{"entry": {"accession": "MF7000911", "general": {"name": "H49N, H51N double mutant dTDP-4-keto-6-deoxy-D-glucose-3,4-ketoisomerase with TDP (Aneurinibacillus thermoaerophilus)", "pdb_id": "2pam", "exp_method": "X-ray", "resolution": "2.50", "assembly": "Homodimer", "source_organism": "Aneurinibacillus thermoaerophilus", "publication": {"pmid": "17459872", "authors": "Davis ML, Thoden JB, Holden HM", "title": "The x-ray structure of dTDP-4-keto-6-deoxy-D-glucose-3,4-ketoisomerase.", "journal": "J. Biol. Chem.", "year": "2007", "issue": "26", "volume": "282", "pages": "19227-36", "abstract": "The repeating unit of the glycan chain in the S-layer of the bacterium Aneurinibacillus thermoaerophilus L420-91(T) is composed of four alpha-d-rhamnose molecules and two 3-acetamido-3,6-dideoxy-alpha-d-galactose moieties (abbreviated as Fucp3NAc). Formation of the glycan layer requires nucleotide-activated sugars as the donor molecules. Whereas the enzymes involved in the synthesis of GDP-rhamnose have been well characterized, less is known regarding the structures and enzymatic mechanisms of the enzymes required for the production of dTDP-Fucp3NAc. One of the enzymes involved in the biosynthesis of dTDP-Fucp3NAc is a 3,4-ketoisomerase, hereafter referred to as FdtA. Here we describe the first three-dimensional structure of this sugar isomerase complexed with dTDP and solved to 1.5 A resolution. The FdtA dimer assumes an almost jellyfish-like appearance with the sole alpha-helices representing the tentacles. Formation of the FdtA dimer represents a classical example of domain swapping whereby beta-strands 2 and 3 from one subunit form part of a beta-sheet in the second subunit. The active site architecture of FdtA is characterized by a cluster of three histidine residues, two of which, His(49) and His(51), appear to be strictly conserved in the amino acid sequences deposited to date. Site-directed mutagenesis experiments, enzymatic assays, and x-ray crystallographic analyses suggest that His(49) functions as an active site base."}}, "function": {"molecular_function": {"go": {"accession": "GO:0016853", "name": "isomerase activity"}}}, "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": "TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase", "source_organism": "Aneurinibacillus thermoaerophilus", "uniprot": {"id": "Q6T1W8", "start": "2", "end": "136", "coverage": "97%", "sequence": "MENKVINFKKIIDSRGSLVAIEENKNIPFSIKRVYYIFDTKGEEPRGFHAHKKLEQVLVCLNGSCRVILDDGNIIQEITLDSPAVGLYVGPAVWHEMHDFSSDCVMMVLASDYYDETDYIRQYDNFKKYIAKINLEKEG", "length": "139"}, "regions": {"region": [{"region_type": "secondary structure", "region_name": "helix", "region_start": "117", "region_end": "119"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "124", "region_end": "138"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "7", "region_end": "9"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "12", "region_end": "15"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "18", "region_end": "24"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "35", "region_end": "40"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "48", "region_end": "53"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "58", "region_end": "64"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "67", "region_end": "72"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "77", "region_end": "82"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "87", "region_end": "91"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "96", "region_end": "100"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "107", "region_end": "112"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "121", "region_end": "122"}, {"region_type": "pfam", "region_id": "PF05523", "region_name": "WxcM-like, C-terminal", "region_start": "1", "region_end": "130"}]}}, {"id": "B", "name": "TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase", "source_organism": "Aneurinibacillus thermoaerophilus", "uniprot": {"id": "Q6T1W8", "start": "2", "end": "135", "coverage": "96%", "sequence": "MENKVINFKKIIDSRGSLVAIEENKNIPFSIKRVYYIFDTKGEEPRGFHAHKKLEQVLVCLNGSCRVILDDGNIIQEITLDSPAVGLYVGPAVWHEMHDFSSDCVMMVLASDYYDETDYIRQYDNFKKYIAKINLEKEG", "length": "139"}, "regions": {"region": [{"region_type": "secondary structure", "region_name": "helix", "region_start": "117", "region_end": "119"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "124", "region_end": "136"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "7", "region_end": "9"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "12", "region_end": "15"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "18", "region_end": "24"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "35", "region_end": "40"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "48", "region_end": "53"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "58", "region_end": "64"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "67", "region_end": "72"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "77", "region_end": "82"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "87", "region_end": "91"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "96", "region_end": "100"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "107", "region_end": "112"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "121", "region_end": "122"}, {"region_type": "pfam", "region_id": "PF05523", "region_name": "WxcM-like, C-terminal", "region_start": "1", "region_end": "130"}]}}]}, "evidence": {"evidence_level": "Insufficient evidence (candidate)", "evidence_coverage": "The full structure participates in mutual synergistic folding.", "sequence_domain": "WxcM-like, C-terminal", "complex_evidence": "Domain-swapped dimer with extensive subunit-subunit interface mainly contributed by beta sheet augmentation (PMID:17459872).", "chain_evidence": [{"chain_id": "A", "support": "N/A"}, {"chain_id": "B", "support": "N/A"}]}, "related_structures": {"id": ["MF7000908", "MF7000909", "MF7000910", "MF7000911"]}}}