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Overview for MACiE Entry M0243

Version history

General Information

EC Number: 2.6.99.2 (A member of the Transferases, Transferring nitrogenous groups, Transferring other nitrogenous groups)

Enzyme Name: pyridoxine 5'-phosphate synthase

Biological Species: Escherichia coli (Bacteria)

Catalytic Chain UniprotKB Accession Codes:

  • P0A794 - Pyridoxine 5'-phosphate synthase

Representative PDB Code: 1ho1 - CRYSTAL STRUCTURE OF PYRIDOXINE 5'-PHOSPHATE SYNTHASE (Resolution = 2.00 Å).

Catalytic CATH Codes:

"Other" CATH Codes:

Display structure information

Overall Reaction:

Image of 3-amino-2-oxopropyl phosphate

Image of 1-deoxy-D-xylulose 5-phosphate

right arrow

Image of pyridoxine 5'-phosphate

Image of phosphate

Image of water

3-amino-2-oxopropyl phosphate
C11638
1-deoxy-D-xylulose 5-phosphate
C11437
CHEBI:57792
pyridoxine 5'-phosphate
C00627
CHEBI:28803
phosphate
C00009
CHEBI:18367
2 water
C00001
CHEBI:15377

Overall Comment: This enzyme forms part of the vitamin B6 biosynthesis pathway in bacteria.


View similar reactions


Stepwise Description of the Reaction

Step 1The 3-amino-2-oxopropyl phosphate substrate initiates a nucleophilic attack upon the 1-deoxy-D-xylulose 5-phosphate in the first step of a Schiff base formation. The carbonyl oxygen is assumed to deprotonate the amine.
Step 2The newly formed secondary amine initiates a intramolecular elimination of water, which obtains its proton first from Glu72, and then from water.
Step 3His45 deprotonates the C3 of the intermediate, which initiates double bond rearrangement, with the Schiff base acting as an electron sink.
Step 4The Schiff base reforms, initiating a double bond rearrangement and resulting in the elimination of water, which obtains it's proton from Glu72.
Step 5Glu72 deprotonates the remaining hydroxide, which initiates a double bond rearrangement and eliminates phosphate.
Step 6His12 activates water, which initiates a nucleophilic addition to the newly formed C=C. This causes ring closure, and the resulting oxyanion is protonated by His193. Glu72 is activated by a water molecule.
Step 7Glu72 deprotonates the C4 carbon, initiating the elimination of hydroxide, which obtains a proton from His12.
Step 8His193 deprotonates C6, initiating a double bond rearrangement that results in the protonation of O3' by His45.

View similar reactions (composite manual annotation)


Catalytic Residues Involved

Type Number Chain Location of Function
His 12 A Side Chain
Arg 51 A Side Chain
Thr 103 A Side Chain
His 45 A Side Chain
Arg 47 A Side Chain
Glu 72 A Side Chain
Glu 153 A Side Chain
Asn 9 A Side Chain
His 193 A Side Chain

References

  1. M. Garrido-Franco et al. (2002), J. Mol. Biol., 321, 601-612. Enzyme-Ligand Complexes of Pyridoxine 5'-Phosphate Synthase: Implications for Substrate Binding and Catalysis.
    Medline: 12206776
  2. J. I. Yeh et al. (2002), Biochemistry, 41, 11649-11657. Multistate Binding in Pyridoxine 5'-Phosphate Synthase: 1.96 A Crystal Structure in Complex with 1-Deoxy-D-xylulose Phosphate.
    Medline: 12269807

Homologue information for M0243 (1ho1)

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)



Entries with at least one Catalytic CATH code in common (different mechanisms):

MACiE Entry Enzyme Name
EC Number
PDB code CATH code Composite
Reaction Similarity
Catalytic Machinery
Similarity
M0102 L-lactate dehydrogenase (cytochrome)
1.1.2.3
1fcb 3.20.20.70
0.17410.1496Compare
M0108 2,4-dienoyl-CoA reductase (NADPH)
1.3.1.34
1ps9 3.20.20.70
0.46150.3803Compare
M0109 dihydroorotate oxidase
1.3.3.1
1d3g 3.20.20.70
0.31060.0408Compare
M0111 glutamate synthase (ferredoxin)
1.4.7.1
1ofd 3.20.20.70
0.6680.188Compare
M0114 trimethylamine dehydrogenase
1.5.8.2
2tmd 3.20.20.70
0.19060.1420Compare
M0319 NADPH dehydrogenase
1.6.99.1
1oya 3.20.20.70
0.18380.2825Compare
M0148 transaldolase
2.2.1.2
1onr 3.20.20.70
0.71520.135Compare
M0008 nicotinate-nucleotide diphosphorylase (carboxylating)
2.4.2.19
1qpr 3.20.20.70
0.18860.2019Compare
M0050 orotidine-5'-phosphate decarboxylase
4.1.1.23
1dbt 3.20.20.70
0.0630Compare
M0252 indole-3-glycerol-phosphate synthase
4.1.1.48
1igs 3.20.20.70
0.45740.1996Compare
M0236 3-dehydro-L-gulonate-6-phosphate decarboxylase
4.1.1.85
1q6l 3.20.20.70
0.16190.2499Compare
M0052 fructose-bisphosphate aldolase (Class II)
4.1.2.13
1b57 3.20.20.70
0.34670.1563Compare
M0222 fructose-bisphosphate aldolase (Class I)
4.1.2.13
2qut 3.20.20.70
0.72520.1454Compare
M0054 3-dehydroquinate dehydratase (type I)
4.2.1.10
1qfe 3.20.20.70
0.61780.2646Compare
M0230 porphobilinogen synthase
4.2.1.24
1gzg 3.20.20.70
0.86610Compare
M0267 dihydrodipicolinate synthase
4.2.1.52
1dhp 3.20.20.70
0.50760Compare
M0270 ribulose-phosphate 3-epimerase
5.1.3.1
1h1z 3.20.20.70
0.17870.0105Compare
M0324 triosephosphate isomerase
5.3.1.1
1tph 3.20.20.70
0.17050.2499Compare
M0223 pyruvate carboxylase
6.4.1.1
2qf7 3.20.20.70
0.43390.0084Compare

View a comparison of the other reactions in MACiE with the CATH domain 3.20.20.70


Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
Link to MetaCyc Link to KEGG Link to BRENDA Link to ExplorENZ

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catalytic activity (molecular function)
cytoplasm (cellular component)
metabolic process (biological process)
pyridoxine biosynthetic process (biological process)
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