Pyridoxine 5'-phosphate synthase - Escherichia coli (strain K12)

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P0A794 (PDXJ_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 81. 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 5'-phosphate synthase
Short name=PNP synthase
EC=2.6.99.2

Gene names

Name:	pdxJ
Ordered Locus Names:	b2564, JW2548

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	243 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 complicated ring closure reaction between the two acyclic compounds 1-deoxy-D-xylulose-5-phosphate (DXP) and 3-amino-2-oxopropyl phosphate (1-amino-acetone-3-phosphate or AAP) to form pyridoxine 5'-phosphate (PNP) and inorganic phosphate. Ref.7
Catalytic activity	1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = pyridoxine 5'-phosphate + phosphate + 2 H₂O. HAMAP-Rule MF_00279
Pathway	Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 5/5. HAMAP-Rule MF_00279
Subunit structure	Homooctamer; tetramer of dimers. Ref.10 Ref.11
Subcellular location	Cytoplasm HAMAP-Rule MF_00279.
Sequence similarities	Belongs to the PNP synthase family.
Sequence caution	The sequence D64044 differs from that shown. Reason: Frameshift at several positions.

Ontologies

Keywords
Biological process	Pyridoxine biosynthesis
Cellular component	Cytoplasm
Molecular function	Transferase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	pyridoxine biosynthetic process Inferred from mutant phenotype Ref.1. Source: EcoliWiki
Cellular_component	cytosol Inferred from direct assay PubMed 16858726. Source: UniProtKB
Molecular_function	pyridoxine 5'-phosphate synthase activity Inferred from direct assay Ref.7. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed HAMAP-Rule MF_00279

Chain

2 – 243

242

Pyridoxine 5'-phosphate synthase HAMAP-Rule MF_00279

PRO_0000190114

Regions

Region

11 – 12

1-deoxy-D-xylulose 5-phosphate binding HAMAP-Rule MF_00279

Region

215 – 216

3-amino-2-oxopropyl phosphate binding HAMAP-Rule MF_00279

Sites

Active site

Proton acceptor

Active site

Proton acceptor

Active site

193

Proton donor

Binding site

3-amino-2-oxopropyl phosphate

Binding site

3-amino-2-oxopropyl phosphate

Binding site

1-deoxy-D-xylulose 5-phosphate

Binding site

1-deoxy-D-xylulose 5-phosphate

Binding site

102

1-deoxy-D-xylulose 5-phosphate

Binding site

194

3-amino-2-oxopropyl phosphate; via amide nitrogen

Site

153

Transition state stabilizer

Natural variations

Natural variant

194

G → S in pdxH null mutation suppressor. Ref.6

Secondary structure

243

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P0A794 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: BF513A5B844E8CB2
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FASTA

243

26,384

        10         20         30         40         50         60 
MAELLLGVNI DHIATLRNAR GTAYPDPVQA AFIAEQAGAD GITVHLREDR RHITDRDVRI 

        70         80         90        100        110        120 
LRQTLDTRMN LEMAVTEEML AIAVETKPHF CCLVPEKRQE VTTEGGLDVA GQRDKMRDAC 

       130        140        150        160        170        180 
KRLADAGIQV SLFIDADEEQ IKAAAEVGAP FIEIHTGCYA DAKTDAEQAQ ELARIAKAAT 

       190        200        210        220        230        240 
FAASLGLKVN AGHGLTYHNV KAIAAIPEMH ELNIGHAIIG RAVMTGLKDA VAEMKRLMLE 


ARG

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Locating essential Escherichia coli genes by using mini-Tn10 transposons: the pdxJ operon." Takiff H.E., Baker T., Copeland T., Chen S.-M., Court D.L. J. Bacteriol. 174:1544-1553(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE. Strain: K12.
[2]	"Suppression of insertions in the complex pdxJ operon of Escherichia coli K-12 by lon and other mutations." Lam H.-M., Tancula E., Dempsey W.B., Winkler M.E. J. Bacteriol. 174:1554-1567(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[3]	Nashimoto H., Saito N. Submitted (SEP-1995) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[4]	"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.
[5]	"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.
[6]	"Isolation of a pdxJ point mutation that bypasses the requirement for the PdxH oxidase in pyridoxal 5'-phosphate coenzyme biosynthesis in Escherichia coli K-12." Man T.K., Zhao G., Winkler M.E. J. Bacteriol. 178:2445-2449(1996) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANT SER-194.
[7]	"Vitamin B6 biosynthesis: formation of pyridoxine 5'-phosphate from 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose-5-phosphate by PdxA and PdxJ protein." Laber B., Maurer W., Scharf S., Stepusin K., Schmidt F.S. FEBS Lett. 449:45-48(1999) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION. Strain: K12 / ATCC 35607 / JM83.
[8]	"Crystallization and preliminary X-ray crystallographic analysis of PdxJ, the pyridoxine 5'-phosphate synthesizing enzyme." Garrido Franco M., Huber R., Schmidt F.S., Laber B., Clausen T. Acta Crystallogr. D 56:1045-1048(2000) [PubMed] [Europe PMC] [Abstract] Cited for: CRYSTALLIZATION.
[9]	"Pyridoxine 5'-phosphate synthase: de novo synthesis of vitamin B6 and beyond." Garrido-Franco M. Biochim. Biophys. Acta 1647:92-97(2003) [PubMed] [Europe PMC] [Abstract] Cited for: REVIEW.
[10]	"Structural basis for the function of pyridoxine 5'-phosphate synthase." Garrido Franco M., Laber B., Huber R., Clausen T. Structure 9:245-253(2001) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH PRODUCT, SUBUNIT.
[11]	"Multistate binding in pyridoxine 5'-phosphate synthase: 1.96 A crystal structure in complex with 1-deoxy-D-xylulose phosphate." Yeh J.I., Du S., Pohl E., Cane D.E. Biochemistry 41:11649-11657(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.96 ANGSTROMS) OF APOENZYME AND COMPLEX WITH SUBSTRATE, SUBUNIT.
[12]	"Enzyme-ligand complexes of pyridoxine 5'-phosphate synthase: implications for substrate binding and catalysis." Garrido-Franco M., Laber B., Huber R., Clausen T. J. Mol. Biol. 321:601-612(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEXES WITH SUBSTRATE AND SUBSTRATE ANALOG, REACTION MECHANISM.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M76470 Genomic DNA. Translation: AAA21845.1.
M74526 Genomic DNA. Translation: AAA24315.1.
D64044 Genomic DNA. No translation available.
U36841 Genomic DNA. Translation: AAA79826.1.
U00096 Genomic DNA. Translation: AAC75617.1.
AP009048 Genomic DNA. Translation: BAE76740.1.

PIR

A42293.

RefSeq

NP_417059.1. NC_000913.2.
YP_490792.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1HO1	X-ray	2.00	A/B/C/D	2-243	[»]
1HO4	X-ray	2.30	A/B/C/D	2-243	[»]
1IXN	X-ray	2.30	A/B/C/D	2-243	[»]
1IXO	X-ray	2.30	A/B/C/D	2-243	[»]
1IXP	X-ray	2.30	A/B/C/D	2-243	[»]
1IXQ	X-ray	2.30	A/B/C/D	2-243	[»]
1M5W	X-ray	1.96	A/B/C/D/E/F/G/H	1-243	[»]

ProteinModelPortal

P0A794.

SMR

P0A794. Positions 2-243.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-36215N.

IntAct

P0A794. 5 interactions.

MINT

MINT-1227457.

STRING

511145.b2564.

Proteomic databases

PaxDb

P0A794.

PRIDE

P0A794.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC75617; AAC75617; b2564.
BAE76740; BAE76740; BAE76740.

GeneID

12931607.
947039.

KEGG

ecj:Y75_p2517.
eco:b2564.

PATRIC

32120527. VBIEscCol129921_2666.

Organism-specific databases

EchoBASE

EB0687.

EcoGene

EG10693. pdxJ.

Phylogenomic databases

eggNOG

COG0854.

HOGENOM

HOG000258095.

K03474.

OMA

LHYHNVK.

ProtClustDB

PRK05265.

Enzyme and pathway databases

BioCyc

EcoCyc:PDXJ-MONOMER.
ECOL316407:JW2548-MONOMER.
MetaCyc:PDXJ-MONOMER.

UniPathway

UPA00244; UER00313.

Gene expression databases

Genevestigator

P0A794.

Family and domain databases

Gene3D

3.20.20.70. 1 hit.

HAMAP

MF_00279. PdxJ.

InterPro

IPR013785. Aldolase_TIM.
IPR004569. PyrdxlP_synth_PdxJ.
[Graphical view]

Pfam

PF03740. PdxJ. 1 hit.
[Graphical view]

SUPFAM

SSF63892. PyrdxlP_synth_PdxJ. 1 hit.

TIGRFAMs

TIGR00559. pdxJ. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P0A794.

Entry information

Entry name

PDXJ_ECOLI

Accession

Primary (citable) accession number: P0A794
Secondary accession number(s): P24223, Q2MAG6

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 7, 2005
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 81 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

Natural variations

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