc:PDXH-MON.

Family and domain databases

HAMAP

MF_01629.
[Tree]

InterPro

IPR011576. PNPOx_rel_FMN_bd_core.
IPR000659. Pyridoxamine_oxidase.
IPR019740. Pyridoxamine_oxidase_CS.
IPR019576. Pyridoxamine_oxidase_dimer_C.
IPR012349. Split_barrel_FMN_bd.
[Graphical view]

Gene3D

G3DSA:2.30.110.10. PNPOx_FMN_bd. 1 hit.

PANTHER

PTHR10851. Pyridox_oxidase. 1 hit.

Pfam

PF10590. PNPOx_C. 1 hit.
PF01243. Pyridox_oxidase. 1 hit.
[Graphical view]

ProDom

PD006312. Pyridox_oxidase. 1 hit.
[Graphical view] [Entries sharing at least one domain]

TIGRFAMs

TIGR00558. pdxH. 1 hit.

PROSITE

PS01064. PYRIDOX_OXIDASE. 1 hit.
[Graphical view]

ProtoNet

Search...

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Entry information

Entry name

PDXH_ECOLI

Accession

Primary (citable) accession number: P0AFI7
Secondary accession number(s): P28225

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 20, 2005
Last sequence update:	January 23, 2007
Last modified:	June 16, 2009
This is version 40 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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