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Overview for MACiE Entry M0253

Version history

General Information

EC Number: 2.5.1.10 (A member of the Transferases, Transferring alkyl or aryl groups, other than methyl groups, Transferring alkyl or aryl groups, other than methyl groups (only sub-subclass identified to date))

Enzyme Name: geranyltranstransferase

Biological Species: Gallus gallus (Chicken)

Catalytic Chain UniprotKB Accession Codes:

  • P22939 - Farnesyl diphosphate synthase

Representative PDB Code: 1uby - STRUCTURE OF FARNESYL PYROPHOSPHATE SYNTHETASE (Resolution = 2.40 Å).

Catalytic CATH Codes:

Display structure information

Overall Reaction:

Image of isopentenyl diphosphate

Image of geranyl diphosphate

right arrow

Image of trans,trans-farnesyl diphosphate

Image of diphosphate

isopentenyl diphosphate
C00129
CHEBI:128769
geranyl diphosphate
C00341
CHEBI:58057
trans,trans-farnesyl diphosphate
C00448
CHEBI:17407
diphosphate
C00013
CHEBI:33019

Overall Comment: This enzyme is annotated as catalysing the reactions for both EC 2.5.1.10 and 2.5.1.1. It is known that the residue at the fifth position before the first DDxxD motif [1], in this case Phe112 (Phe240 in E. coli) is responsible for determining product chain length. It has also been shown for the avian enzyme that Phe113 also helps to determine product chain length. It is not clear if any other active site amino acid residues are involved in the catalysis of the Avian enzyme. However, in the E. coli enzyme, which utilises a three metal mechanism and performs the elongation with cis- stereochemistry, rather than two metal trans- stereochemistry, the main chain carbonyl of Lys202 (Lys214 in avian protein) and side chain oxygens of Thr203 and Gln241 form the carbocation binding (and stabilisation) site [2].


View similar reactions


Stepwise Description of the Reaction

Step 1The substrate undergoes heterolysis. The diphosphate product remains associated with the active site, and the cabocation is delocalised over the three terminal carbon atoms of the intermediate.
Step 2The double bond of isopentenyl diphosphate adds to the terminal carbocation in an electrophilic addition.
Step 3The diphosphate formed in the initial heterolysis deprotonates the carbon adjacent to the newly formed carbocation, forming a new double bond in the trans,trans-farnesyl diphosphate product.

View similar reactions (composite manual annotation)


Catalytic Residues Involved

Type Number Chain Location of Function
Phe 112 A Side Chain
Lys 214 A Side Chain

Metal Cofactors for M0253

Type Het group Number Chain
magnesium MG 402 A Overview
magnesium MG 403 A Overview
magnesium No Available PDB Information

References

  1. P.-H. Liang et al. (2002), Eur. J. Biochem., 269, 3339-3354. Structure, mechanism and function of prenyltransferases.
    Medline: 12135472
  2. D. J. Hosfield et al. (2004), J. Biol. Chem., 279, 8526-8529. Structural Basis for Bisphosphonate-mediated Inhibition of Isoprenoid Biosynthesis.
    Medline: 14672944
  3. L. C. Tarshis et al. (1996), Proc. Natl Acad. Sci. USA, 93, 15018-15023. Regulation of product chain length by isoprenyl diphosphate synthases.
    Medline: 8986756

Homologue information for M0253 (1uby)

CSA Homologues

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
M0264 squalene synthase
2.5.1.21
1ezf 1.10.600.10
0.29160.1285Compare
M0262 trichodiene synthase
4.2.3.6
1jfg 1.10.600.10
0.35130.0805Compare
M0089 pentalenene synthase
4.2.3.7
1ps1 1.10.600.10
0.31810.2719Compare
M0261 aristolochene synthase
4.2.3.9
1di1 1.10.600.10
0.33330.4608Compare
M0265 aristolochene synthase
4.2.3.9
5eat 1.10.600.10
0.22850.0081Compare
M0259 bornyl diphosphate synthase
5.5.1.8
1n20 1.10.600.10
0.33330.18Compare

View a comparison of the other reactions in MACiE with the CATH domain 1.10.600.10


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
Link to EzCatDB Link to SFLD

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isoprenoid biosynthetic process (biological process)
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