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Overview for MACiE Entry M0300

Version history

General Information

EC Number: 3.1.4.46 (A member of the Hydrolases, Acting on ester bonds, Phosphoric-diester hydrolases)

Enzyme Name: glycerophosphodiester phosphodiesterase

Biological Species: Thermoanaerobacter tengcongensis (Bacteria)

Catalytic Chain UniprotKB Accession Codes:

Representative PDB Code: 2pz0 - CRYSTAL STRUCTURE OF GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE (GDPD)FROM T. TENGCONGENSIS (Resolution = 1.91 Å).

Catalytic CATH Codes:

  • 3.20.20.190 - Phosphatidylinositol (PI) phosphodiesterase

"Other" CATH Codes:

  • 3.20.20.190 - Phosphatidylinositol (PI) phosphodiesterase

Display structure information

Overall Reaction:

Image of water

Image of glycerophosphodiester

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Image of sn-Glycerol 3-phosphate

Image of alcohol

water
C00001
CHEBI:15377
glycerophosphodiester
C03120
sn-Glycerol 3-phosphate
C00093
CHEBI:15978
alcohol
C00069
CHEBI:30879

Overall Comment: This enzyme will function with Ca(II) ions, but it more active with Mg(II) ions.


View similar reactions


Stepwise Description of the Reaction

Step 1His17 deprotonates the substrate alcohol, which initiates a nucleophilic attack on the phosphate group, eliminating the product alcohol with concomitant deprotonation of His59
Step 2His59 deprotonates water, which initiates a nucleophilic attack on the phosphate group, destroying the cyclic intermediate with concomitant deprotonation of His17

View similar reactions (composite manual annotation)


Catalytic Residues Involved

Type Number Chain Location of Function
Asp 239 A Side Chain
His 17 A Side Chain
His 59 A Side Chain
Arg 18 A Side Chain
Lys 121 A Side Chain

Metal Cofactors for M0300

Type Het group Number Chain
magnesium CA 502 B Overview

References

  1. L. Shi et al. (2008), Proteins, 72, 280-288. Crystal structure of glycerophosphodiester phosphodiesterase (GDPD) from Thermoanaerobacter tengcongensis, a metal ion-dependent enzyme: insight into the catalytic mechanism.
    Medline: 18214974

Homologue information for M0300 (2pz0)

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
M0028 phosphoinositide phospholipase C
3.1.4.11
1djx 3.20.20.190
0.69230.3999Compare
M0242 sphingomyelin phosphodiesterase D
3.1.4.41
2f9r 3.20.20.190
0.47820.488Compare
M0026 phosphatidylinositol diacylglycerol-lyase
4.6.1.13
1ptd 3.20.20.190
0.88230.7107Compare

View a comparison of the other reactions in MACiE with the CATH domain 3.20.20.190


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

GOA logo
glycerol metabolic process (biological process)
lipid metabolic process (biological process)
phosphoric diester hydrolase activity (molecular function)
glycerophosphodiester phosphodiesterase activity (molecular function)
metal ion binding (molecular function)
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