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Overview for MACiE Entry M0090

Version history

General Information

EC Number: 3.3.1.1 (A member of the Hydrolases, Acting on ether bonds, Thioether and trialkylsulfonium hydrolases)

Enzyme Name: adenosylhomocysteinase

Biological Species: Rattus norvegicus (Rat)

Catalytic Chain UniprotKB Accession Codes:

  • P10760 - Adenosylhomocysteinase

Representative PDB Code: 1b3r - RAT LIVER S-ADENOSYLHOMOCYSTEIN HYDROLASE (Resolution = 2.80 Å).

Catalytic CATH Codes:

Display structure information

Overall Reaction:

Image of S-adenosyl-L-homocysteine

Image of water

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Image of adenosine

Image of L-homocysteine

S-adenosyl-L-homocysteine
C00021
CHEBI:57856
water
C00001
CHEBI:15377
adenosine
C00212
CHEBI:16335
L-homocysteine
C00155
CHEBI:58199

View similar reactions


Stepwise Description of the Reaction

Step 1Asp189 deprotonates Lys185, which in turn deprotonates 3'-OH of the substrate. This cause the elimination of a hydride ion, which is transferred to the NAD cofactor.
Step 2Asp130 deprotonates the 4'-CH of the substrate, forming a carbanion.
Step 3The 4'-carbanion initiates the elimination of the homocysteine thiolate.
Step 4His54 deprotonates water, which initiates a nucleophilic attack upon the C=C in an addition reaction, re-forming the carbanion.
Step 5The homocysteine thiolate deprotonates His54 in an inferred step.
Step 6The carbanion deprotonates Asp130.
Step 7The NAD cofactor eliminates the hydride ion, which adds to the 3'-C initiating the oxyanion to deprotonate Lys185, which in turn deprotonates Asp189.

View similar reactions (composite manual annotation)


Catalytic Residues Involved

Type Number Chain Location of Function
His 54 A Side Chain
Asp 130 A Side Chain
Lys 185 A Side Chain
Asp 189 A Side Chain
Asn 190 A Side Chain
Cys 194 A Side Chain
His 300 A Side Chain
Ser 360 A Side Chain

Organic Cofactors for M0090

Type Identity Chain
NAD NAD 432 A Overview

References

  1. J. Komoto et al. (2000), J. Biol. Chem., 275, 32147-32156. Effects of site-directed mutagenesis on structure and function of recombinant rat liver S-adenosylhomocysteine hydrolase. Crystal structure of D244E mutant enzyme.
    Medline: 10913437
  2. Y. Hu et al. (1999), Biochemistry, 38, 8323-8333. Crystal structure of S-adenosylhomocysteine hydrolase from rat liver.
    Medline: 10387078
  3. Y. Takata et al. (2002), J. Biol. Chem., 277, 22670-22676. Catalytic mechanism of S-adenosylhomocysteine hydrolase. Site-directed mutagenesis of Asp-130, Lys-185, Asp-189, and Asn-190.
    Medline: 11927587

Homologue information for M0090 (1b3r)

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
M0255 alcohol dehydrogenase
1.1.1.1
1mg5 3.40.50.720
0.41530.1509Compare
M0092 UDP-glucose 6-dehydrogenase
1.1.1.22
1dli 3.40.50.720
0.68830.3575Compare
M0021 malate dehydrogenase (oxaloacetate-decarboxylating)
1.1.1.38
1do8 3.40.50.720
0.6610.2868Compare
M0227 GDP-L-fucose synthase
1.1.1.271
1e6u 3.40.50.720
0.65280.3992Compare
M0110 D-amino-acid oxidase
1.4.3.3
1c0p 3.40.50.720
0.56960.1384Compare
M0237 pteridine reductase
1.5.1.33
2c7v 3.40.50.720
0.66660.1384Compare
M0116 NAD(P)+ transhydrogenase (AB-specific)
1.6.1.2
1hzz 3.40.50.720
0.36660.2653Compare
M0142 ferredoxin-NADP+ reductase
1.18.1.2
1e6e 3.40.50.720
0.26080.3159Compare
M0226 UDP-sulfoquinovose synthase
3.13.1.1
1qrr 3.40.50.720
0.81150.2768Compare
M0228 dTDP-glucose 4,6-dehydratase
4.2.1.46
1bxk 3.40.50.720
0.70.1927Compare
M0188 UDP-glucose 4-epimerase
5.1.3.2
1xel 3.40.50.720
0.53570.1525Compare

View a comparison of the other reactions in MACiE with the CATH domain 3.40.50.720


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)
adenosylhomocysteinase activity (molecular function)
binding (molecular function)
one-carbon metabolic process (biological process)
metabolic process (biological process)
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