{"entry": {"accession": "MF7000061", "general": {"name": "YdcE", "pdb_id": "1gyj", "exp_method": "X-ray", "resolution": "2.10", "assembly": "Homodimer", "source_organism": "Escherichia coli", "publication": {"pmid": "12356301", "authors": "Almrud JJ, Kern AD, Wang SC, Czerwinski RM, Johnson WH, Murzin AG, Hackert ML, Whitman CP", "title": "The crystal structure of YdcE, a 4-oxalocrotonate tautomerase homologue from Escherichia coli, confirms the structural basis for oligomer diversity.", "journal": "Biochemistry", "year": "2002", "issue": "40", "volume": "41", "pages": "12010-24", "abstract": "The tautomerase superfamily consists of three major families represented by 4-oxalocrotonate tautomerase (4-OT), 5-(carboxymethyl)-2-hydroxymuconate isomerase (CHMI), and macrophage migration inhibitory factor (MIF). The members of this superfamily are structurally homologous proteins constructed from a simple beta-alpha-beta fold that share a key mechanistic feature; they use an amino-terminal proline, which has an unusually low pK(a), as the general base in a keto-enol tautomerization. Several new members of the 4-OT family have now been identified using PSI-BLAST and categorized into five subfamilies on the basis of multiple-sequence alignments and the conservation of key catalytic and structural residues. The members of subfamily 5, which includes a hypothetical protein designated YdcE from Escherichia coli, are predicted not to form hexamers. The crystal structure of YdcE has been determined to 1.35 A resolution and confirms that it is a dimer. In addition, YdcE complexed with (E)-2-fluoro-p-hydroxycinnamate, identified as a potent competitive inhibitor of this enzyme, as well as N-(2-hydroxyethyl)piperazine-N'-2-ethanesulfonic acid (HEPES) and benzoate are also presented. These latter crystal structures reveal the location of the active site and suggest a mechanism for the observed YdcE-catalyzed tautomerization reaction. The dimeric arrangement of YdcE represents a new structure in the 4-OT family and demonstrates structural diversity within the 4-OT family not previously reported."}}, "function": {"molecular_function": {"go": [{"accession": "GO:0016862", "name": "intramolecular oxidoreductase activity, interconverting keto- and enol-groups"}, {"accession": "GO:0042803", "name": "protein homodimerization activity"}]}, "cellular_component": {"go": {"accession": "GO:0005737", "name": "cytoplasm"}}, "biological_process": {"go": {"accession": "GO:0006725", "name": "cellular aromatic compound metabolic process"}}}, "macromolecules": {"general": {"nr_of_chains": "2", "nr_of_unique_protein_segments": "1", "class": "Homooligomeric enzymes", "subclass": "Homodimeric enzymes", "note": "All chains according to the most probable oligomerization state stored in PDBe were considered."}, "chain": [{"id": "A", "name": "Tautomerase PptA", "source_organism": "Escherichia coli", "uniprot": {"id": "P31992", "start": "2", "end": "77", "coverage": "98%", "sequence": "MPHIDIKCFPRELDEQQKAALAADITDVIIRHLNSKDSSISIALQQIQPESWQAIWDAEIAPQMEALIKKPGYSMNA", "length": "77"}, "regions": {"region": [{"region_type": "secondary structure", "region_name": "helix", "region_start": "13", "region_end": "33"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "35", "region_end": "39"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "50", "region_end": "58"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "59", "region_end": "63"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "2", "region_end": "7"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "40", "region_end": "45"}, {"region_type": "pfam", "region_id": "PF01361", "region_name": "Tautomerase enzyme", "region_start": "2", "region_end": "54"}]}}, {"id": "B", "name": "Tautomerase PptA", "source_organism": "Escherichia coli", "uniprot": {"id": "P31992", "start": "2", "end": "77", "coverage": "98%", "sequence": "MPHIDIKCFPRELDEQQKAALAADITDVIIRHLNSKDSSISIALQQIQPESWQAIWDAEIAPQMEALIKKPGYSMNA", "length": "77"}, "regions": {"region": [{"region_type": "secondary structure", "region_name": "helix", "region_start": "13", "region_end": "33"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "47", "region_end": "58"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "59", "region_end": "66"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "2", "region_end": "7"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "40", "region_end": "45"}, {"region_type": "pfam", "region_id": "PF01361", "region_name": "Tautomerase enzyme", "region_start": "2", "region_end": "54"}]}}]}, "evidence": {"evidence_level": "Direct evidence", "evidence_coverage": "The full structure participates in mutual synergistic folding.", "sequence_domain": "Tautomerase enzyme", "complex_evidence": "Two-state unfolding from dimers to unfolded monomers proved experimentally (PMID:11914096).", "chain_evidence": [{"chain_id": "A", "support": "N/A"}, {"chain_id": "B", "support": "N/A"}]}, "related_structures": {"id": ["MF7000061", "MF7000062", "MF7000063"]}}}