1TXZ

Crystal structure of yeast ymx7, an ADP-ribose-1''-monophosphatase, complexed with ADP-ribose

Summary for 1TXZ

• Entry DOI: 10.2210/pdb1txz/pdb
• Related: 1NJR
• Descriptor: Hypothetical 32.1 kDa protein in ADH3-RCA1 intergenic region, SULFATE ION, SODIUM ION, ... (6 entities in total)
• Functional Keywords: structural genomics, dimer, two domain organization, adp-ribose complex, psi, protein structure initiative, new york sgx research center for structural genomics, nysgxrc, unknown function
• Biological source: Saccharomyces cerevisiae (baker's yeast)
• Total number of polymer chains: 1
• Total formula weight: 32942.75

Authors

Kumaran, D.,Swaminathan, S.,Burley, S.K.,New York SGX Research Center for Structural Genomics (NYSGXRC) (deposition date: 2004-07-06, release date: 2004-11-30, Last modification date: 2023-08-23)

Primary citation

Kumaran, D.,Eswaramoorthy, S.,Studier, F.W.,Swaminathan, S.
Structure and mechanism of ADP-ribose-1''-monophosphatase (Appr-1''-pase), a ubiquitous cellular processing enzyme.
Protein Sci., 14:719-726, 2005

PubMed Abstract: Appr-1''-pase, an important and ubiquitous cellular processing enzyme involved in the tRNA splicing pathway, catalyzes the conversion of ADP-ribose-1''monophosphate (Appr-1''-p) to ADP-ribose. The structures of the native enzyme from the yeast and its complex with ADP-ribose were determined to 1.9 A and 2.05 A, respectively. Analysis of the three-dimensional structure of this protein, selected as a target in a structural genomics project, reveals its putative function and provides clues to the catalytic mechanism. The structure of the 284-amino acid protein shows a two-domain architecture consisting of a three-layer alphabetaalpha sandwich N-terminal domain connected to a small C-terminal helical domain. The structure of Appr-1''-pase in complex with the product, ADP-ribose, reveals an active-site water molecule poised for nucleophilic attack on the terminal phosphate group. Loop-region residues Asn 80, Asp 90, and His 145 may form a catalytic triad.

PubMed: 15722447
DOI: 10.1110/ps.041132005

Experimental method

X-RAY DIFFRACTION (2.05 Å)