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

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P0AFI7 (PDXH_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 74. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

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) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

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

General annotation (Comments)

Function	Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP). HAMAP-Rule MF_01629
Catalytic activity	Pyridoxamine 5'-phosphate + H₂O + O₂ = pyridoxal 5'-phosphate + NH₃ + H₂O₂. HAMAP-Rule MF_01629 Pyridoxine 5'-phosphate + O₂ = pyridoxal 5'-phosphate + H₂O₂. HAMAP-Rule MF_01629
Cofactor	Binds 1 FMN per subunit.
Pathway	Cofactor biosynthesis; B6 vitamer interconversion; pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate: step 1/1. HAMAP-Rule 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-Rule 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 Ref.9

Ontologies

Keywords
Biological process	Pyridoxine biosynthesis
Ligand	FMN Flavoprotein
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	pyridoxal 5'-phosphate salvage Inferred from experiment PubMed 12686112. Source: EcoCyc pyridoxine biosynthetic process Inferred from direct assay Ref.5. Source: EcoCyc
Molecular_function	FMN binding Inferred from direct assay Ref.5. Source: EcoCyc pyridoxamine-phosphate oxidase activity Inferred from direct assay Ref.5. Source: EcoCyc
Complete GO annotation...

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-Rule MF_01629

PRO_0000167706

Regions

Nucleotide binding

82 – 83

FMN HAMAP-Rule MF_01629

Nucleotide binding

146 – 147

FMN HAMAP-Rule MF_01629

Region

14 – 17

Substrate binding HAMAP-Rule MF_01629

Region

197 – 199

Substrate binding HAMAP-Rule MF_01629

Sites

Binding site

FMN

Binding site

FMN; via amide nitrogen

Binding site

Substrate

Binding site

FMN

Binding site

129

Substrate

Binding site

133

Substrate

Binding site

137

Substrate

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...

Sequences

Sequence

Length

Mass (Da)

Tools

P0AFI7 [UniParc].

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

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

« Hide

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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL 5'-PHOSPHATE AND FMN, SUBUNIT.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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

PIR

B43261.

RefSeq

NP_416155.1. NC_000913.2.
YP_489902.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P0AFI7.

SMR

P0AFI7. Positions 5-218.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-48024N.

IntAct

P0AFI7. 12 interactions.

STRING

511145.b1638.

Proteomic databases

PaxDb

P0AFI7.

PRIDE

P0AFI7.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC74710; AAC74710; b1638.
BAA15399; BAA15399; BAA15399.

GeneID

12934494.
946806.

KEGG

ecj:Y75_p1615.
eco:b1638.

PATRIC

32118578. VBIEscCol129921_1709.

Organism-specific databases

EchoBASE

EB1450.

EcoGene

EG11487. pdxH.

Phylogenomic databases

eggNOG

COG0259.

HOGENOM

HOG000242755.

K00275.

OMA

ERIEFWQ.

ProtClustDB

PRK05679.

Enzyme and pathway databases

BioCyc

EcoCyc:PDXH-MONOMER.
ECOL316407:JW1630-MONOMER.
MetaCyc:PDXH-MONOMER.

UniPathway

UPA00190; UER00304.
UPA00190; UER00305.

Gene expression databases

Genevestigator

P0AFI7.

Family and domain databases

Gene3D

2.30.110.10. 1 hit.

HAMAP

MF_01629. PdxH.

InterPro

IPR000659. Pyridox_Oxase.
IPR019740. Pyridox_Oxase_CS.
IPR011576. Pyridox_Oxase_FMN-bd.
IPR019576. Pyridoxamine_oxidase_dimer_C.
IPR012349. Split_barrel_FMN-bd.
[Graphical view]

PANTHER

PTHR10851. PTHR10851. 1 hit.

Pfam

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

PIRSF

PIRSF000190. Pyd_amn-ph_oxd. 1 hit.

SUPFAM

SSF50475. FMN_binding. 1 hit.

TIGRFAMs

TIGR00558. pdxH. 1 hit.

PROSITE

PS01064. PYRIDOX_OXIDASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P0AFI7.

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:	May 1, 2013
This is version 74 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents