Database accession: MF7000062
Name: YdcE
PDB ID: 1gyx
Experimental method: X-ray (1.35 Å)
Assembly: Homodimer
Source organism: Escherichia coli
Primary publication of the structure:
Almrud JJ, Kern AD, Wang SC, Czerwinski RM, Johnson WH, Murzin AG, Hackert ML, Whitman CP
The crystal structure of YdcE, a 4-oxalocrotonate tautomerase homologue from Escherichia coli, confirms the structural basis for oligomer diversity.
(2002) Biochemistry 41: 12010-24
PMID: 12356301
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.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
intramolecular oxidoreductase activity, interconverting keto- and enol-groups intramolecular oxidoreductase activity, interconverting keto- and enol-groups
protein homodimerization activity protein homodimerization activity
Biological process:
cellular aromatic compound metabolic process obsolete cellular aromatic compound metabolic process
Cellular component:
cytoplasm cytoplasm
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, B
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: Tautomerase PptA
Source organism: Escherichia coli
Length: 77 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMPHIDIKCFPRELDEQQKAALAADITDVIIRHLNSKDSSISIALQQIQPESWQAIWDAEIAPQMEALIKKPGYSMNA
UniProtKB AC: P31992 (positions: 2-77)
Coverage: 98%
Name: Tautomerase PptA
Source organism: Escherichia coli
Length: 77 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMPHIDIKCFPRELDEQQKAALAADITDVIIRHLNSKDSSISIALQQIQPESWQAIWDAEIAPQMEALIKKPGYSMNA
UniProtKB AC: P31992 (positions: 2-77)
Coverage: 98%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: Tautomerase enzyme
Evidence level: Direct evidence
Evidence coverage: The full structure participates in mutual synergistic folding.
Complex Evidence:
Two-state unfolding from dimers to unfolded monomers proved experimentally (PMID:11914096).
Chain A:
N/A
Chain B:
N/A
Surface and contacts features:
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). Download the CIF file (.cif)
Download this entry's XML file (.xml)
Download this entry's JSON file (.json)
