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Catalytic Site Atlas

CSA LITERATURE entry for 1b3r

E.C. nameadenosylhomocysteinase
SpeciesRattus norvegicus (Rat)
E.C. Number (IntEnz) 3.3.1.1
CSA Homologues of 1b3rThere are 15 Homologs
CSA Entries With UniProtID P10760
CSA Entries With EC Number 3.3.1.1
PDBe Entry 1b3r
PDBSum Entry 1b3r
MACiE Entry M0090

Literature Report

IntroductionAdenosylhomocysteinase (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.
MechansimIt 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.
Reaction

Catalytic Sites for 1b3r

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
HisA5455macie:sideChainIt 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.
LysA185186macie:sideChainIt acts as a general acid-base catalyse, protonating and deprotonating the 3'-OH group during the reaction.
AspA189190macie:sideChainIt 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.
HisA300301macie:sideChainIt polarises a water molecule to activate it for the nucleophilic attack on C5' of 3'-keto-4',5'-dehydroadenosine during hydrolysis.
AspA130131macie:sideChainIt acts as a general acid-base catalyst, protonating and deprotonating the 4'-carbon.
CysA194195macie:sideChainIt modulates the oxidation state of the bound NAD+ and facilitates abstraction of the C3'-H of the substrate.
AsnA190191macie:sideChainIt facilitates the formation of neutral Lys185 to promote the reduction of the keto-intermediate by NADH.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
HisB5455macie:sideChainIt 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.
LysB185186macie:sideChainIt acts as a general acid-base catalyse, protonating and deprotonating the 3'-OH group during the reaction.
AspB189190macie:sideChainIt 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.
HisB300301macie:sideChainIt polarises a water molecule to activate it for the nucleophilic attack on C5' of 3'-keto-4',5'-dehydroadenosine during hydrolysis.
AspB130131macie:sideChainIt acts as a general acid-base catalyst, protonating and deprotonating the 4'-carbon.
CysB194195macie:sideChainIt modulates the oxidation state of the bound NAD+ and facilitates abstraction of the C3'-H of the substrate.
AsnB190191macie:sideChainIt facilitates the formation of neutral Lys185 to promote the reduction of the keto-intermediate by NADH.

Annotated By Reference To The Literature - Site 3 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
HisC5455macie:sideChainIt 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.
LysC185186macie:sideChainIt acts as a general acid-base catalyse, protonating and deprotonating the 3'-OH group during the reaction.
AspC189190macie:sideChainIt 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.
HisC300301macie:sideChainIt polarises a water molecule to activate it for the nucleophilic attack on C5' of 3'-keto-4',5'-dehydroadenosine during hydrolysis.
AspC130131macie:sideChainIt acts as a general acid-base catalyst, protonating and deprotonating the 4'-carbon.
CysC194195macie:sideChainIt modulates the oxidation state of the bound NAD+ and facilitates abstraction of the C3'-H of the substrate.
AsnC190191macie:sideChainIt facilitates the formation of neutral Lys185 to promote the reduction of the keto-intermediate by NADH.

Annotated By Reference To The Literature - Site 4 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
HisD5455macie:sideChainIt 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.
LysD185186macie:sideChainIt acts as a general acid-base catalyse, protonating and deprotonating the 3'-OH group during the reaction.
AspD189190macie:sideChainIt 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.
HisD300301macie:sideChainIt polarises a water molecule to activate it for the nucleophilic attack on C5' of 3'-keto-4',5'-dehydroadenosine during hydrolysis.
AspD130131macie:sideChainIt acts as a general acid-base catalyst, protonating and deprotonating the 4'-carbon.
CysD194195macie:sideChainIt modulates the oxidation state of the bound NAD+ and facilitates abstraction of the C3'-H of the substrate.
AsnD190191macie:sideChainIt facilitates the formation of neutral Lys185 to promote the reduction of the keto-intermediate by NADH.

Literature References

Notes:
Hu Y
Crystal structure of S-adenosylhomocysteine hydrolase from rat liver.
Biochemistry 1999 38 8323-8333
PubMed: 10387078
Takata Y
Catalytic mechanism of S-adenosylhomocysteine hydrolase. Site-directed mutagenesis of Asp-130, Lys-185, Asp-189, and Asn-190.
J Biol Chem 2002 277 22670-22676
PubMed: 11927587
Yuan CS
Chemical modification and site-directed mutagenesis of cysteine residues in human placental S-adenosylhomocysteine hydrolase.
J Biol Chem 1996 271 28009-28016
PubMed: 8910410
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