1GYX

The Crystal Structure of YdcE, a 4-Oxalocrotonate Tautomerase Homologue from Escherichia coli, Confirms the Structural Basis for Oligomer Diversity

Summary for 1GYX

• Entry DOI: 10.2210/pdb1gyx/pdb
• Related: 1GYJ 1GYY
• Descriptor: HYPOTHETICAL PROTEIN YDCE, BENZOIC ACID, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ... (4 entities in total)
• Functional Keywords: tautomerase, isomerase, hypothetical protein, complete proteo
• Biological source: ESCHERICHIA COLI
• Total number of polymer chains: 2
• Total formula weight: 17461.88

Authors

Almrud, J.,Kern, A.,Wang, S.,Czerwinski, R.,Johnson, W.,Murzin, A.,Hackert, M.,Whitman, C. (deposition date: 2002-04-30, release date: 2002-10-10, Last modification date: 2024-05-08)

Primary citation

Almrud, J.,Kern, A.,Wang, S.,Czerwinski, R.,Johnson, W.,Murzin, A.,Hackert, M.,Whitman, C.
The Crystal Structure of Ydce, a 4-Oxalocrotonate Tautomerase Homologue from Escherichia Coli, Confirms the Structural Basis for Oligomer Diversity
Biochemistry, 41:12010-12024, 2002

PubMed 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.

PubMed: 12356301
DOI: 10.1021/BI020271H

Experimental method

X-RAY DIFFRACTION (1.35 Å)