1B54

CRYSTAL STRUCTURE OF A YEAST HYPOTHETICAL PROTEIN-A STRUCTURE FROM BNL'S HUMAN PROTEOME PROJECT

Summary for 1B54

• Entry DOI: 10.2210/pdb1b54/pdb
• Descriptor: YEAST HYPOTHETICAL PROTEIN, PYRIDOXAL-5'-PHOSPHATE (3 entities in total)
• Functional Keywords: yeast hypothetical protein, proteome, pyridoxal phosphate, tim barrel, structural genomics, psi, protein structure initiative, new york sgx research center for structural genomics, nysgxrc, hypothetical protein
• Biological source: Saccharomyces cerevisiae (baker's yeast)
• Total number of polymer chains: 1
• Total formula weight: 29411.38

Authors

Swaminathan, S.,Eswaramoorthy, S.,Burley, S.K.,New York SGX Research Center for Structural Genomics (NYSGXRC) (deposition date: 1999-01-12, release date: 1999-01-27, Last modification date: 2025-03-26)

Primary citation

Eswaramoorthy, S.,Gerchman, S.,Graziano, V.,Kycia, H.,Studier, F.W.,Swaminathan, S.
Structure of a yeast hypothetical protein selected by a structural genomics approach.
Acta Crystallogr.,Sect.D, 59:127-135, 2003

PubMed Abstract: Yeast hypothetical protein YBL036C (SWISS-PROT P38197), initially thought to be a member of an 11-protein family, was selected for crystal structure determination since no structural or functional information was available. The structure has been determined independently by MIR and MAD methods to 2.0 A resolution. The MAD structure was determined largely through automated model building. The protein folds as a TIM barrel beginning with a long N-terminal helix, in contrast to the classic triose phosphate isomerase (TIM) structure, which begins with a beta-strand. A cofactor, pyridoxal 5'-phosphate, is covalently bound near the C-terminal end of the barrel, the usual active site in TIM-barrel folds. A single-domain monomeric molecule, this yeast protein resembles the N-terminal domain of alanine racemase or ornithine decarboxylase, both of which are two-domain dimeric proteins. The yeast protein has been shown to have amino-acid racemase activity. Although selected as a member of a protein family having no obvious relationship to proteins of known structure, the protein fold turned out to be a well known and widely distributed fold. This points to the need for a more comprehensive base of structural information and better structure-modeling tools before the goal of structure prediction from amino-acid sequences can be realised. In this case, similarity to a known structure allowed inferences to be made about the structure and function of a widely distributed protein family.

PubMed: 12499548

Experimental method

X-RAY DIFFRACTION (2.1 Å)