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Catalytic Site Atlas Version 2.2.12
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CSA entry for 1b3r
Original Entry
Title:
Hydrolase
Compound:
S-adenosylhomocysteine hydrolase
Mutant:
No
UniProt/Swiss-Prot:
P10760-SAHH_RAT
EC Class:
3.3.1.1
Other CSA Entries:
Overview of all sites for 1b3r
Homologues of 1b3r
Entries for UniProt/Swiss-Prot: P10760
Entries for EC: 3.3.1.1
Other Databases:
PDB entry: 1b3r
PDBsum entry: 1b3r
UniProt/Swiss-Prot: P10760
IntEnz entry: 3.3.1.1
Literature Report:
Introduction:
Adenosylhomocysteinase (AdoHcyase) catalyses the reversible hydrolysis of S-adenosylhomocysteine (AdoHcy). AdoHcyase is a tetrameric enzyme with 431 amino acid residues in each identical subunit. The subunit is composed of the catalytic domain, the NAD+-binding domain, and the small C-terminal domain. Both catalytic and NAD+-binding domains are folded into an ellipsoid with a typical alpha / beta twisted open sheet structure. The catalytic domain is quite mobile, whereas the NAD+-binding domain and the small C-terminal domain are less mobile. The high mobility of the catalytic domain is due to the unique architecture of the tetramer.
Mechanism:
It is likely that binding of AdoHcy induces a large conformational change so as to place the ribose moiety of AdoHcy in close proximity to the nicotinamide moiety of NAD+. A catalytic mechanism is proposed based on crystal structures and results from site-directed mutagenesis.

In the hydrolysis, the neutral side chain of Lys185 serves as a base to accept a proton from 3'-OH in concomitant to the abstraction of the 3'-CH proton by NAD+, forming a 3'keto-AdoHcy intermediate and a NADH molecule. Asp130 then acts as a base to abstract the proton from C4'and the 3'-keto-AdoHcy carbanion intermediate is produced. His54 donates a proton to Hcy delta-S of the resulting carbanion, leading to the release of Hcy to form 3'-keto-4',5'-dehydroadenosine. A water molecule, activated by His54 and His300, then acts as a nucleophile to attack C5' of 3'-keto-4',5'-dehydroadenosine and the proton abstracted from C4' by Asp130 is donated back. Reduction of the keto intermediate by NADH forms the product adenosine.

Asp189 acts as a general acid-base catalyst, protonating and deprotonating Lys185, in order to retain the proton removed by Lys185 from ribose 3'-OH group in the enzyme to ensure catalytic efficiency. Asn190 facilitates the formation of neutral Lys185 to promote the reduction of the keto-intermediate by NADH. Cys194 modulates the oxidation state of the bound NAD+ and facilitates abstraction of the C3'-H of the substrate.
Sites:

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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
HISA 54 55Sidechain
ElectrostaticWater
Acid/baseSubstrate
It acts as an acid to donate a proton to the leaving Hcy/H2O. It polarises a water molecule to activate it for the nucleophilic attack on C5' of 3'-keto-4',5'-dehydroadenosine in hydrolysis.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11927587 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ASPA 130 131Sidechain
Acid/baseSubstrate
It acts as a general acid-base catalyst, protonating and deprotonating the 4'-carbon.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11927587 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 11927587 Current protein Mutagenesis of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
LYSA 185 186Sidechain
Acid/baseSubstrate
It acts as a general acid-base catalyse, protonating and deprotonating the 3'-OH group during the reaction.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11927587 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 11927587 Current protein Mutagenesis of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ASPA 189 190Sidechain
Acid/baseResidue
It acts as a general acid-base catalyst, protonating and deprotonating Lys185, in order to retain the proton removed by Lys185 from ribose 3'-OH group in the enzyme to ensure catalytic efficiency.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11927587 Current protein Mutagenesis of residue
PubMed ID 11927587 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ASNA 190 191Sidechain
ElectrostaticResidue
It facilitates the formation of neutral Lys185 to promote the reduction of the keto-intermediate by NADH.
Evidence from paper Evidence concerns Evidence type

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
CYSA 194 195Sidechain
ElectrostaticCofactor
It modulates the oxidation state of the bound NAD+ and facilitates abstraction of the C3'-H of the substrate.
Evidence from paper Evidence concerns Evidence type
PubMed ID 8910410 Current protein Mutagenesis of residue
PubMed ID 10387078 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
HISA 300 301Sidechain
ElectrostaticWater
It polarises a water molecule to activate it for the nucleophilic attack on C5' of 3'-keto-4',5'-dehydroadenosine during hydrolysis.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11927587 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
NADA 432 0
Substrate
It oxidises the ribose C3' to a keto and then reduces C3'-keto back to a hydroxyl group again.
Evidence from paper Evidence concerns Evidence type
PubMed ID 10387078 Current protein Ligand is essential for catalysis
References:
1
Catalytic mechanism of S-adenosylhomocysteine hydrolase. Site-directed mutagenesis of Asp-130, Lys-185, Asp-189, and Asn-190.
Y. Takata and T. Yamada and Y. Huang and J. Komoto and T. Gomi and H. Ogawa and M. Fujioka and F. Takusagawa
J Biol Chem 277, (25) 22670-6, (2002).
11927587
2
Chemical modification and site-directed mutagenesis of cysteine residues in human placental S-adenosylhomocysteine hydrolase.
C. S. Yuan and D. B. Ault-Riché and R. T. Borchardt
J Biol Chem 271, (45) 28009-16, (1996).
8910410
3
Crystal structure of S-adenosylhomocysteine hydrolase from rat liver.
Y. Hu and J. Komoto and Y. Huang and T. Gomi and H. Ogawa and Y. Takata and M. Fujioka and F. Takusagawa
Biochemistry 38, (26) 8323-33, (1999).
10387078
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