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CATH domain | Related DB codes (homologues) |
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3.90.245.10 : Inosine-uridine Nucleoside N-ribohydrolase; Chain A | S00751,S00910 |
Enzyme Name | UniProtKB | KEGG |
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| P83851 | Q27546 |
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Protein name | Inosine-uridine preferring nucleoside hydrolase | Inosine-uridine preferring nucleoside hydrolase | inosine-uridine preferring nucleoside hydrolaseIU-NHIU-nucleoside hydrolasenon-specific nucleoside hydrolasepurine nucleosidase |
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Synonyms | IU-nucleoside hydrolaseIU-NHEC 3.2.2.-Purine nucleosidaseNon-specific nucleoside hydrolase | IU-nucleoside hydrolaseIU-NHEC 3.2.2.-Purine nucleosidaseNon-specific nucleoside hydrolase |
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Pfam | PF01156 (IU_nuc_hydro) [Graphical view]
| PF01156 (IU_nuc_hydro) [Graphical view]
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KEGG pathways | MAP code | Pathways |
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MAP00230 | Purine metabolism | MAP00760 | Nicotinate and nicotinamide metabolism |
UniProtKB:Accession Number | P83851 | Q27546 |
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Entry name | IUNH_LEIMA | IUNH_CRIFA |
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Activity | A purine nucleoside + H(2)O = D-ribose + a purine base. | A purine nucleoside + H(2)O = D-ribose + a purine base. |
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Subunit | Homotetramer. | Homotetramer. |
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Subcellular location |
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Cofactor | Calcium. | Calcium. |
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References for Catalytic Mechanism | References | Sections | No. of steps in catalysis |
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[2] | p.5968-5970, Fig.7 |
| [3] | p.5979 |
| [4] | p.21717-21719 |
| [5] | p.3533-3534 |
| [6] | Fig.1, p.6279, p.6283 | 2 | [7] | p.21117-21120 |
| [9] | p.1368-1375 |
| [10] | p.15943-15944, p.15945 |
| [11] | Scheme 1, p.8830-8833 | 2 | [12] | Scheme 1, p.14598-14600 | 2 |
references | [1] |
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PubMed ID | 7577992 |
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Journal | Biochemistry |
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Year | 1995 |
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Volume | 34 |
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Pages | 13961-6 |
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Authors | Parkin DW, Schramm VL |
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Title | Binding modes for substrate and a proposed transition-state analogue of protozoan nucleoside hydrolase. |
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[2] |
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PubMed ID | 8634237 |
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Journal | Biochemistry |
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Year | 1996 |
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Volume | 35 |
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Pages | 5963-70 |
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Authors | Gopaul DN, Meyer SL, Degano M, Sacchettini JC, Schramm VL |
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Title | Inosine-uridine nucleoside hydrolase from Crithidia fasciculata. Genetic characterization, crystallization, and identification of histidine 241 as a catalytic site residue. |
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[3] |
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Comments | X-ray crystallography (2.5 Angstroms) |
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PubMed ID | 8634238 |
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Journal | Biochemistry |
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Year | 1996 |
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Volume | 35 |
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Pages | 5971-5981 |
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Authors | Degano M, Gopaul DN, Scapin G, Schramm VL, Sacchettini JC |
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Title | Three-dimensional structure of the inosine-uridine nucleoside N-ribohydrolase from Crithidia fasciculata. |
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Related PDB | 1mas |
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[4] |
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PubMed ID | 8702965 |
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Journal | J Biol Chem |
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Year | 1996 |
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Volume | 271 |
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Pages | 21713-9 |
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Authors | Parkin DW |
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Title | Purine-specific nucleoside N-ribohydrolase from Trypanosoma brucei brucei. Purification, specificity, and kinetic mechanism. |
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[5] |
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PubMed ID | 9132003 |
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Journal | Biochemistry |
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Year | 1997 |
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Volume | 36 |
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Pages | 3528-34 |
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Authors | Parkin DW, Limberg G, Tyler PC, Furneaux RH, Chen XY, Schramm VL |
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Title | Isozyme-specific transition state inhibitors for the trypanosomal nucleoside hydrolases. |
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[6] |
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Comments | X-ray crystallography (2.3 Angstroms) |
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PubMed ID | 9572842 |
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Journal | Biochemistry |
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Year | 1998 |
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Volume | 37 |
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Pages | 6277-6285 |
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Authors | Degano M, Almo SC, Sacchettini JC, Schramm VL |
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Title | Trypanosomal nucleoside hydrolase. A novel mechanism from the structure with a transition-state inhibitor. |
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Related PDB | 2mas |
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[7] |
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Comments | X-ray crystallography (2.5 Angstroms) |
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PubMed ID | 10409664 |
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Journal | J Biol Chem |
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Year | 1999 |
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Volume | 274 |
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Pages | 21114-21120 |
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Authors | Shi W, Schramm VL, Almo SC |
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Title | Nucleoside hydrolase from Leishmania major. Cloning, expression, catalytic properties, transition state inhibitors, and the 2.5-a crystal structure. |
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Related PDB | 1ezr |
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[8] |
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PubMed ID | 11282633 |
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Journal | Appl Environ Microbiol |
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Year | 2001 |
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Volume | 67 |
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Pages | 1783-7 |
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Authors | Ogawa J, Takeda S, Xie SX, Hatanaka H, Ashikari T, Amachi T, Shimizu S |
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Title | Purification, characterization, and gene cloning of purine nucleosidase from Ochrobactrum anthropi. |
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[9] |
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PubMed ID | 11292348 |
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Journal | J Mol Biol |
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Year | 2001 |
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Volume | 307 |
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Pages | 1363-79 |
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Authors | Versees W, Decanniere K, Pelle R, Depoorter J, Brosens E, Parkin DW, Steyaert J |
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Title | Structure and function of a novel purine specific nucleoside hydrolase from Trypanosoma vivax. |
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[10] |
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PubMed ID | 11854281 |
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Journal | J Biol Chem |
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Year | 2002 |
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Volume | 277 |
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Pages | 15938-46 |
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Authors | Versees W, Decanniere K, Van Holsbeke E, Devroede N, Steyaert J |
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Title | Enzyme-substrate interactions in the purine-specific nucleoside hydrolase from Trypanosoma vivax. |
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[11] |
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PubMed ID | 12137535 |
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Journal | J Am Chem Soc |
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Year | 2002 |
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Volume | 124 |
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Pages | 8825-33 |
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Authors | Mazumder D, Kahn K, Bruice TC |
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Title | Computer simulations of trypanosomal nucleoside hydrolase: determination of the protonation state of the bound transition-state analogue. |
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[12] |
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PubMed ID | 12465969 |
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Journal | J Am Chem Soc |
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Year | 2002 |
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Volume | 124 |
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Pages | 14591-600 |
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Authors | Mazumder D, Bruice TC |
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Title | Exploring nucleoside hydrolase catalysis in silico: molecular dynamics study of enzyme-bound substrate and transition state. |
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comments | This enzyme belongs to the IU-nuceloside hydrolase family. This enzyme is homologous to ribosylpyrimidine nucleosidase (EC 3.2.2.8; S00751 in EzCatDB). According to the literature [2] & [4], The oxocarbonium ion is formed in the transition state, which is characterstic of an SN1-like catalytic mechanism. The paper [3] on crystal structure suggested that His241 can act as proton donor for the leaving nitrogenous base, whilst the paper [5] mentioned that His82 as well as His241 can protonates the leaving group. Asp14 is reported to have a hydrogen-bonding interaction with His241 [3]. Moreover, the papers [5], [6] and [7] suggested that metal or Ca2+ -bound water can attack the C1' atom after the oxocarbonium ion has been formed. One of the aspartic acid residues, Asp10, Asp15, Thr126 and Asp242, is proposed to be the group which will act as a general base, extracting the proton from the incoming water nucleophile, according to the paper [3]. The paper [12] based on molecular simulation suggested that the proton will be transferred from the activated water through Asp10 to Asp15 to water pool.
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created | updated |
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2002-07-11 | 2011-09-27 |
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