{"entry": {"accession": "MF7000975", "general": {"name": "Domain-swapped guanine deaminase (Bacillus subtilis)", "pdb_id": "1wkq", "exp_method": "X-ray", "resolution": "1.17", "assembly": "Homodimer", "source_organism": "Bacillus subtilis", "publication": {"pmid": "15180998", "authors": "Liaw SH, Chang YJ, Lai CT, Chang HC, Chang GG", "title": "Crystal structure of Bacillus subtilis guanine deaminase: the first domain-swapped structure in the cytidine deaminase superfamily.", "journal": "J. Biol. Chem.", "year": "2004", "issue": "34", "volume": "279", "pages": "35479-85", "abstract": "Guanine deaminase, a key enzyme in the nucleotide metabolism, catalyzes the hydrolytic deamination of guanine into xanthine. The crystal structure of the 156-residue guanine deaminase from Bacillus subtilis has been solved at 1.17-A resolution. Unexpectedly, the C-terminal segment is swapped to form an intersubunit active site and an intertwined dimer with an extensive interface of 3900 A(2) per monomer. The essential zinc ion is ligated by a water molecule together with His(53), Cys(83), and Cys(86). A transition state analog was modeled into the active site cavity based on the tightly bound imidazole and water molecules, allowing identification of the conserved deamination mechanism and specific substrate recognition by Asp(114) and Tyr(156'). The closed conformation also reveals that substrate binding seals the active site entrance, which is controlled by the C-terminal tail. Therefore, the domain swapping has not only facilitated the dimerization but has also ensured specific substrate recognition. Finally, a detailed structural comparison of the cytidine deaminase superfamily illustrates the functional versatility of the divergent active sites found in the guanine, cytosine, and cytidine deaminases and suggests putative specific substrate-interacting residues for other members such as dCMP deaminases."}}, "function": {"molecular_function": {"go": [{"accession": "GO:0008892", "name": "guanine deaminase activity"}, {"accession": "GO:0047974", "name": "guanosine deaminase activity"}, {"accession": "GO:0008270", "name": "zinc ion binding"}]}, "biological_process": {"go": [{"accession": "GO:0006147", "name": "guanine catabolic process"}, {"accession": "GO:0006152", "name": "purine nucleoside catabolic 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": "Guanine deaminase", "source_organism": "Bacillus subtilis", "uniprot": {"id": "O34598", "start": "1", "end": "156", "coverage": "100%", "sequence": "MNHETFLKRAVTLACEGVNAGIGGPFGAVIVKDGAIIAEGQNNVTTSNDPTAHAEVTAIRKACKVLGAYQLDDCILYTSCEPCPMCLGAIYWARPKAVFYAAEHTDAAEAGFDDSFIYKEIDKPAEERTIPFYQVTLTEHLSPFQAWRNFANKKEY", "length": "156"}, "regions": {"region": [{"region_type": "secondary structure", "region_name": "helix", "region_start": "10", "region_end": "28"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "51", "region_end": "56"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "61", "region_end": "75"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "91", "region_end": "102"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "111", "region_end": "118"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "121", "region_end": "130"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "132", "region_end": "136"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "149", "region_end": "158"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "35", "region_end": "40"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "43", "region_end": "49"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "83", "region_end": "88"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "105", "region_end": "110"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "140", "region_end": "142"}, {"region_type": "pfam", "region_id": "PF00383", "region_name": "Cytidine and deoxycytidylate deaminase zinc-binding region", "region_start": "2", "region_end": "101"}]}}, {"id": "B", "name": "Guanine deaminase", "source_organism": "Bacillus subtilis", "uniprot": {"id": "O34598", "start": "2", "end": "156", "coverage": "99%", "sequence": "MNHETFLKRAVTLACEGVNAGIGGPFGAVIVKDGAIIAEGQNNVTTSNDPTAHAEVTAIRKACKVLGAYQLDDCILYTSCEPCPMCLGAIYWARPKAVFYAAEHTDAAEAGFDDSFIYKEIDKPAEERTIPFYQVTLTEHLSPFQAWRNFANKKEY", "length": "156"}, "regions": {"region": [{"region_type": "secondary structure", "region_name": "helix", "region_start": "10", "region_end": "28"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "51", "region_end": "56"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "61", "region_end": "75"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "91", "region_end": "102"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "111", "region_end": "118"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "121", "region_end": "131"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "132", "region_end": "136"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "149", "region_end": "158"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "35", "region_end": "40"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "43", "region_end": "49"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "83", "region_end": "88"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "105", "region_end": "110"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "140", "region_end": "142"}, {"region_type": "pfam", "region_id": "PF00383", "region_name": "Cytidine and deoxycytidylate deaminase zinc-binding region", "region_start": "2", "region_end": "101"}]}}]}, "evidence": {"evidence_level": "Indirect evidence", "evidence_coverage": "The full structure participates in mutual synergistic folding.", "sequence_domain": "-", "complex_evidence": "Analytical ultracentrifugation experiments demonstrated that the guanine deaminase enzyme exists in solution as a homodimer. The C-terminal segment is swapped to form an intersubunit active site and an intertwined dimer with an extensive interface. The dimer is stabilized mainly by the formation of the wide interhelical hydrophobic packing of helices. Interestingly, analysis of unswapped bGD model shows that domain swapping contributes not only to oligomerization and structural stability but also to substrate specificity (PMID:15180998).", "chain_evidence": [{"chain_id": "A", "support": "N/A"}, {"chain_id": "B", "support": "N/A"}]}}}